# Patent

## Title
Focused libraries of genetic packages

## Abstract

Focused libraries of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of antibody peptides, polypeptides or proteins and collectively display, display and express, or comprise at least a portion of the focused diversity of the family. The libraries have length and sequence diversities that mimic that found in native human antibodies.

## Background
This application is a continuation of U.S. application Ser. No. 12/762,051, filed on Apr. 16, 2010, now published, which is a continuation of U.S. application Ser. No. 11/416,460, filed on May 1, 2006, now abandoned, which is a continuation of U.S. application Ser. No. 10/026,925, filed on Dec. 18, 2001, now abandoned, which claims the benefit under 35 USC §120 of U.S. provisional application 60/256,380, filed Dec. 18, 2000 the entire content of each of which is herein incorporated by reference. The provisional application and the Tables attached to it are specifically incorporated by reference herein.
The present invention relates to focused libraries of genetic packages that each display, display and express, or comprise a member of a diverse family of peptides, polypeptides or proteins and collectively display, display and express, or comprise at least a portion of the focused diversity of the family. The focused diversity of the libraries of this invention comprises both sequence diversity and length diversity. In a preferred embodiment, the focused diversity of the libraries of this invention is biased toward the natural diversity of the selected family. In more preferred embodiment, the libraries are biased toward the natural diversity of human antibodies and are characterized by variegation in their heavy chain and light chain complementarity determining regions (“CDRs”).
The present invention further relates to vectors and genetic packages (e.g., cells, spores or viruses) for displaying, or displaying and expressing a focused diverse family of peptides, polypeptides or proteins. In a preferred embodiment the genetic packages are filamentous phage or phagemids or yeast. Again, the focused diversity of the family comprises diversity in sequence and diversity in length.
The present invention further relates to methods of screening the focused libraries of the invention and to the peptides, polypeptides and proteins identified by such screening.


BACKGROUND OF THE INVENTION
It is now common practice in the art to prepare libraries of genetic packages that individually display, display and express, or comprise a member of a diverse family of peptides, polypeptides or proteins and collectively display, display and express, or comprise at least a portion of the amino acid diversity of the family. In many common libraries, the peptides, polypeptides or proteins are related to antibodies (e.g., single chain Fv (scFv), Fv, Fab, whole antibodies or minibodies (i.e., dimers that consist of VH linked to VL)). Often, they comprise one or more of the CDRs and framework regions of the heavy and light chains of human antibodies.
Peptide, polypeptide or protein libraries have been produced in several ways in the prior art. See e.g., Knappik et al., J. Mol. Biol., 296, pp. 57-86 (20004, which is incorporated herein by references. One method is to capture the diversity of native donors, either naive or immunized. Another way is to generate libraries having synthetic diversity. A third method is combination of the first two. Typically, the diversity produced by these methods is limited to sequence diversity, i.e., each member of the library differs from the other members of the family by having different amino acids or variegation at a given position in the peptide, polypeptide or protein chain. Naturally diverse peptides, polypeptides or proteins, however, are not limited to diversity only in their amino acid sequences. For example, human antibodies are not limited to sequence diversity in their amino acids, they are also diverse in the lengths of their amino acid chains.
For antibodies, diversity in length occurs, for example, during variable region rearrangements. See e.g., Corbett et al., J. Mol. Biol., 270, pp. 587-97 (1997). The joining of V genes to J genes, for example, results in the inclusion of a recognizable D segment in CDR3 in about half of the heavy chain antibody sequences, thus creating regions encoding varying lengths of amino-acids. The following also may occur during joining of antibody gene segments: (i) the end of the V gene may have zero to several base deleted or changed; (ii) the end of the D segment may have zero to many bases removed or changed; (iii) a number of random bases may be inserted between V and D or between D and J; and (iv) the 5′ end of J may be edited to remove or to change several bases. These rearrangements result in antibodies that are diverse both in amino acid sequence and in length.
Libraries that contain only amino acid sequence diversity are, thus disadvantaged in that they do not reflect the natural diversity of the peptide, polypeptide or protein that the library is intended to mimic. Further, diversity in length may be important to the ultimate functioning of the protein, peptide or polypeptide. For example, with regard to a library comprising antibody regions, many of the peptides, polypeptides, proteins displayed, displayed and expressed, or comprised by the genetic packages of the library may not fold properly or their binding to an antigen may be disadvantaged, if diversity both in sequence and length are not represented in the library.
An additional disadvantage of prior art libraries of genetic packages that display, display and express, or comprise peptides, polypeptides and proteins is that they are not focused on those members that are based on natural occurring diversity and thus on members that are most likely to be functional. Rather, the prior art libraries, typically, attempt to include as much diversity or variegation at every amino acid residue as possible. This makes library construction time-consuming and less efficient than possible. The large number of members that are produced by trying to capture complete diversity also makes screening more cumbersome than it needs to be This is particularly true given that many members of the library will not be functional.
SUMMARY OF THE INVENTION
One objective of this invention is focused libraries of vectors or genetic packages that encode members of a diverse family of peptides, polypeptides or proteins wherein the libraries encode populations that are diverse in both length and sequence. The diverse length comprising components contain motifs that are likely to fold and function in the context of the parental peptide, polypeptide or protein.
Another object of this invention is focused libraries of genetic packages that display, display and express, or comprise a member of a diverse family of peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the focused diversity of the family. These libraries are diverse not only in their amino acid sequences, but also in their lengths. And, their diversity is focused so as to more closely mimic or take into account the naturally-occurring diversity of the specific family that the library represents.
Another object of this invention is diverse, but focused, populations of DNA sequences encoding peptides, polypeptides or proteins suitable for display or display and expression using genetic packages (such as phage or phagemids) or other regimens that allow selection of specific binding components of a library.
A further object of this invention is focused libraries comprising the CDRs of human antibodies that are diverse in both their amino acid sequence and in their length (examples of such libraries include libraries of single chain Fv(scFv), Fv, Fab, whole antibodies or minibodies (i.e., dimers that consist of VH linked to VL). Such regions may be from the heavy or light chains or both and may include one or, more of the CDRs of those chains. More preferably, they diversity or variegation occurs in all of the heavy chain and light chain CDRs.
It is another object of this invention to provide methods of making and screening the above libraries and the peptides, polypeptides and proteins obtained in such screening.
Among the preferred embodiments of this invention are the following:
1. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a heavy chain CDR1 selected from the group consisting of:

    
    
        (1) <1>1Y2<1>3M4<1>5 (SEQ ID NO:100), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y;
        (2) (S/T)1(S/G/X)2(S/G/X)3Y4Y5W6(S/G/X)7 (SEQ ID NO:101) wherein (S/T) is a 1:1 mixture of S and T residues, (S/G/X) is a mixture of 0.2025 S, 0.2025 G and 0.035 of each of amino acid residues A, D, E, F, H, I, K, L, H, N, P, Q, R, T, V, W, and Y;
        (3) V1S2G3G4S5I6S7<1>8<l>9<l>10Y11Y12W13<1>14 (SEQ ID NO:1), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; and
        (4) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably in the ratio: HC CDR1s (1):(2):(3)::0.80:0.17:0.02.
    
    


2. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express or comprise at least a portion of the diversity of the antibody facility, the vectors or genetic packages being characterized by variegated DNA sequences that encode a heavy chain CDR2 selected from the group consisting of:

    
    
        (1) <2>I<2><3>SGG<1>T<1>YADSVKG (SEQ ID NO:2), wherein <1> is an equimolar mixture of each of amino acid residues 211,. 0, E, F, G, H, I, K, L, M, N, P, 0, P, S, T, V, W, and Y; <2> is an equimolar mixture of each of amino acid residues Y, R, W, V, G, and S; and <3> is an equimolar mixture of each of amino acid residues P, S, and G or an equimolar mixture of P and S;
        (2) <1>I<4><1><1><G><5><1><1><1>YADSVKG (SEQ ID NO:3), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; <4> is an equimolar mixture of residues D, I, N, S, W, Y; and <5> is an equimolar mixture of residues S, G, D and N;
        (3) <1>I<4><1><1>G<5><1><1>YNPSLKG (SEQ ID NO:4), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, I, K, L, M, N; P, Q, R, S, T, V, W and Y, and <4> and <5> are as defined above;
        (4) <1>I<8>S<1><1><1>GGYY<1>YAASVKG (SEQ ID NO:5), wherein <1> is an equimolar mixture of each amino acid residues A, D, E, F, Gill, I, K, L, M, N, P, Q, R, S, T, V, and Y; <8> is 0.27 R and 0.027 of each of ADEFGHIKLMNPQSTVWY; and
        (5) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably in the ratio: HC CDR2s: (1)/(2) (equimolar): (3):(4)::0.54:0.43:0.03.
    
    


3. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a heavy chain CDR3 was selected from the group consisting of:

    
    
        (1) YYCA21111YFDYWG (SEQ ID NO:6), Wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of K and R;
        (2) YYCA2111111YFDYWG (SEQ ID NO:7), wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of K and R;
        (3) YYCA211111111YFDAYTG (SEQ ID NO:8), wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, 1, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of K and R;
        (4) YYCAR111S2S3111YFDYWG (SEQ ID NO:9), wherein 1 is an equimolar mixture of each amino acid residues A, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of S and G; and 3 is an equimolar mixture of Y and W;
        (5) YYCA2111CSG11CY1YFDYWG (SEQ ID NO:10), wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of K and R;
        (6) YYCA211S1TIFG11111YFDYWG (SEQ ID NO:11), wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of K and R.
        (7) YYCAR111YY2S3344111YFDYWG (SEQ ID NO:12), wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; 2 is an equimolar mixture of D and S; and 3 is an equimolar mixture of S and G;
        (8) YYCAR1111YC2231CY111YFDYWG (SEQ ID NO:13), wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; 2 is an equimolar mixture of S and G; and 3 is an equimolar mixture of T, D and G; and
        (9) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably the HC CDR3s (1) through (8) are in the following proportions in the mixture:
        (1) 0.10
        (2) 0.14
        (3) 0.25
        (4) 0.13
        (5) 0.13
        (6) 0.11
        (7) 0.04 and
        (8) 0.10; and more preferably the HC CDR3s (1) through (8) are in the following proportions in the mixture:
        (1) 0.02
        (2) 0.14
        (3) 0.25
        (4) 0.14
        (5) 0.14
        (6) 0.12
        (7) 0;08 and
        (8) 0.11.
    
    


Preferably, 1 in one or all of HC CDR3s (1) through (8) is 0.095 of each of G and Y and 0.048 of each of A, D, E, F H, 1, K, L, M, N, P, Q, R, S, T, V, and W.
4. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encodes a kappa light chain CDR1 selected from the group consisting of:

    
    
        (1) RASQ<1>V<2><2><3>LA (SEQ ID NO:14)
        (2) RASQ<1>V<2><2><2><3>LA (SEQ ID NO:15);

wherein <1> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY; <2> is 0.2 S and 0.044 of each of ADEFGHIKLMNPQRTVWY; and <3> is 0.2Y and 0.044 each of ADEFGHIKLMNPQRTVW and Y; and

    
    


(3) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably in the ratio CDR1s (1):(2)::0.68:0.32.
5. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the-antibody family the vectors or genetic packages being characterized by variegated DNA sequences that encode a kappa light-chain CDR2 having the sequence:

    
    
        <1>AS<2>R<4><1> (SEQ ID NO:102),

wherein <1> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY; <2> is 0.2 S and 0.044 of each of ADEFGHIKLMNPQRTVWY; and <4> is 0.2.A and 0.044 each of DEFGHIKLMNPQRSTVWY.

    
    


6. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a kappa light chain CDR3 selected from the groups consisting of:

    
    
        (1) QQ<3><1><1><1>P<1>T (SEQ ID NO:16), wherein <1> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY; <3> is 0.2 Y and 0.044 each of ADEFGHIKIMNPQRTVW;
        (2) QQ33111P (SEQ ID NO:103), wherein 1 and 3 are as defined in (1) above;
        (3) QQ3211PP1T (SEQ ID NO:17), wherein 1 and 3 are as defined in (1) above and 2 is 0.2 S and 0.044 each of ADEFGHIKLMNPQRTVWY; and
        (4) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably in the ratio CDA3s (1):(2):(3)::0.65:0.1:0.25.
    
    


7. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a lambda light chain CDR1 selected from the group consisting of:

    
    
        (1) TG<1>SS<2>VG<1><3><2><3>VS (SEQ ID NO:18), wherein <1> is 0.27 T, 0.27 G and 0.027 each of ADEFRIKLMNPQRSVWY: <2> is 0.27 D, 0.27 N and 0.027 each of AEFGHIKLMPQRSTVWY, and <3> is 0.36 Y and 0.036 each of ADEFGHIKLMNPQRSTVW;
        (2) G<2><4>L<4><4><4><3><4><4> (SEQ ID NO:104),

wherein <2> is as defined in (1) above and <4> is an equimolar mixture of amino acid residues ADEFGHIKIMNPQRSTVWY; and

        (3) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably in the ratio CDR1 (1):(2)::0.67:0.33;
    
    


8. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a lambda light chain CDR2 has the sequence:

    
    
        <4><4><4><2>RPS (SEQ ID NO:105)

wherein <2> is 0.27 D, 0.27 N, and 0.027 each of AEFGHIKIMPQRSTVWY and <4> is an equimolar mixture of amino acid residues ADEFGHIKLONPQRSTVW.

    
    


9. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a lambda light chain CDR3 selected from the group consisting of:

    
    
        (1) <4><5><4><2><4>S<4><4><4><4>V (SEQ ID NO:106), wherein <2> is 0.27 D, 0.27 N, and 0.027 each of AEFGHIKIMPQRSTVWY; <4> is an equimolar mixture of amino acid residues ADEFGHIKLMVPQRSTVW; and <5> is 0.36 S and 0.6355 each of ADEFGHIKLMNPQRTVWY;
        (2) <5>SY<1><5>S<5><1><4>V (SEQ ID NO:19), wherein <1> is an equimolar mixture of ADEFGHIKLMNPQRSTVWY; and <4> and 5 <5> are as defined in (1) above; and
        (3) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably in the ratio CDR3s
    
    


10. A focused library comprising variegated-DNA sequences that encode a heavy chain CDR selected from the group consisting of:

    
    
        (1) one or more of the heavy chain CDR's of paragraph 1 above;
        (2) one or more of the heavy chin CDR2s of paragraph 2 above;
        (3) one or more of the heavy chain CDR3s of paragraph 3 above; and
        (4) mixtures of vectors or genetic-packages characterized by (1), (2) and (3).
    
    


11. The focused library comprising one or more of the variegated DNA sequences that encodes a heavy chain CDR of paragraphs 1, 2 and 3 and further comprising variegated DNA sequences that encodes a light chain CDR selected from the group consisting of

    
    
        (1) one or more the kappa light chain CDR1s of paragraph 4;
        (2) the kappa light chain. CDR2 of paragraph 5;
        (3) one or more of the kappa light chain CDR3s of paragraph 6;
        (4) one or more of the kappa light chain CDR1s of paragraph 7;
        (5) the lambda light chain ‘CDR2’ of paragraph 8
        (6) one or more of the lambda light chain CDR3s of paragraph. 9; and
        (7) mixtures of vectors and genetic packages characterized by one or more of (1) through (6).
    
    


12. A population of variegated DNA sequences as. described in paragraphs 1-11 above.
13. A population of vectors comprising the variegated DNA sequences as described in paragraphs 1-11 above.


DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
Antibodies (“Ab”) concentrate their diversity into those regions that are involved in determining affinity and specificity of the Ab for particular targets. These regions may be diverse in sequence or in length. Generally, they are diverse In both ways. However, within families of human antibodies the diversities, both in sequence and in length, are not truly random. Rather, some amino acid residues are preferred at certain positions of the CDRs and some CDR lengths are preferred. These preferred diversities account for the natural diversity of the antibody family.
According to this invention, and as more fully described below, libraries of vectors and genetic packages that more closely mirror the natural diversity, both in sequence and in length, of antibody families, or portions thereof are prepared and used.
Human Antibody Heavy Chain Sequence and Length Diversity
(a) Framework
The heavy chain (“HC”) Germ-Line Gene (GLG) 3-23 (also known as 1/1)-47) accounts for about 12% of all human Abs and is preferred as the framework in the preferred embodiment of the invention. It should, however, be understood that other well-known frameworks, such as 4-34, 3-30, 3-30.3 and 4-30.1, may also be used without departing from the principles of the focused diversities of this invention.
In addition, JH4(YFDYWGQGTLVTVSS; SEQ ID NO:20) occurs more often than JH3 in native antibodies. Hence, it is preferred for the focused libraries of this invention. However, JH3 (AFDIWGQGTMVTVSS; SEQ ID NO:21) could as well be used.
(b) Focused Length Diversity: CDR1, 2 and 3
(i) CDR1
For CDR1, GLGs provide CDR1s only Of the lengths 5, 6, and 7. Mutations during the maturation of the v-domain gene, however, can lead to CDR1s having lengths as short as 2 and as long as 16. Nevertheless, length 5, predominates. Accordingly, in the preferred embodiment of this invention the preferred HC CDR1 is 5 amino acids, with less preferred CDR1s having lengths of 7 and 14. In the most preferred libraries of this invention, all three lengths are used in proportions similar to those found in natural antibodies.
(ii) CDR2
GLGs provide CDR2s only of the lengths 15:19, but mutations during maturation may result in CDR2s of lengths from 16 to 28 amino acids. The lengths 16 and 17 predominate in mature Ab genes. Accordingly, length 17 is the preferred length for HC CDR2 of the present invention. Less preferred HC CDR2s of this invention have lengths 16 and 19. In the most preferred focused libraries of this invention, all three lengths are included in proportions similar to those found in natural antibody families.
(iii) CDR3
HC CDR3s vary in length. About half of human HCs consist of the components: V::nz::D::ny::JHn where V is a V gene, nz is a series of bases (mean 12) that are essentially random, D is a D segment, often with heavy editing at both ends, ny is a series of bases (mean 6) that are essentially random, and JH is one of the six JH segments, often with heavy editing at the 5′ end. The D segments appear to provide spacer segments that allow folding of the IgG. The greatest diversity is at the junctions of y with D and of D with JH.
In the preferred-libraries of this invention both types of HC CDR3s are used. In HC CDR3s that have no identifiable D segment, the structure is V::nz::JHn where JH is usually edited at the 5′ end. In HC CDR3s that have an identifiable D segment, the structure is V::nz::D::ny::JHn.
(c) Focused Sequence Diversity: CDR1, 2 and 3
(i) CDR1
In 5 amino acid length CDR1, examination of a 3D model of a humanized Ab showed that the side groups of residues 1, 3, and 5 were directed toward the combining pocket. Consequently, in the focused libraries of this invention, each of these positions may be selected from any of the native amino acid residues, except cysteine (“C”). Cysteine can form disulfide bonds, which are an important component of the canonical Ig fold. Having free thiol groups Could, thus, interfere with proper folding of the HC and could lead to problems in production or manipulation of selected Abs. Thus, in the focused libraries of this invention cysteine is excluded from positions 1; 3 and 5 of the preferred 5 amino acid CDR1s. The other 19 natural amino acids residues may be used at positions 1, 3 and 5. Preferably, each is present in equimolar ratios in the variegated libraries of this invention.
3D modeling also suggests that the side groups of residue 2 in a 5 amino acid CDR1 are directed away from the combining pocket. Although this position shows substantial diversity, both in GLG and mature genes, in the focused libraries of this invention this residue is preferably Tyr (Y) because it occurs in 681/820 mature antibody genes. However, any of the other native amino acid residues, except Cys (C), could also be used at this position.
For position 4, there is also some diversity in GLG and mature antibody genes. However, almost all mature genes have uncharged hydrophobic amino acid residues: A, G, L, P, F, M, W, I, V, at this position. Inspection of a 3D model also shows that the side group of residue 4 is packed into the innards of the HC. Thus, in the preferred embodiment of this invention which uses framework 3-23, residue 4 is preferably Met because it Is likely to fit very well into the framework of 3-23. With other frameworks, a similar fit consideration is used to assign residue 4.
Thus, the most preferred HC−CDR1 of this invention consists of the amino acid sequence <1>Y<I>M<1> where <1> can be any one of amino acid residues: A, D, E, G, H, I, K, L, M, N, R, Q, S, T, V, W, Y. (not C), preferably present at each position in an equimolar amount. This diversity is shown in the context of a framework 3-23:JH4 in Table 1. It has a diversity of 6859-fold.
The two less preferred HC CDR1s of this invention have length 7 and length 14. For length 7, a preferred variegation is (S/T)1(S/G/<1>)2(S/G/<1>)3Y4Y5W6(S/G/<1>)7 (SEQ ID NO:107); where (S/T) indicates an equimolar mixture of Ser and Thr codons; (S/G/<1>) indicates a mixture Of 0.2025 S, 0.2025 G, and 0.035 for each of A, D, E, F, H, I, K, L, M, N, P, Q, R, T, V, W, Y. This design gives a predominance of Ser and Gly at positions 2, 3, and 7, as occurs in mature HC genes. For length 14, a preferred variegation is VSGGSIS<1><1><1>YYW<1> (SEQ ID NO:108), where <1> is an equimolar mixture of the 19 native amino acid residues, except Cys (C).
The DNA that encodes these preferred HC CDR1s is preferably synthesized using trinucleotide building blocks so that each amino acid residue ii present in essentially equimolar or other described amounts. The preferred codons for the <1> amino acid residues are gct, gat, gag, ttt, ggt, cat, att, aag, ctt, atg, aat, cct, cag, cgt, tct, act, gtt, tgg, and tat. Of course, other codons for the chosen amino acid residue could also be used.
The diversity oligonucleotide (ON). is preferably synthesized from BspEI to BstXI (as shown in Table 1) and can, therefore, be incorporated either by PCR synthesis using overlapping ONs or introduced by ligation of BspEI/BstXI-cut fragments. Table 2 shows the oligonucleotides that embody the specified variegations of the preferred length 5 HC CDR1s of this invention. PCR using ON-R1V1vg, ON-R1top, and ON-R1bot gives a dsDNA product of 73 base-pairs, cleavage with 14spEI and BstXI trims 11 and 13 bases from the ends and provides cohesive ends that can be ligated to similarly cut vector having the 3-23 domain shown in Table 1. Replacement of ON-R1V1vg with either ONR1V2vg or ONR1V3vg (see Table 2) allows synthesis of the two alternative diversity patterns—the 7 residue length and the 14 residue length HC CDR1.
The more preferred libraries of this invention comprise the 3 preferred HC CDR1 length diversities. Most preferably, the 3 lengths should be incorporated in approximately the ratios in which they are observed in antibodies selected without reference to the length of the CDRs. For example, one sample of 1095 HC genes have the three lengths present in the ratio:
L=5:L=7:L=14::820:175:23::0.80:0.17:0.02. This is the preferred ratio in accordance with this invention.
(ii) CDR2
Diversity in HC CDR2 was designed with the same considerations as for HC CORI: GLG sequences, mature sequences and 3D structure. A preferred length for CDR2 is 17, as shown in Table 1. For this preferred 17 length CDR2, the preferred variegation in accordance with the invention is: <2>I<2><3>SGG<1>T<1>YADSVKG (SEQ ID NO:2), where <2> indicates any amino acid residue selected from the group of Y, R, W, V, G and S (equimolar mixture), <3> is P, S and G or P and S only (equimolar mixture), and <1> is any native amino acid residue except C (equimolar mixture).
ON-R2V1vg shown in Table 3 embodies this diversity pattern. It is preferably synthesized so that fragments of dsDNA containing the BstXI and XbaI site can be generated by PCR. PCR with ON-R2V1vg, ON-R2top, and ONR2bot gives a dsDNA product of 122 base pairs. Cleavage with BstXI and XbaI removes about 10 bases from each end and produces cohesive ends that can be ligated to similarly cut vector that contains the 3-23 gene-shown in Table 1.
In an alternative embodiment for a 17 length HC CDR2, the following variegation may be used; <1>I<4><1><1>G<5><1><1><1>YADSVKG(SEQ ID NO:3), where <1> is as described above for the more preferred alternative of HC CDR2; <4> indicates an equimolar mixture of DINSWY, and <5> indicates an equimolar mixture of SGDN. This diversity pattern is embodied in ON-R2V2vg shown in Table 3. Preferably, the two embodiments are used in equimolar mixtures in the libraries of this invention.
Other preferred HC CDR2s have lengths 16 and 19. Length 16: <1>I<4><1><1>G<5<1><1>YNPSLKG (SEQ ID NO:4); Length: 19: <1>I<8>S<1><1><1>GGYY<1>YAASVKG (SEQ ID NO:5), wherein <1> is an equimolar mixture of all native amino acid residues except C; <4> is a equimolar mixture of DINSWY; <5> is an equimolar mixture of SGDN; and <8> is 0.27 R and 0:0 7 of each of residues ADEFGHIKLMNPQSTVWY. Table 3 shows ON-R2V3vg which embodies a preferred aDR2 variegation of length 16 and ON7R2V4vg which embodies a preferred CDR2 variegation of length 19. To prepare these variegations ON-R2V3vg may be PCR amplified with ON-A2top and ON-R2bo3 and ON-R2V4vg may be PCR amplified with ON-R2top and ON-R2-bo4. See Table 3. In the most preferred embodiment of this invention, all three HC CDR2 lengths are used. Preferably, they are present in a ratio 17:16:19::579:464:31::0.54:0.43:0.03.
(iii) CDR3
The preferred libraries of this invention comprise several BC CDR3 components. Some of these will have only sequence diversity. Others will have sequence diversity with embedded D segments to extend the length, while also incorporating sequences known to allow Igs to fold. The HC CDR3 components of the preferred libraries of this invention and their diversities are depicted in Table 4: Components 1-8.
This set of components was chosen after studying the sequences of 1383 human BC sequences. The proposed components are meant to fulfill the following goals:
1) approximately the same distribution of lengths as seen in native Ab genes;
2) high level of sequence diversity at places having high diversity in native Ab genes; and
3) incorporation of constant sequences often seen in native Ab genes.
Component 1 represents all the genes having lengths 0 to 8 (counting from the YYCAR motif at the end of FR3 to the WG dipeptide motif near the start of the J region, i.e., FR4). Component 2 corresponds the all the genes having lengths 9 or 10. Component 3.corresponds to the genes having lengths 11 or 12 plus half the genes having length 13. Component 4 corresponds to those having length 14 plus half those having length 13. Component 5 corresponds to the genes having length 15 and half of those having length 16. Component. 6 corresponds to genes of length 17 plus half of those with length 16. Component 7 corresponds to those with length 18. Component 8 corresponds to those having length 19 and greater. See Table 4.
For each HC CDR3 residue having the diversity <1>, equimolar ratios are preferably not used. Rather, the following ratios are used 0.095 [G and Y] and 0.048 [A, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, and W]. Thus, there is a double dose of G and Y with the other residues being in equimolar ratios. For the other diversities, e.g., KR or SG, the residues are present in equimolar mixtures.
In the preferred libraries of this invention the eight components are present in the following fractions: 1 (0.10), 2 (0.14), 3 (0.25), 4 (0.13), 5 (0.13), 6 (0.11), 7 (0.04) and 8 (0.10). See Table 4.
In the more preferred embodiment of this invention, the amounts of the eight components is adjusted because the first component is not complex enough to justify including it as 10% of the library. For example, if the final library were to have 1×109 members, then 1×108 sequences would come from component 1, but it has only 2.6×105 CDR3 sequences so that each one would occur in  ̃385 CDR1/2 contexts. Therefore, the more preferred amounts of the eight components are 1(0.02), 2(0.14), 3(0.25), 4(0.14), 510.14), 6(0.12), 7(0.68), 8(0.11). In accordance with the more preferred embodiment component 1 occurs in  ̃77 CDR1/2 contexts and the other, longer CDR3s occur more often.
Table 5 shows vgDNA that embodies each of the eight HC CDR3 components shown in Table 4. In Table 5, the oligonucleotides (ON) Ctop25, CtprmA, C8prmB, and CBot25 allow PCR amplification of each of the variegated ONs (vgDNA): C1t08, C2t10, C3t12, C4t14, C5t15, C6t17, C7t18, and C8t19. After amplification, the dsDNA can be cleaved with AfiII and BstEII (or KpnI) and ligated to similarly cleaved vector that contains the remainder of the 3-23 domain. Preferably, this vector already contains diversity in one, or both, of CDR1 and CDR2 as disclosed herein. Most preferably, it contains diversity in both the CDR1 and CDR2 regions. It is, of course, to be understood that the various diversities can be incorporated into the vector in any order.
Preferably, the recipient vector originally contains a stuffer in place of CDR1, CDR2 and CDR3 so that there will be no parental sequence that would then occur in the resulting library. Table 6 shows a version of the V3-23 gene segment with each CDR replaced by a short segment that contains both stop codons and restriction sites that will allow specific cleavage of any vector that does not have the stuffer removed. The stuffer can either be short and contain a restriction enzyme site that will not occur in the finished library, allowing removal of vectors that are not cleaved by both AfiII and BstEII (or Aionl) and religated. Alternatively, the stuffer could be 200-400 bases long so that uncleaved or once-cleaved vector can be readily separated from doubly cleaved vector.
Human Antibody Light Chain: Sequence and Length Diversity
(i) Kappa Chain
(a) Framework
In the preferred embodiment of this invention, the kappa light chain is built in an A27 framework with a JK1 region. These are the most common V and J regions in the native genes. Other frameworks, such as 012, L2, and All, and other J regions, such as JK4, however, may be used without departing from the scope of this invention.
(b) CDR1
In native human kappa chains, CDR1s with lengths of 11, 12, 13, 16, and 17 were observed with length 11 being predominant and length 12 being well represented. Thus, in the preferred embodiments of this invention LC CDR1s of length 11 and 12 are used in an and mixture similar to that observed in native antibodies), length 11 being most preferred. Length 11 has the following sequence: RASQ<1>V<2><2><3>LA (SEQ ID NO:14) and Length 12 hag the following sequence: RASQ<1>V<25<2><2><3>LA (SEQ ID NO:15), wherein <1> is an equimolar mixture of ill of the native. amino acid residues, except C, <2> is 0.2 S and 0.044 of each of ADEFGHIKLMNPQRTVWY, and <3> is 0.2.Y and 0.044 each of A. D, E, F, G, H, 1, K, L, M, N, Q, R, T, V, W and Y. In the most preferred embodiment of this invention, both CDR1. lengths are used. Preferably, they are present in a ratio of 11:12::154:73:0.68:0.32.
(c) CDR2
In native kappa, CDR2 exhibits only length 7. This length is used in the preferred embodiments of-this invention. It has the sequence <1>AS<2>R<4><1>, wherein <1> is an-equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY; <2> is 0.2 S and 0.004 of each of ADEFGHIKLMNPQRTVWY; and <4> is 0.2 A and 0.044 of each of DEFGHIKLMNPQRSTUWY.
(d) CDR3
In native kappa, CDR3 exhibits lengths of 4, 6, 7; 8, 9, 10, 11, 12, 13, 0.0 . . . and 19. While any of these lengths and mixtures of them can be employed in this invention, we prefer lengths 8, 9 and 10, length 9 being more preferred. For the preferred Length 9, the sequence is, QQ<3><1><1><1>P<1>T, wherein <1> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY and <3> is 0.2? and 0.044 each of ADEFGHIKLWQRSVW. Length 8 is preferably QQ33111P and Length 10 is Preferably QQ3211PP1T, wherein 1 and 3 are as defined for Length 9 and 2 is S (0.2) and 0.044 each of ADEFGHIKLMNPQRTVWY. A mixture of all 3 lengths being most preferred (ratios as in native antibodies), i.e., 8:9:10i28:166:63::0.1:0.65:0.25.
Table 7 shows a kappa chain gene of this invention, including a PlacZ promoter a ribosome-binding site, and signal sequence (MI3 III signal). The DNA sequence encodes the GLG amino acid sequence but does not comprise the GLG DNA sequence. Restriction sites are designed to fall within each framework region so that diversity can be cloned into the CDRs. XmaI and Espl are in FR1, SexAI is in FR2, RsrII is in FR3, and KpnI (or Acc65I), are in FR4. Additional sites are provided in the constant kappa chain to facilitate construction of the gene.
Table 7 also shows a suitable scheme of variegation for kappa. In.CDR1, the most preferred length 11 is depicted. However, most preferably both lengths 11 and 12 are used. Length 12 in CDR1 can be construed by introducing codon 51 as <2> (i.e. a Ser-biased mixture). CDR2 of kappa is always 7 codons. Table 7 shows a preferred variegation scheme for CDR2. Table 7 Shows a variegation scheme for the most preferred CDR3 (length 9). Similar variegations can be lied for CDRs of length 8 and 10. In the preferred embodiment of this invention, those three lengths (8, 9 and 10) are included in the libraries of this invention in the native ratios, as described above.
Table 9 shows series of diversity oligonucleotides and primers that may be used to construct the kappa chain diversities depicted in Table 7.
(ii) Lambda Chain
(a) Framework
The lambda chain is preferably built in a 2a2 framework with an L2J region. These are the most common V and J regions in the native genes. Other frameworks, such as 31, 4b, la and 6a, and other J regions, such as L1J, L3J and L7J, however, may be used without departing from the scope of this invention.
(b) CDR1
In native human lambda chains, CDR1s with length 14. predominate, lengths 11, 12 and 13 also occur. While any of these can be used in this invention, lengths 11 and 14 are preferred. For length 11 the sequence is: TG<2><4>L<4><4><4><3><4><4> (SEQ ID NO:22) and for Length 14 the sequence is: TG<1>SS<2>VG<1><3><2><3>VS (SEQ ID NO:18), wherein <1> is 0.27 T, 0.21 G and 0.027 each of ADEFHIKLMNPQRSVWY; <2> is 0.27 D, 0.27 N and 0.027 each of AEFGHIKLMPQRSTVWY; <3> is 0.36 Y and 0.0355 each of ADEFGHIKLMNPQRSTVW; and <4> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY. Most preferably, Mixtures (similar to those occurring in native antibodies) preferably, the ratio is 11:14::23:46::0.33: 0.67 of the three lengths are used.
(c) CDR2
In native human lambda chains4.CDR2s with length 7 are by far the most common. This length is preferred in this invention. The sequence of this Length 7 CDR2 is <4><4><4><2>RPS, wherein <2> is 0.27 D, 0.27 N, and 0.027 each of AEFGHIKLMPQRTVWY and <4> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVW.
(d) CDR3
In native human lambda chains, CDR3s of length 10 and 11 predominate, while length 9 is also common. Any of these three lengths can be used in the invention. Length 11 is preferred and mixtures of 10 and 11 more preferred. The sequence of Length 11 is <4><5><4><2><4>S<4><4><4><4>V, where <2> and <4> are as defined for the lambda CORI and <5> is 0.36 S and 0.0355 each of ADFFGHIKLMNFORTVWY. The sequence of Length 10 is <5>SY<1><5>S<5><1><4>V (SEQ ID NO:19), wherein <1> is an equimolar mixture of ADEFGHIKLMNPQRSTVWY; and <4> and <5> are as defined for Length 11. The preferred mixtures of this invention comprise an equimolar mixture of Length 10 and Length 11. Table 8 shows a preferred focused lambda light chain diversity in accordance with this invention.
Table 9 shows a series of diversity oligonucleotides and primers that may be used to construct 10 the lambda chain diversities depicted in Table 7.
Method of Construction of the Genetic Package
The diversities of heavy chain and the kappa and lambda light chains are best constructed in separate vector's. First a synthetic gene is designed to embody each of the synthetic variable domains. The light chains are bounded by restriction sites for ApaLI (positioned at the very end of the signal sequence) and AscI (positioned after the stop codon). The heavy chain is bounded by SfiI (positioned within the PelB signal sequence) and NotI (positioned in the linker between CH1 and the anchor protein). Signal sequences other than PelB may also need, e.g., a M13 pIII signal sequence.
The initial genes are made with “stuffer” sequences in place of the desired CDRs. A “stuffer” is a sequence that is to be cut away and replaced by diverse DNA but which does not allow expression ‘of a functional antibody gene. For example, the stuffer may contain several stop codons and restriction sites that will not occur in the correct finished library vector. For example, in Table 10, the stuffer for CDR1 of kappa A27 contains a StuI site. The vgDNA for CDR1 is introduced as a cassette from EspI, XmaI, or Af1II to dither SexAI or KasI. After the ligation, the DNA is cleaved with Still; there should be no StuI sites in the desired vectors.
The sequences of the heavy chain gene with stuffers is depicted in Table 6. The sequences of the kappa light chain gene with stuffers is depicted in Table 10. The sequence of the lambda light chain gene with stuffers is depicted in Table 11.
In another embodiment of the present invention the diversities of heavy chain and the kappa or lambda light chains are constructed in a single vector or genetic packages (e.g., for display or display and expression) having appropriate restriction sites that allow cloning of these chains. The processes to construct such vectors are well known and widely used in the art. Preferably, a heavy chain and Kappa light Chain library and a heavy chain and lambda light chain library would be prepared separately. The two libraries, most preferably, will then be mixed in equimolar amounts to attain maximum diversity.
Most preferably, the display is had on the surface of a derivative of M13 phage. The most preferred vector contains all the genes of M13, an antibiotic resistance-gene, and the display cassette. The preferred vector is provided with restriction sites that allow introduction and excision of members of the diverse family of genes, as cassettes. The preferred vector is stable against rearrangement under the growth conditions used to amplify phage.
In another embodiment of this invention, the diversity captured by the methods of the present invention may be displayed and/or expressed in a phagemid vector (e.g., pCES1) that displays and/or expresses the peptide, polypeptide or protein. Such vectors may also be used to store the diversity for subsequent display and/or expression using other vectors or phage.
In another embodiment of this invention, the diversity captured by the methods of the present invention may be displayed and/or expressed in a yeast vector.







TABLE 1





3-23: JH4 CDR1/2 diversity = 1.78 × 108















                                 FR1(VP47/V3-23)---------------


                20  21  22       23  24  25  26  27  28  29  30


(SEQ ID NO: 99) A   M   A        E   V   Q   L   L   E   S   G


ctgtctgaac      cc atg gcc      gaa/gtt/caa/ttg/tta/gag/tct/ggt/


Scab......      NcoI....             MfeI


 


      --------------FR1------------------------------


       31  32  33  34  35  36  37  38  39  40  41  42  43  44  45


        G   G   L   V   Q   P   G   G   S   L   R   L   S   C   A


      /ggc/ggt/ctt/gtt/cag/cct/ggt/ggt/tct/tta/cgt/ctt/tct/tgc/gct/


 


          Sites of variegation       <1><1> <1> <1>   6859-fold diversity


      ----FR1-------------->/.....CDR1............./---FR2-----


       46  47  48  49  50  51  52   53  54   55  56  57  58  59  60


        A   S   G   F   T   F   S   -   Y   -   M   -   W   V   R


      /gct/tcc/gga/ttc/act/ttc/tct/ - /tac/ - /atg/ - /tgg/gtt/cgc/


           BspEI                      BsiWI                      BstXI.


 


                         Sites of variegation-><2>     <2> <3>


      -------FR2-------------------->/...CDR2


       61  62  63  64  65  66  67  68  69  70  71  72  73  74  75


        Q   A   P   G   K   G   L   E   W   V  S   -   I   -   -


      /caa/gct/cct/ggt/aaa/ggt/ttg/gag/tgg/gtt/tct/ - /atc/ - / - /


   ...BstXI


 


                <1>     <1>  25992-fold diversity in CDR2


  .....CDR2......................................./---FR3-----


    76  77  78  79  80  81  82  83  84  85  86  87  88  89  90


     S   G   G   -   T   -   Y   A   D   S   V   K   G   R   F


  /tct/ggt/ggc/ - /act/ - /tat/gct/gac/tcc/gtt/aaa/ggt/cgc/ttc/


 


  --------FR3--------------------------------------------------


    91  92  93  94  95  96  97  98  99 100 101 102 103 104 105


    T   I   S   R   D   N   S   K   N   T   L   Y   L   Q   M


  /act/atc/tct/aga/gac/aac/tct/aag/aat/act/ctc/tac/ttg/cag/atg/


           XbaI


 


  ---FR3------------------------------------------------------


   106 107 108 109 110 111 112 113 114 115 116 117 118 119 120


    N   S   L   R   A   E   D   T   A   V   Y   Y   C   A   K


  /aac/agc/tta/agg/gct/gag/gac/acc/gct/gtc/tac/tac/tgc/gcc/aaa/


        AflII


 


  .......CDR3................./ Replaced by the various components!


   121 122 123 124 125 126 127


    D   Y   E   G   T   G   Y   (SEQ ID NO: 24)


  /gac/tat/gaa/ggt/act/ggt/tat/ (SEQ ID NO: 23)


 


  /----- FR4 ---(JH4)-----------------------------------------


    Y   F   D   Y   W   G   Q   G   T   L   V   T   V   S   S    (SEQ ID NO: 26)


  /tat/ttc/gat/tat/tgg/ggt/caa/ggt/acc/ctg/gtc/acc/gtc/tct/agt/. (SEQ ID NO: 25)


                                KpnI       BstEII





<1> = Codons for ADEFGHIKLMNPQRSTVWY (equimolar mixture)


<2> = Codons for YRWVGS (equimolar mixture)


<3> = Codons for PS or PS and G (equimolar mixture)













TABLE 2





Oligonucleotides used to variegate CDR1 of human HC















CDR1 - 5 residues








(ON-R1V1vg):
5′-ct/tcc/gga/ttc/act/ttc/tct/<1>/tac/<1>/atg/<1>/tgg/gtt/cgc/caa/gct/cct/gg-3′



(SEQ ID NO: 27)







<1> = Codons of ADEFGHIKLMNPQRSTVWY 1:1








(ON-R1top):
5′-cctactgtct/tcc/gga/ttc/act/ttc/tct-3′ (SEQ ID NO: 28)


(ON-R1bot) [RC]:
5′-tgg/gtt/cgc/caa/gct/cct/ggttgctcactc-3′ (SEQ ID NO: 29)







CDR1 - 7 residues








(ON-R1V2vg):
5′-ct/tcc/gga/ttc/act/ttc/tct/<6>/<7>/<7>/tac/tac/tgg/<7>/tgg/gtt/cgc/caa/gct/



cct/gg-3′ (SEQ ID NO: 30)







<6> = Codons for ST, 1:1


<7> = 0.2025(Codons for SG) + 0.035(Codons for ADEFHIKLMNPQRTVWY)


CDR1 - 14 residues








(ON-R1V3vg):
5′-ct/tcc/gga/ttc/act/ttc/tct/atc/agc/ggt/ggt/tct/atc/tcc/<1>/<1>/<1>/-



tac/tac/tgg/<1>/tgg/gtt/cgc/caa/gct/cct/gg-3′ (SEQ ID NO: 31)







<1> = Codons for ADEFGHIKLMNPQRSTVWY 1:1
















TABLE 3





Oligonucleotides used to variegate CDR2 of human HC















CDR2 - 17 residues








(ON-R2V1vg):
5′-ggt/ttg/gag/tgg/gtt/tct/<2>/atc/<2>/<3>/tct/ggt/ggc/<1>/act/<1>/tat/gct/-



gac/tcc/gtt/aaa/gg-3′ (SEQ ID NO: 32)


(ON-R2top):
5′-ct/tgg/gtt/cgc/caa/gct/cct/ggt/aaa/ggt/ttg/gag/tgg/gtt/tct-3′ (SEQ ID NO: 33)


(ON-R2bot) [RC]:
5′-tat/gct/gac/tcc/gtt/aaa/ggt/cgc/ttc/act/atc/tct/aga/ttcctgtcac-3′



(SEQ ID NO: 34)







<1> = Codons for A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y


(equimolar mixture)


<2> = Codons for Y, R, W, V, G and S (equimolar mixture)


<3> = Codons for P and S (equimolar mixture) or P, S and G (equimolar mixture)


 








(ON-R2V2vg):
5′-ggt/ttg/gag/tgg/gtt/tct/<1>/atc/<4>/<1>/<1>/ggt/<5>/<1>/<1>/



<1>/tat/gct/-gac/tcc/gtt/aaa/gg-3′ (SEQ ID NO: 35)







<4> = Codons for DINSWY (equimolar mixture)


<5> = Codons for SGDN, (equimolar mixture)


CDR2 - 16 residues








(ON-R2V3vg):
5′-ggt/ttg/gag/tgg/gtt/tct/<1>/atc/<4>/<1>/<1>/ggt/



<5>/<1>/<1>/tat/aac/cct/tcc/ctt/aag/gg-3′ (SEQ ID NO: 36)


(ON-R2bo3)[RC]:
5′-tat/aac/cct/tcc/ctt/aag/ggt/cgc/ttc/act/atc/tct/aga/ttcctgtcac-3′



(SEQ ID NO: 37)







CDR2 - 19 residues








(ON-R2V4vg):
5′-ggt/ttg/gag/tgg/gtt/tct/<1>/atc/<8>/agt/<1>/<1>/



<1>/ggt/ggt/act/act/<1>/tat/gcc/gct/tcc/gtt/aag/gg-3′ (SEQ ID NO: 38)


(ON-R2bo4)[RC]:
5′-tat/gcc/gct/tcc/gtt/aag/ggt/cgc/ttc/act/atc/tct/aga/ttcctgtcac-3′



(SEQ ID NO: 39)



<1>, <2>, <3>, <4> and <5> are as defined above







<8> is 0.27 R and 0.027 each of ADEFGHIKLMNPQSTVWY
















TABLE 4







Preferred Components

















Preferred






Fraction of
Adjusted


Component

Length
Complexity
Library
Fraction















1
YYCA21111YFDYWG.
8
2.6 × 105
.10
.02



(SEQ ID NO: 6)







(1 = any amino acid residue, except C; 2 = K and R)






 


2
YYCA2111111YFDYWG.
10
9.4 × 107
.14
.14



(SEQ ID NO: 7)







(1 = any amino acid residue, except C; 2 = K and R)






 


3
YYCA211111111YFDYTG.
12
3.4 × 1010
.25
.25



(SEQ ID NO: 8)







(1 = any amino acid residue, except C; 2 = K and R)






 


4
YYCAR111S2S3111YFDYWG.
14
1.9 × 108
.13
.14



(SEQ ID NO: 9)







(1 = any amino acid residue, except C; 2 = S and G







3 = Y and W)






 


5
YYCA2111CSG11CY1YFDYWG.
15
9.4 × 107
.13
.14



(SEQ ID NO: 10)







(1 = any amino acid residue, except C; 2 = K and R)






 


6
YYCA211S1TIFG11111YFDYWG.
17
1.7 × 1010
.11
.12



(SEQ ID NO: 11)







(1 = any amino acid residue, except C; 2 = K and R)






 


7
YYCAR111YY2S33YY111YFDYWG.
18
3.8 × 108
.04
.08



(SEQ ID NO: 12)







(1 = any amino acid residue, except C; 2 = D or G;







3 = S and G)






 


8
YYCAR1111YC2231CY111YFDYWG.
19
2.0 × 1011
.10
.11



(SEQ ID NO: 13)







(1 = any amino acid residue, except C; 2 = S and G;







3 = T, D and G)
















TABLE 5





Oligonucleotides used to variegate the eight components of HC CDR3
















(Ctop25):
5′-gctctggtcaac/tta/agg/gct/gag/g-3′ (SEQ ID NO: 40)


(CtprmA):
5′-gctctggtcaac/tta/agg/gct/gag/gac/acc/gct/gtc/tac/tac/tgc/gcc-3′



          AflII...  (SEQ ID NO: 41)


(CBprmB) [RC]:
5′-/tac/ttc/gat/tac/tgg/ggc/caa/ggt/acc/ctg/gtc/acc/tcgctccacc-3′



(SEQ ID NO: 42)                              BstEII...


(CBot25) [RC]:
5′-/ggt/acc/ctg/gtc/acc/tcgctccacc-3′ (SEQ ID NO: 43)







The 20 bases at 3′ end of CtprmA are identical to the most 5′ 20 bases


of each of the vgDNA molecules.


Ctop25 is identical to the most 5′ 25 bases of CtprmA.


The 23 most 3′ bases of CBprmB are the reverse complement of the


most 3′ 23 bases of each of the vgDNA molecules.


CBot25 is identical to the 25 bases at the 5′ end of CBprmB.


Component 1








(C1t08):
5′-cc/gct/gtc/tac/tac/tgc/gcc/<2>/<1>/<1>/<1>/<1>/tac/ttc/gat/tac/tgg/ggc/caa/gg-3′



(SEQ ID NO: 44)







<1> = 0.095 Y + 0.095 G + 0.048 each of the residues ADEFHIKLMNPQRSTVW, no C; <2> = K and R


(equimolar mixture)


Component 2








(C2t10):
5′-cc/gct/gtc/tac/tac/tgc/gcc/<2>/<1>/<1>/<1>/<1>/<1>/<1>/tac/ttc/gat/tac/tgg/ggc/caa/gg-3′



(SEQ ID NO: 45)







<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C; <2> = K and R (equimolar


mixture)


Component 3








(C3t12):
5′-cc/gct/gtc/tac/tac/tgc/gcc/<2>/<1>/<1>/<1>/<1>/<1>/<1>/<1>/<1>/tac/ttc/gat/tac/-



tgg/ggc/caa/gg-3′ (SEQ ID NO: 46)







<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C; <2> = K and R (equimolar


mixture)


Component 4








(C4t140):
5′-cc/gct/gtc/tac/tac/tgc/gcc/cgt/<1>/<1>/<1>/tct/<2>/tct/<3>/<1>/<1>/<1>/tac/ttc/gat/-



tac/tgg/ggc/caa/gg-3′ (SEQ ID NO: 47)







<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C; <2> = S and G (equimolar


mixture); <3> = Y and W (equimolar mixture)


Component 5








(C5t15):
5′-cc/gct/gtc/tac/tac/tgc/gcc/<2>/<1>/<1>/<1>/tgc/tct/ggt/<1>/<1>/tgc/tat/<1>/tac/-



ttc/gat/tac/tgg/ggc/caa/gg-3′ (SEQ ID NO: 48)







<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C; <2> = K and R (equimolar


mixture)


Component 6








(C6t17):
5′-cc/gct/gtc/tac/tac/tgc/gcc/<2>/<1>/<1>/tct/<1>/act/atc/ttc/ggt/<1>/<1>/<1>/<1>/-



<1>/tac/ttc/gat/tac/tgg/ggc/caa/gg-3′ (SEQ ID NO: 49)







<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C; <2> = K and R (equimolar


mixture)


Component 7








(C7t18):
5′-cc/gct/gtc/tac/tac/tgc/gcc/cgt/<1>/<1>/<1>/tat/tac/<2>/tct/<3>/<3>/tac/tat/-



<1>/<1>/<1>/tac/ttc/gat/tac/tgg/ggc/caa/gg-3′ (SEQ ID NO: 50)







<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C; <2> = D and G (equimolar


mixture); <3> = S and G (equimolar mixture)


Component 8








(c8t19):
5′-cc/gct/gtc/tac/tac/tgc/gcc/cgt/<1>/<1>/<1>/<1>/tat/tgc/<2>/<2>/<3>/<1>/tgc/tat/-



<1>/<1>/<1>/tac/ttc/gat/tac/tgg/ggc/caa/gg-3′ (SEQ ID NO: 51)







<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C; <2> = S and G (equimolar


mixture); <3> = TDG (equimolar mixture);
















TABLE 6





3-23:: JH4 Stuffers in place of CDRs















                                 FR1(DP47/V3-23)---------------


            20 21  22            23  24  25  26  27  28  29  30


            A   M   A             E   V   Q   L   L   E   S   G


ctgtctgaac  cc atg gcc           gaa/gtt/caa/ttg/tta/gag/tct/ggt/


(SEQ ID NO: 99)


Scab......  NcoI....                      MfeI


 


     --------------FR1--------------------------------------------


      31  32  33  34  35  36  37  38  39  40  41  42  43  44  45


       G   G   L   V   Q   P   G   G   S   L   R   L   S   C   A


     /ggc/ggt/ctt/gtt/cag/cct/ggt/ggt/tct/tta/cgt/ctt/tct/tgc/gct/


 


     ----FR1-------------------->/...CDR1 stuffer..../---FR2------


      46  47  48  49  50  51  52  53  54  55  56  57  58  59  60


       A   S   G   F   T   F   S   S   Y   A   /   /   W   V   R


     /gct/tcc/gga/ttc/act/ttc/tct/tcg/tac/gct/tag/taa/tgg/gtt/cgc/


           BspEI                     BsiWI                       BstXI.


 


     -------FR2--------------------------------->/...CDR2 stuffer.


      61  62  63  64  65  66  67  68  69  70  71  72  73  74  75


       Q   A   P   G   K   G   L   E   W   V   S   /   p   r   /


    /caa/gct/cct/ggt/aaa/ggt/ttg/gag/tgg/gtt/tct/taa/cct/agg/tag/


...BstXI                                         AvrII..


 


      ....CDR2 stuffer..................................../---FR3---


       91  92  93  94  95  96  97  98  99  100 101 102 103 104 105


       T   I   S   R   D   N   S   K   N   T   L   Y   L   Q   M


      /act/atc/tct/aga/gac/aac/tct/aag/aat/act/ctc/tac/ttg/cag/atg/


              XbaI


 


     ---FR3-----------..> CDR3 Stuffer------------->/


      106 107 108 109 110


       N   S   L   R   A   (SEQ ID NO: 53)


     /aac/agc/tta/agg/gct/tag taa agg cct taa


             AflII                StuI...


 


 /----- FR4 ---(JH4)-----------------------------------------


  Y   F   D   Y   W   G   Q   G   T   L   V   T   V   S   S (SEQ ID NO: 26)


/tat/ttc/gat/tat/tgg/ggt/caa/ggt/acc/ctg/gtc/acc/gtc/tct/agt/... (SEQ ID NO: 25)


                              KpnI       BstEII
















TABLE 7





A27:JH1 Human Kappa light chain gene















 gaggacc attgggcccc ctccgagact ctcgagcgca


 Scab...... Eco0109I           XhoI


           ApaI


 


acgcaattaa tgtgagttag ctcactcatt aggcacccca ggctttacac tttatgcttc


      ..-35..          Plac                    ..-10.


 


cggctcgtat gttgtgtgga attgtgagcg gataacaatt tcacacagga


 


aacagctatg accatgatta


 


cgccaagctt tggagccttt tttttggaga ttttcaac  (SEQ ID NO: 54)


  PflMI.......


      Hind III


 


M13 III signal sequence (AA seg)---------------------------


  1   2   3   4   5   6   7   8   9  10  11  12  13  14  15


  M   K   K   L   L   F   A   I   P   L   V   V   P   F   Y


 gtg aag aag ctc cta ttt gct atc ccg ctt gtc gtt ccg ttt tac


 


--Signal-->FR1--------------------------------------------->


 16  17  18  19  20  21  22  23  24  25  26  27  28  29  30


  S   H   S   A   Q   S   V   L   T   Q   S   P   G   T   L


/agc/cat/agt/gca/caa/tcc/gtc/ctt/act/caa/tct/cct/ggc/act/ctt/


          ApaLI...


 


----- FR1 ------------------------------------->/ CDR1----->


 31  32  33  34  35  36  37  38  39  40  41  42  43  44  45


  S   L   S   P   G   E   R   A   T   L   S   C   R   A   S  (SEQ ID NO: 55)


 /tcg/cta/agc/ccg/ggt/gaa/cgt/gct/acc/tta/agt/tgc/cgt/gct/tcc/ (SEQ ID NO: 54; Cont'd)


    EspI.....                       AflII...


            XmaI....


For CDR1:


<1> ADEFGHIKLMNPQRSTVWY 1:1


<2> S(0.2) ADEFGHIKLMNPQRTVWY (0.044 each)


<3> Y(0.2) ADEFGHIKLMNPQRSTVW (0.044 each)


(CDR1 installed as AflII-(SexAI or KasI) cassette.) For the most preferred 11 length codon 51


(XXX) is omitted; for the preferred 12 length this codon is <2>


 


         ------- CDR1 --------------------->/--- FR2 --------------->


             <1>     <2> <2> xxx <3>


         46  47  48  49  50  51  52  53  54  55  56  57  58  59  60


          Q   -   V   -   -   -   -  L   A   W   Y   Q   Q   K   P (SEQ ID NO: 55; Cont'd)


        /cag/ - /gtt/ - / - / - / - /ctt/gct/tgg/tat/caa/cag/aaa/cct/(SEQ ID NO: 54; Cont'd)


                                                              SexAI...


For CDR2:


<1> ADEFGHIKLMNPQRSTVWY 1:1


<2> S(0.2) ADEFGHIKLMNPQRTVWY (0.044 each)


<4> A(0.2) DEFGHIKLMNPQRSTVWY (0.044 each)


CDR2 installed as (SexAI or KasI) to (BamHI or RsrII) cassette.)


 


         ----- FR2 ------------------------>/------ CDR2 ---------->


                                            <1>         <2>     <4>


         61  62  63  64  65  66  67  68  69  70  71  72  73  74  75


          G   Q   A   P   R   L   L   I   Y   -   A   S   -   R   - (SEQ ID NO: 55; Cont'd)


        /ggt/cag/gcg/ccg/cgt/tta/ctt/att/tat/ - /gct/tct/ - /cgc/ - (SEQ ID NO: 54; Cont'd)


        SexAI....   KasI....


 


         CDR2-->/--- FR3 -------------------------------------------->


           <1>


           76  77  78  79  80  81  82  83  84  85  86  87  88  89  90


            -   G   I   P   D   R   F   S   G   S   G   S   G   T   D


          / - /ggg/atc/ccg/gac/cgt/ttc/tct/ggc/tct/ggt/tca/ggt/act/gac/


                BamHI


                       RsrII.....


 


         ------ FR3 ------------------------------------------------->


          91  92  93  94  95  96  97  98  99 100 101 102 103 104 105


            F   T   L   T   I   S   R   L   E   P   E   D   F   A   V (SEQ ID NO: 55' Cont'd)


         /ttt/acc/ctt/act/att/tct/aga/ttg/gaa/cct/gaa/gac/ttc/gct/gtt/ (SEQ ID NO: 54; Cont'd)


                              XbaI


For CDR3 (Length 9):


<1> ADEFGHIKLMNPQRSTVWY  1:1


<3> Y(0.2) ADEFGHIKLMNPQRTVW (0.044 each)


For CDR3 (Length 8): QQ33111P


1 and 3 as defined for Length 9


For CDR3 (Length 10): QQ3211PP1T


1 and 3 as defined for Length 9


2 S(0.2) and 0.044 each of ADEFGHIKLMNPQRTVWY


CDR3 installed as XbaI to (StyI or BsiWI) cassette.


 


         ------------>/----CDR3-------------------------->/-----FR4--->


                              <3> <1> <1> <1>    <1>


         106 107 108 109 110 111 112 113 114 115 116 117 118 119 120


           Y   Y   C   Q   Q   -   -   -   -   P   -   T   F   G   Q (SEQ ID NO: 55; Cont'd)


         /tat/tat/tgc/caa/cag/ - / - / - / - /cct/ - /act/ttc/ggt/caa/ (SEQ ID NO: 54; Cont'd)


                    BstXI...........


 


-----FR4------------------->/     <------- Ckappa ------------


121 122 123 124 125 126 127       128 129 130 131 132 133 134


  G   T   K   V   E   I   K        R   T   V   A   A   P   S


/ggt/acc/aag/gtt/gaa/atc/aag/    /cgt/acg/gtt/gcc/gct/cct/agt/


      StyI....                     BsiWI..


 


135 136 137 138 139 140 141 142 143 144 145 146 147 148 149


  V   F   I   F   P   P   S   D   E   Q   L   K   S   G   T


/gtg/ttt/atc/ttt/cct/cct/tct/gac/gaa/caa/ttg/aag/tca/ggt/act/


                                      MfeI...


 


150 151 152 153 154 155 156 157 158 159 160 161 162 163 164


  A   S   V   V   C   L   L   N   N   F   Y   P   R   E   A (SEQ ID NO: 55; Cont'd)


/gct/tct/gtc/gta/tgt/ttg/ctc/aac/aat/ttc/tac/cct/cgt/gaa/gct/ (SEQ ID NO: 54; Cont'd)


                                              BssSI...


 


 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179


  K   V   Q   W   K   V   D   N   A   L   Q   S   G   N   S


/aaa/gtt/cag/tgg/aaa/gtc/gat/aac/gcg/ttg/cag/tcg/ggt/aac/agt/


                              MluI....


 


 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194


  Q   E   S   V   T   E   Q   D   S   K   D   S   T   Y   S


/caa/gaa/tcc/gtc/act/gaa/cag/gat/agt/aag/gac/tct/acc/tac/tct/


 


 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209


  L   S   S   T   L   T   L   S   K   A   D   Y   E   K   H


/ttg/tcc/tct/act/ctt/act/tta/tca/aag/gct/gat/tat/gag/aag/cat/


 


 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224


  K   V   Y   A   C   E   V   T   H   Q   G   L   S   S   P (SEQ ID NO: 55; Cont'd)


/aag/gtc/tat/GCt/TGC/gaa/gtt/acc/cac/cag/ggt/ctg/agc/tcc/cct/ (SEQ ID NO: 54; Cont'd)


                                               SacI....


 


 225 226 227 228 229 230 231 232 233 234


  V   T   K   S   F   N   R   G   E   C                     (SEQ ID NO: 55; Cont'd)


/gtt/acc/aaa/agt/ttc/aac/cgt/ggt/gaa/tgc/taa/tag ggcgcgcc


                       DsaI....                  AscI....


                                                  BssHII


 


acgcatctctaa gcggccgc aacaggaggag                           (SEQ ID NO: 54; Cont'd)


             NotI....
















TABLE 8





2a2:JH2 Human lambda-chain gene















     gaggaccatt gggcccc   ttactccgtgac


     Scab...... Eco0109I


                ApaI..


              ----------FR1------------------------------------------->


              1   2   3   4   5   6   7   8   9  10  11  12  13  14  15


      S   A   Q   S   A   L   T   Q   P   A   S   V   S   G   S   P   G (SEQ ID NO: 57)


     agt/gca/caa/tcc/gct/ctc/act/cag/cct/gct/agc/gtt/tcc/ggg/tca/cct/ggt/ (SEQ ID NO: 56)


      ApaLI...                           NheI...          BstEII...


                                                               SexAI....


For CDR1 (length 14):


<1> = 0.27 T, 0.27 G, 0.027 each of ADEFHIKLMNPQRSVWY, no C


<2> = 0.27 D, 0.27 N, 0.027 each of AEFGHIKLMPQRSTVWY, no C


<3> = 0.36 Y, 0.0355 each of ADEFGHIKLMNPQRSTVW, no C


 


                                   T   G  <1>  S   S  <2>  V   G


     ------FR1------------------> /-----CDR1---------------------


      16  17  18  19  20  21  22  23  24  25  26  27  28  29  30


       Q   S   I   T   I   S   C   T   G   -   S   S   -   V   G


     /caa/agt/atc/act/att/tct/tgt/aca/ggt/ - /tct/tct/ - /gtt/ggc/


                              BsrGI..


 


      <1> <3> <2> <3>  V   S = vg Scheme #1, length = 14


      -----CDR1-------------> /--------FR2-----------------------


      31  32  33  34  35  36  37  38  39  40  41  42  43  44  45


       -   -   -   -   V   S   W   Y   Q   Q   H   P   G   K   A (SEQ ID NO: 57; Cont'd)


     / - / - / - / - /gtt/tct/tgg/tat/caa/caa/cac/ccg/ggc/aag/gcg/ (SEQ ID NO: 56; Cont'd)


                                                XmaI....    KasI.....


                                                AvaI....


 


A second Vg scheme for CDR1 gives segments of length 11:


T22G<2><4>L<4><4><4><3><4><4> where


<4> = equimolar mixture of each of ADEFGHIKLMNPQRSTVWY, no C


<3> = as defined above for the alternative CDR1


For CDR2:


<2> and <4> are the same variegation as for CDR1


 


                                  <4> <4> <4> <2>  R   P   S


           --FR2---------------> /------CDR2---------------->/-----FR3-


           46  47  48  49  50  51  52  53  54  55  56  57  58  59  60


            P   K   L   M   I   Y   -   -   -   -   R   P   S   G   V


          /ccg/aag/ttg/atg/atc/tac/ - / - / - / - /cgt/cct/tct/ggt/gtt/


     KasI....


 


          -------FR3----------------------------------------------------


           61  62  63  64  65  66  67  68  69  70  71  72  73  74  75


            S   N   R   F   S   G   S   K   S   G   N   T   A   S   L (SEQ ID NO: 57; Cont'd)


          /agc/aat/cgt/ttc/tcc/gga/tct/aaa/tcc/ggt/aat/acc/gca/agc/tta/ (SEQ ID NO: 56; Cont'd)


                           BspEI..                           HindIII.


                                BsaBI........(blunt)


 


      -------FR3-------------------------------------------------->


      76  77  78  79  80  81  82  83  84  85  86  87  88  89  90


       T   I   S   G   L   Q   A   E   D   E   A   D   Y   Y   C (SEQ ID NO: 57; Cont'd)


     /act/atc/tct/ggt/ctg/cag/gct/gaa/gac/gag/gct/gac/tac/tat/tgt/ (SEQ ID NO: 56; Cont'd)


                      PstI...


CDR3 (Length 11):


<2> and <4> are the same variegation as for CDR1


<5> = 0.36 S, 0.0355 each of ADEFGHIKLMNPQRTVWY no C


 


CDR3 (Length 10): <5> SY <1> <5> S <5> <1> <4> V


<1> is an equimolar mixture of ADEFGHIKLMNPQRSTVWY, no C


<4> and <5> are as defined for Length 11


 


     <4> <5> <4> <2> <4> S <4> <4> <4> <4> V


     -----CDR3----------------------------------->/---FR4--------


       91  92  93  94  95  96  97  98  99  100 101 102 103 104 105


       -   -   -   -   -   S   -   -   -   -    V   F   G   G   G


     / - / - / - / - / - /tct/ - / - / - / - /gtc/ttc/ggc/ggt/ggt/


                                                              KpnI...


 


     -------FR4-------------->


      106 107 108 109 110 111 112 113 114 115 116 117 118 119 120


       T   K   L   T   V   L   G   Q   P   K   A   A   P   S   V


     /acc/aaa/ctt/act/gtc/ctc/ggt/caa/cct/aag/gct/gct/cct/tcc/gtt/


  KpnI...                      HincII..


                                     Bsu36I...


 


      121 122 123 124 125 126 127 128 129 130 131 132 133 134 135


       T   L   F   P   P   S   S   E   E   L   Q   A   N   K   A (SEQ ID NO: 57; Cont'd)


     /act/ctc/ttc/cct/cct/agt/tct/gaa/gag/ctt/caa/gct/aac/aag/gct/ (SEQ ID NO: 56; Cont'd)


                                  SapI.....


 


      136 137 138 139 140 141 142 143 144 145 146 147 148 149 150


       T   L   V   C   L   I   S   D   F   Y   P   G   A   V   T


     /act/ctt/gtt/tgc/ttg/atc/agt/gac/ttt/tat/cct/ggt/gct/gtt/act/


                       BclI....


 


     151 152 153 154 155 156 157 158 159 160 161 162 163 164 165


      V   A   W   K   A   D   S   S   P   V   K   A   G   V   E


    /gtc/gct/tgg/aaa/gcc/gat/tct/tct/cct/gtt/aaa/gct/ggt/gtt/gag/


                                                                 BsmBI...


 


      166 167 168 169 170 171 172 173 174 175 176 177 178 179 180


        T   T   T   P   S   K   Q   S   N   N   K   Y   A   A   S


      /acg/acc/act/cct/tct/aaa/caa/tct/aac/aat/aag/tac/gct/gcg/agc/


  BsmBI....                                              SacI....


 


      181 182 183 184 185 186 187 188 189 190 191 192 193 194 195


       S   Y   L   S   L   T   P   E   Q   W   K   S   H   K   S (SEQ ID NO: 57; Cont'd)


     /tct/tat/ctt/tct/ctc/acc/cct/gaa/caa/tgg/aag/tct/cat/aaa/tcc/ (SEQ ID NO: 56; Cont'd)


SacI...


 


 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210


  Y   S   C   Q   V   T   H   E   G   S   T   V   E   K   T


/tat/tcc/tgt/caa/gtt/act/cat/gaa/ggt/tct/acc/gtt/gaa/aag/act/


                       BspHI...


 


 211 212 213 214 215 216 217 218 219


  V   A   P   T   E   C   S (SEQ ID NO: 57; Cont'd)


/gtt/gcc/cct/act/gag/tgt/tct/tag/tga/ggcgcgcc


                                    AscI....


                                     BssHII


 


aacgatgttc aag gcggccgc aacaggaggag (SEQ ID NO: 56; Cont'd)


               NotI.... Scab.......
















TABLE 9





Oligonucleotides For Kappa and Lambda Light Chain Variegation
















(Ctop25):
5′-gctctggtcaac/tta/agg/gct/gag/g-3′  (SEQ ID NO: 58)


(CtprmA):
5′-gctctggtcaac/tta/agg/gct/gag/gac/acc/gct/gtc/tac/tac/tgc/gcc-3′ 



(SEQ ID NO: 59) AflII...


 


(CBprmB) [RC]:
5′-/tac/ttc/gat/tac/ttg/ggc/caa/ggt/acc/ctg/gtc/acc/tcgctccacc-3′ 



(SEQ ID NO: 60)                           BstEII...


(CBot25) [RC]:
5′-/ggt/acc/ctg/gtc/acc/tcgctccacc-3′ (SEQ ID NO: 61)







Kappa chains: CDR1 (“1”), CDR2 (“2”), CDR3 (“3”)


CDR1








(Ka1Top610):
5′-ggtctcagttg/cta/agc/ccg/ggt/gaa/cgt/gct/acc/tta/agt/tgc/cgt/gct/tcccag-3′



(SEQ ID NO: 62)


(Ka1STp615):
5′-ggtctcagttg/cta/agc/ccg/ggt/g-3′ (SEQ ID NO: 63)


(Ka1Bot620) [RC]:
5′-ctt/gct/tgg/tat/caa/cag/aaa/cct/ggt/cag/gcg/ccaagtcgtgtc-3′



(SEQ ID NO: 64)


(Ka1SB625) [RC]:
5′-cct/ggt/cag/gcg/ccaagtcgtgtc-3′ (SEQ ID NO: 65)


(Ka1vg600):
5′-gct/acc/tta/agt/tgc/cgt/gct/tcc/cag-



/<1>/gtt/<2>/<2>/<3>/ctt/gct/tgg/tat/caa/cag/aaa/cc-3′ (SEQ ID NO: 66)


(Ka1vg600-12):
5′-gct/acc/tta/agt/tgc/cgt/gct/tcc/cag-



/<1>/gtt/<2>/<2>/<2>/<3>/ctt/gct/tgg/tat/caa/cag/aaa/cc-3′ (SEQ ID NO: 67)







CDR2








(Ka2Tshort657):
5′-cacgagtccta/cct/ggt/cag/gc-3′ (SEQ ID NO: 68)


(Ka2Tlong655):
5′-cacgagtccta/cct/ggt/cag/gcg/ccg/cgt/tta/ctt/att/tat-3′ (SEQ ID NO: 69)


(Ka2Bshort660): [RC]:
5′-/gac/cgt/ttc/tct/ggt/tctcacc-3′ (SEQ ID NO: 70)


(Ka2vg650):
5′-cag/gcg/ccg/cgt/tta/ctt/att/tat/<1>/gct/tct/<2>/-



     /cgc/<4>/<1>/ggg/atc/ccg/gac/cgt/ttc/tct/ggt/tctcacc-3′ (SEQ ID NO: 71)







CDR3








(Ka3Tlon672):
5′-gacgagtccttct/aga/ttg/gaa/cct/gaa/gac/ttc/gct/gtt/tat/tat/tgc/caa/c-3′



(SEQ ID NO: 72)


(Ka3BotL682) [RC]:
5′-act/ttc/ggt/caa/ggt/acc/aag/gtt/gaa/atc/aag/cgt/acg/tcacaggtgag-3′



(SEQ ID NO: 73)


(Ka3Bsho694) [RC]:
5′-gaa/atc/aag/cgt/acg/tcacaggtgag-3′ (SEQ ID NO: 74)


(Ka3vg670):
5′-gac/ttc/gct/gtt/-



/tat/tat/tgc/caa/cag/<3>/<1>/<1>/<1>/cct/<1>/act/ttc/ggt/caa/-



/ggt/acc/aag/gtt/g-3′ (SEQ ID NO: 75)


(Ka3vg670-8):
5′-gac/ttc/gct/gtt/- (



/tat/tat/tgc/caa/cag/<3>/<3>/<1>/<1>/<1>/cct/ttc/ggt/caa/-



/ggt/acc/aag/gtt/g-3′ SEQ ID NO: 76)


(Ka3vg670-10):
5′-gac/ttc/gct/gtt/tat/-



/tat/tgc/caa/cag/<3>/<2>/<1>/<1>/cct/cct/<1>/act/ttc/ggt/caa/-



/ggt/acc/aag/gtt/g-3′ (SEQ ID NO: 77)







Lambda Chains: CDR1 (“1”), CDR2 (“2”), CDR3 (“3”)


CDR1








(Lm1TPri75):
5′-gacgagtcctgg/tca/cct/ggt/-3′ (SEQ ID NO: 78)


(Lm1tlo715):
5′-gacgagtcctgg/tca/cct/ggt/caa/agt/atc/act/att/tct/tgt/aca/ggt-3′



(SEQ ID NO: 79)


(Lm1blo724) [rc]:
5′-gtt/tct/tgg/tat/caa/caa/cac/ccg/ggc/aag/gcg/agatcttcacaggtgag-3′



(SEQ ID NO: 80)


(Lm1bsh737) [rc]:
5′-gc/aag/gcg/agatcttcacaggtgag-3′ (SEQ ID NO: 81)


(Lm1vg710b):
5′-gt/atc/act/att/tct/tgt/aca/ggt/<2>/<4>/ctc/<4>/<4>/<4>/-



      /<3>/<4>/<4>/tgg/tat/caa/caa/cac/cc-3′ (SEQ ID NO: 82)


(Lm1vg710):
5′-gt/atc/act/att/tct/tgt/aca/ggt/<1>/tct/tct/<2>/gtt/ggc/-



/<1>/<3>/<2>/<3>/gtt/tct/tgg/tat/caa/caa/cac/cc-3′ (SEQ ID NO: 83)


CDR2



(Lm2TSh757):
5′-gagcagaggac/ccg/ggc/aag/gc-3′ (SEQ ID NO: 84)


(Lm2TLo753):
5′-gagcagaggac/ccg/ggc/aag/gcg/ccg/aag/ttg/atg/atc/tac/-3′ (SEQ ID NO: 85)


(Lm2BLo762) [RC]:
5′-cgt/cct/tct/ggt/gtc/agc/aat/cgt/ttc/tcc/gga/tcacaggtgag-3′



(SEQ ID NO: 86)


(Lm2BSh765) [RC]:
5′-cgt/ttc/tcc/gga/tcacaggtgag-3′ (SEQ ID NO: 87)


(Lm2vg750):
5′-g/ccg/aag/ttg/atg/atc/tac/-







             <4>/<4>/<4>/<2>/cgt/cct/tct/ggt/gtc/agc/aat/c-3′ (SEQ ID NO: 88)


CDR3








(Lm3TSh822):
5′-ctg/cag/gct/gaa/gac/gag/gct/gac-3′ (SEQ ID NO: 89)


(Lm3TLo819):
5′-ctg/cag/gct/gaa/gac/gag/gct/gac/tac/tat/tgt/-3′ (SEQ ID NO: 90)


(Lm3BLo825) [RC]:
5′-gtc/ttc/ggc/ggt/ggt/acc/aaa/ctt/act/gtc/ctc/ggt/caa/cct/



aag/g-acacaggtgag-3′ (SEQ ID NO: 91)


(Lm3BSh832) [RC]:
5′-c/ggt/caa/cct/aag/gacacaggtgag (SEQ ID NO: 92)


(Lm3vg817):
5′-gac/gag/gct/gac/tac/tat/tgt/-



/<4>/<5>/<4>/<2>/<4>/tct/<4>/<4>/<4>/<4>/-



            Gtc/ttc/ggc/ggt/ggt/acc/aaa/ctt/ac-3′ (SEQ ID NO: 93)


(Lm3vg817-10):
5′-gac/gag/gct/gac/tac/tat/tgt/-



/<5>/agc/tat/<1>/<5>/tct/<5>/<1>/<4>/gtc/ttc/ggc/ggt/ggt/-



/acc/aaa/ctt/ac-3′ (SEQ ID NO: 94)
















TABLE 10





A27:JH1 Kappa light chain geen with stuffers in place of CDRs















Each stuffer contains at least one stop codon and a


restriction site that will be unique within the diversity vector.


gaggacc attgggcccc ctccgagact ctcgagcgca


  Scab.....Eco0109I


           ApaI.


                              XhoI..


 


acgcaattaa tgtgagttag ctcactcatt aggcacccca ggctttacac tttatgcttc


      ..-35..         Plac                    ..-10.


 


cggctcgtat gttgtgtgga attgtgagcg gataacaatt tcacacagga aacagctatgac


 


catgatta cgccaagctt tggagccttt tttttggaga ttttcaac     (SEQ ID NO: 95)


           PflMI..............


            Hind3.


 


M13 III signal sequence (AA seq)--------------------------->


  1   2   3   4   5   6   7   8   9  10  11  12  13  14  15


  M   K   K   L   L   F   A   I   P   L   V   V   P   F   Y


 gtg aag aag ctc cta ttt gct atc ccg ctt gtc gtt ccg ttt tac


 


--Signal--> FR1--------------------------------------------


 16  17  18  19  20  21  22  23  24  25  26  27  28  29  30


  S   H   S   A   Q   S   V   L   T   Q   S   P   G   T   L


/agc/cat/agt/gca/caa/tcc/gtc/ctt/act/caa/tct/cct/ggc/act/ctt/


         ApaLI...


 


----- FR1 --------------------------------->/-------Stuffer->


 31  32  33  34  35  36  37  38  39  40  41  42  43


  S   L   S   P   G   E   R   A   T   L   S   /   / (SEQ ID NO: 96)


/tcg/cta/agc/ccg/ggt/gaa/cgt/gct/acc/tta/agt/tag/taa/gct/ccc/ (SEQ ID NO: 95; Cont'd)


   EspI.....                      AflII...


           XmaI....


 


 - Stuffer for CDR1--> FR2 ----------------FR2---->/  Stuffer for CDR2


                       59  60  61  62  63  64  65  66


                        K   P   G   Q   A   P   R


/agg/cct/ctt/tga/tct/g/aaa/cct/ggt/cag/gcg/ccg/cgt/taa/tga/aagcgctaatggccaacagtg


 StuI...                SexAI...    KasI....               AfeI..   MscI..


 


Stuffer-------->/--- FR3 ------------------------------------------->


       76  77  78  79  80  81  82  83  84  85  86  87  88  89  90


        T   G   I   P   D   R   F   S   G   S   G   S   G   T   D (SEQ ID NO: 96; Cont'd)


      /act/ggg/atc/ccg/gac/cgt/ttc/tct/ggc/tct/ggt/tca/ggt/act/gac/ (SEQ ID NO: 95; Cont'd)


             BamHI...


                   RsrII.....


 


-------FR3------->----------------STUFFER for CDR3------------------>


 91  92  93  94  95  96  97


  F   T   L   T   I   S   R   /   /


/ttt/acc/ctt/act/att/tct/aga/taa/tga/ gttaac tag acc tacgta acc tag


                XbaI...        HpaI..         SnaBI.


 


-----------------CDR3 stuffer--------------->/--------FR4--->


                                                118 119 120


                                                  F   G   Q


                                                /ttc/ggt/caa/


 


-----FR4------------------->/      <------- Ckappa ------------


121 122 123 124 125 126 127        128 129 130 131 132 133 134


  G   T   K   V   E   I   K         R   T   V   A   A   P   S (SEQ ID NO: 96; Cont'd)


/ggt/acc/aag/gtt/gaa/atc/aag/           /cgt/acg/gtt/gcc/gct/cct/agt/


      StyI....                     BsiWI..                   (SEQ ID NO: 95; Cont'd)


 


 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149


  V   F   I   F   P   P   S   D   E   Q   L   K   S   G   T


/gtg/ttt/atc/ttt/cct/cct/tct/gac/gaa/caa/ttg/aag/tca/ggt/act/ (SEQ ID NO: 96; Cont'd)


                                      MfeI...


 


acgcatctctaa gcggccgc aacaggaggag (SEQ ID NO: 95; Cont'd)


             NotI....


               EagI..
















TABLE 11





2a2:JH2 Human lambda-chain gene with stuffers in place of CDR3















gaggaccatt gggcccc ttactccgtgac


Scab...... Eco0109I


           ApaI


        -----------FR1-------------------------------------------->


         1   2   3   4   5   6   7   8   9  10  11  12  13  14  15


 S   A   Q   S   A   L   T   Q   P   A   S   V   S   G   S   P   G


agt/gca/caa/tcc/gct/ctc/act/cag/cct/gct/agc/gtt/tcc/ggg/tca/cct/ggt/


ApaLI...                            NheI...         BstEII...


                                                           SexAI....


 


------FR1------------------> /-----stuffer for CDR1---------


 16  17  18  19  20  21  22  23


  Q   S   I   T   I   S   C   T (SEQ ID NO: 98)


/caa/agt/atc/act/att/tct/tgt/aca/tct tag tga ctc (SEQ ID NO: 97)


                         BsrGI..


 


 -----Stuffer--------------------------->-------FR2---------->


 31  32  33  34  35  36  37  38  39  40  41  42  43  44  45


  R   S   /   /   P   /                   H   P   G   K   A


aga tct taa tga ccg tag                 cac/ccg/ggc/aag/gcg/


 BglII                                    XmaI....     KasI.....


                                          AvaI....


 


 --/-------------Stuffer for CDR2 ---------------------------------->


  P


/ccg/taa/tga/atc tcg tac g                               ct/ggt/gtt/


KasI....          BsiWI...


 


-------FR3--------------------------------------------------


 61  62  63  64  65  66  67  68  69  70  71  72  73  74  75


  S   N   R   F   S   G   S   K   S   G   N   T   A   S   L (SEQ ID NO: 98; Cont'd)


/agc/aat/cgt/ttc/tcc/gga/tct/aaa/tcc/ggt/aat/acc/gca/agc/tta/ (SEQ ID NO: 97; Cont'd)


                 BspEI..                           HindIII.


                        BsaBI........(blunt)


 


-------FR3------------>/--Stuffer for CDR3----------------->/


 76  77  78  79  80  81  82  83  84  85  86  87  88  89  90


  T   I   S   G   L   Q


/act/atc/tct/ggt/ctg/cag/gtt ctg tag ttc caattg ctt tag tga ccc


                 PstI...                 MfeI..


 


-----Stuffer--------------------------------->/---FR4-------


                                                103 104 105


                                                 G   G   G


                                               /ggc/ggt/ggt/


                                                       KpnI...


 


-------FR4--------------->


 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120


  T   K   L   T   V   L   G   Q   P   K   A   A   P   S   V (SEQ ID NO: 98; Cont'd)


/acc/aaa/ctt/act/gtc/ctc/ggt/caa/cct/aag/gct/gct/cct/tcc/gtt/ (SEQ ID NO: 97; Cont'd)


KpnI...                     HincII..


                                 Bsu36I...


 


 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135


  T   L   F   P   P   S   S   E   E   L   Q   A   N   K   A


/act/ctc/ttc/cct/cct/agt/tct/gaa/gag/ctt/caa/gct/aac/aag/gct/


                             SapI.....


 


 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150


  T   L   V   C   L   I   S   D   F   Y   P   G   A   V   T (SEQ ID NO: 98; Cont'd)


/act/ctt/gtt/tgc/ttg/atc/agt/gac/ttt/tat/cct/ggt/gct/gtt/act/ (SEQ ID NO: 97; Cont'd)


                  BclI....









The invention relates to generation of useful diversity in synthetic antibody (Ab) gene, especially to Ab genes having frameworks derived from human Abs.
BACKGROUND OF THE INVENTION
Antibodies are highly useful molecules because of their ability to bind almost any substance with high specificity and affinity and their ability to remain in circulation in blood for prolonged periods as therapeutic or diagnostic agents. For treatment of humans, Abs derived from human Abs are much preferred to avoid immune response to the Ab. For example, murine Abs very often cause Human Anti Mouse Antibodies (HAMA) which at a minimum prevent the therapeutic effects of the murine Ab. For many medical applications, monoclonal Abs are preferred. Nowadays the preferred method of obtaining a human Ab having a particular binding specificity is to select the Ab from a library of human-derived Abs displayed on a genetic package, such as filamentous phage.
Libraries of phage-displayed Fabs and scFvs have been produced in several ways. One method is to capture the diversity of donors, either naive or immunized. Another way is to generate libraries having synthetic diversity. The present invention relates to methods of generating useful diversity in human Ab scaffolds.
As is well known, typical Abs consist of two heavy chains (HC) and two light chains (LC). There are several types of HCs: gamma, mu, epsilon, delta, etc. Each type has an N-terminal V domain followed by three or more constant domains. The LCs comprise an N-terminal V domain followed by a constant domain. LCs come in two types: kappa and lambda.
Within each V domain (LC or HC) there are seven canonical regions, named FR1, CDR1, FR2, CDR2, FR3, CDR3, and FR4, where “FR” stands for “Framework Region” and “CDR” stands for “Complementarity Determining Region”. For LC and HC, the FR and CDR GLGs have been selected over time to be secretable, stable, non-antigenic and these properties should be preserved as much as possible. Actual Ab genes contain mutations in the FR regions and some of these mutations contribute to binding, but such useful FR mutations are rare and are not necessary to obtain high-affinity binding. Thus, the present invention will concentrate diversity in the CDR regions.
In LC, FR1 up to FR3 and part of CDR3 comes from a genomic collection of genes called “V-genes”. The remainder of CDR3 and FR4 comes from a genomic collection of genes called “J-genes”. The joining may involve a certain degree of mutation, allowing diversity in CDR3 that is not present in the genomic sequences. After the LC gene is formed, somatic mutations can give rise to mature, rearranged LC genes that have higher affinity for an antigen (Ag) than does any LC encoded by genomic sequences. A large fraction of somatic mutations occur in CDRs.
The HC V region is more complicated. A V gene is joined to a J gene with the possible inclusion of a D segment. About half of HC Abs sequences contain a recognizable D segment in CDR3. The joining is achieved with an amazing degree of molecular sloppiness. Roughly, the end of the V gene may have zero to several bases deleted or changed, the D segment may have zero to many bases removed or changed at either end, a number of random bases may be inserted between V and D or between D and J, and the 5′ end of J may be edited to remove or change several bases. Withal, it is amazing that human heavy chains work, but they do. The upshot is that the CDR3 is highly diverse both in encoded amino-acid sequences and in length. In designing synthetic libraries, there is the temptation to just throw in a high degree of synthetic diversity and let the phage sort it out. Nevertheless, D regions serve a function. They cause the Ab repertoire to be rich in sequences that a) allow Abs to fold correctly, and b) are conducive to binding to biological molecules, i.e. antigens.
One purpose of the present invention is to show how a manageable collection of diversified sequences can confer these advantages on synthetic Ab libraries. Another purpose of the present invention is to disclose analysis of known mature Ab sequences that lead to improved designs for diversity in the CDR1 and CDR2 of HC and the three CDRs of lambda and kappa chains.
BRIEF STATEMENT OF THE INVENTION
The invention is directed to methods of preparing synthetically diverse populations of Ab genes suitable for display on genetic packages (such as phage or phagemids) or for other regimens that allow selection of specific binding. Said populations concentrate the diversity into regions of the Ab that are likely to be involved in determining affinity and specificity of the Ab for particular targets. In particular, a collection of actual Ab genes has been analyzed and the sites of actual diversity have been identified. In addition, structural considerations were used to determine whether the diversity is likely to greatly influence the binding activity of the Ab. Schemes of variegation are presented that encode populations in which the majority of members will fold correctly and in which there is likely to be a plurality of members that will bind to any given Ag. Specifically, a plan of variegation is presented for each CDR of the human heavy chain, kappa light chain, and lambda light chain. The variegated CDRs are presented in synthetic HC and LC frameworks.
In one embodiment, the invention involves variegation of human HC variable domains based on a synthetic 3-23 domain joined to a JH4 segment in which the variability in CDR1 and CDR2 comprises sequence variation of segments of fixed length while in CDR3 there are several components such that the population has lengths roughly corresponding to lengths seen in human Abs and having embedded D segments in a portion of the longer segments. In the light chains, the kappa chain is built in an A27 framework and a JK1 while lambda is built in a 2a2 framework with an L2 J region.
EXAMPLES
Choice of a Heavy-Chain V Domain
The HC Germ-Line Gene (GLG) 3-23 (also known as VP-47) accounts for about 12% of all human Abs and it suitable for the framework of the library. Certain types of Ags elicit Abs having particular types of VH genes; in some cases, the types elicited are otherwise rarely found. This apparent Ag/Ab type specificity has been ascribed to possible structural differences between the various families of V genes. It is also possible that the selection has to do with the availability of particular AA types in the GLG CDRs. Suppose, for example, that the sequence YR at positions 4 and 5 of CDR2 is particularly effective in binding a particular type of Ag. Only the V gene 6-1 provides this combination. Most Abs specific for the Ag will come from GLG 6-1. If Y4-R5 were provided in other frameworks, then other frameworks are likely to be as effective in binding the Ag.
Analysis of HC CDR1 and CDR2:
In CDR1 and CDR2 of HCs, the GLGs provide limited length diversity as shown in Table 15P. Note that GLGs provide CDR1s only of the lengths 5, 6, and 7. Mutations during the maturation of the V-domain gene leads to CDR1s having lengths as short as 2 and as long as 16. Nevertheless, length 5 predominates. The preferred length for the present invention is 5 AAs in CDR1 with a possible supplemental components having lengths of 7 and 14.
GLGs provide CDR2s only of the lengths 15-19, but mutations during maturation result in CDR2s of length from 16 to 28 AAs. The lengths 16 and 17 predominate in mature Ab genes and length 17 is the most preferred length for the present invention. Possible supplementary components of length 16 and 19 may also be incorporated.
Table 20P shows the AA sequences of human GLG CDR1s and CDR2. Table 21P shows the frequency of each amino-acid type at each position in the GLGs. The GLGs as shown in Table 20P have been aligned by inserting gaps near the middle of the segment so that the ends align.
The 1398 mature V-domain genes used in studying D segments (vide infra) were scanned for examples in which CDR1 and CDR2 could be readily identified. Of this sample 1095 had identifiable CDR1, 2, and 3. The CDRs were identified by finding subsequences of the GLGs in an open reading frame. There are 51 human HC V genes. At the end of FR1, there are 20 different 9-mers. At the start of FR2, there are 11 different 9-mers. At the end of FR2 there are 14 different 9-mers. At the start of FR3, there are 14 different 9-mers. At the end of FR3, there are 13 different 9-mers. At the start of JH, there are three different 9-mers. These motifs were compared to the reported gene in frame and a match, at the site of maximum similarity, of seven out of nine was deemed acceptable. Only when all three CDRs were identified were any of the CDRs included in the analysis. In addition, the type of the gene was determined by comparing the framework regions to the GLG frameworks; the results are shown in Table 22P.
Design of HC CDR1 and CDR2 Diversity.
Diversity in CDR1 and CDR2 was designed from: a) the diversity of the GLGs, b) observed diversity in mature HC genes, and c) structural considerations. In CDR1, examination of a 3D model of a humanized Ab showed that the side groups of residues 1, 3, and 5 were directed toward the combining pocket. Consequently, we allow each of these positions to be any amino-acid type except cysteine. Cysteine can form disulfide bonds. Disulfide bonds are an important component of the canonical Ig fold. Having free thiol groups could interfere with proper folding of the HC and could lead to problems in production or manipulation of selected Abs. Thus, I exclude cysteine from the menu. The side groups of residue 2 is directed away from the combining pocket. Although this position shows substantial diversity, both in GLG and mature genes, I fixed this residue as Tyr because it occurs in 681/820 mature genes (Table 21P). Position 4 is fixed as Met. There is some diversity here, but almost all mature genes have uncharged hydrophobic AA types: M, W, I, V, etc. (Table 21P). Inspection of a 3D model shows that the side group of residue 4 is packed into the innards of the HC. Since we are using a single framework (3-23), we retain the Met that 3-23 has because it is likely to fit very well into the framework of 3-23. Thus, the most preferred CDR1 library consists of XYXMX (SEQ ID NO:109) where X can be any one of [A,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y] (no C). The DNA that encodes this is preferably synthesized using trinucleotide building blocks so that each AA type is present in essentially equimolar amounts. Specifically, the X codons are synthesized using a mixture of the codons [gct, gat, gag, ttt, ggt, cat, att, aag, atg, aat, cct, cag, cgt, tct, act, gtt, tgg, tat]. This diversity is shown in the context of a synthetic 3-23 gene in Table 18P. The diversity oligonucleotide (ON) is synthesized from BspEI to BstXI and can be incorporated either by PCR synthesis using overlapping ONs or introduced by ligation of BspEI/BstXI-cut fragments. Table 22P shows ONs that embody the specified variegation. PCR using ON-R1V1vg, ON-R1top, and ON-R1bot gives a dsDNA product of 73 base pairs, cleavage with BspEI and BstXI trims 11 and 13 bases from the ends and provides cohesive ends that can be ligated to similarly cut vector having the synthetic 3-23 domain shown in Table 18P. Replacement of ON-R1V1vg with either ONR1V2vg or ONR1V3vg allows synthesis of the two alternative diversity patterns given below.
Alternatively, one can include CDR1s of length 7 and/or 14. For length 7, a preferred diversity is (S/T)1(S/G/x)2(S/G/x)3Y4Y5W6(S/G/x)7 (SEQ ID NO:107); where (S/T) indicates an equimolar mixture of Ser and Thr codons; (S/G/x) indicates a mixture of 0.2025 S, 0.2025 G, and 0.035 for each of A, D, E, F, H, I, K, L, M, N, P, Q, R, T, V, W, Y. Other proportions could be used. The design gives a predominance of Ser and Gly at positions 2, 3, and 7, as occurs in mature HC genes. For length 14, a preferred pattern of diversity is VSGGSISXXXYYWX (SEQ ID NO:1) where X can be any AA type except Cys. This pattern appears to arise by insertions into the GLG sequences (SGGYYWS; SEQ ID NO:110, (4-30.1 and 4-31) and similar sequences. There is a preference for a hydrophobic residue at position 1 (V or C) with a second insertion of SISXXX (SEQ ID NO:111) between GG and YY. Diversity ONs having CDR1s of length 7 or 14 are synthesized from BspEI to BstXI and introduced into the library in appropriate proportions to the CDR1 of length 5. The components should be incorporated in approximately the ratios in which they are observed in antibodies selected without reference to the length of the CDRs. For example, the sample of 1095 HC genes examined here have them in the ratios (L=5:L=7:L=14::820:175:23::0.80:0.17:0.02).
CDR2
Diversity at CDR2 was designed with the same considerations: GLG sequences, mature sequences and 3D structure. A preferred length for CDR2 is 17, as shown in Table 18P. Examination of a 3D model suggests that the residues shown as varied in Table 18P are the most likely to interact directly with Ag. Thus a preferred pattern of variegation is: <2>I<2><3>SGG<1>T<1>YADSVKG (SEQ ID NO:2), where <2> indicates a mixture of YRWVGS, <3> is a mixture of P and S, and <1> is a mixture of ADEFGHIKLMNPQRSTVWY (no C). ON-R2V1vg shown in Table 22P embodies this diversity pattern. PCR with ON-R2V1vg, ON-R2top, and ONR2bot gives a dsDNA product of 122 base pairs. Cleavage with BstXI and XbaI removes about 10 bases from each end and produces cohesive ends that can be ligated to similarly cut vector that contains the 3-23 gene shown in Table 18P.
An alternative pattern would include the variability seen in mature CDR2s as shown in Table 21P: <1>I<4><1><1>G<5><1><1><1>YADSVKG (SEQ ID NO:3), where <4> indicates a mixture of DINSWY, and <5> indicates a mixture of SGDN. This diversity pattern is embodied in ON-R2V2vg shown in Table 22P. For either case, the variegated ONs would be synthesized so that fragments of dsDNA containing the BstXI and XbaI site can be generated by PCR. ON-R2V2vg embodies this diversity pattern.
Alternatively, one can allow shorter or longer CDR2s. Table 22P shows ON-R2V3vg which embodies a CDR2 of length 16 and ON-R2V4vg which embodies a CDR2 of length 19. Table 22P shows ON-R2V3vg is PCR amplified with ON-R2top and ON-R2bo3 while ON-R2V4vg is amplified with ON-R2top and ONR2-bo4.
Analysis of HC CDR3:
CDR3s of HC vary in length and in sequence. About half of human HCs consist of the components: V::nz::D::ny::JHn where V is a V gene, nz is a series of bases (mean 12) that are essentially random, D is a D segment, often with heavy editing at both ends, ny is a series of bases (mean 6) that are essentially random, and JH is one of the six JH segments, often with heavy editing at the 5′ end. In HCs that have no identifiable D segment, the structure is V::nz::JHn where JH is usually edited at the 5′ end. Our goal is to mimic the diversity of CDR3, but not to duplicate it (which would be impossible). The D segments appear to provide spacer segments that allow folding of the IgG. The greatest diversity is at the junctions of V with D and of D with JH. The planned CDR3 library will consist of several components. Some of these will have only sequence diversity. Others will have sequence diversity with embedded D segments to extend the length while incorporating sequences known to allow Igs to fold.
There are many papers on D segments. Corbett et al. (1997) show which D segments are used in which reading frames. My analysis basically confirms their findings. They did not report, however, the level of editing of each D segment and this information is needed for design of an effective library.
The following diversified sequences would be incorporated in the indicated proportions: “1” stands for 0.095 [G, Y] and 0.048 [A, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W]; double dose of Gly and Tyr plus all other AAs except Cys at equal level.
The amount of each component is assigned from the tabulation of lengths of the collection of natural VH genes. Component 1 represents all the genes having length 0 to 8 (counting from the YYCAR (SEQ ID NO:112) motif to the WG dipeptide motif). Component 2 corresponds the all the chains having length 9 or 10. Component 3 corresponds to the genes having length 11 or 12 plus half the genes having length 13. Component 4 corresponds to those having length 14 plus half those having length 13. Component 5 corresponds to the genes having length 15 and half of those having length 16. Component 6 corresponds to genes of length 17 plus half of those with length 16. Component 7 corresponds to those with length 18. Component 8 corresponds to those having length 19 and greater.
The composition has been adjusted because the first component is not complex enough to justify including it as 10% of the library. If the final library were to be 1. E 9, then 1. E 8 sequences would come from component 1, but it has only 2.6 E 5 CDR3 sequences so that each one would occur in  ̃385 CDR1/2 contexts. I think it better to have this short CDR3 diversity occur in  ̃77 CDR1/2 contexts and have the other, longer CDR3s occur more often.
The ONs would be PCR amplified with the primers CtprmA and CBprmB, cut with MB and BstEII, and ligated to similarly cut V3-23.
This set of components was designed after studying the sequences of 1383 human HC sequences as described below. The proposed components are meant to fulfill the goals:
1) approximately the same distribution of lengths as seen in real Ab genes,
2) high level of sequence diversity at places having high diversity in real Ab genes, and
3) incorporation of constant sequences often seen in real Ab genes.
Note that the design uses JH4 (YFDYWGQGTLVTVSS; SEQ ID NO:20), which is found more often, instead of JH3 (AFDIWGQGTMVTVSS; SEQ ID NO:21). This involves three changes in AA sequence, shown as double underscored bold. An alternative JH segment is shown.
How the Library Components were Designed:
The processing of sequence data was accomplished by a series of custom-written FORTRAN programs, each of which carries out a fairly simple transformation on the data and writes its results as one or more ASCII files. The next program then uses these files as input.
A set of 2049 human heavy-chain genes was selected from the version of GenBank that was available at Dyax on the Sun server on 26 Jun. 2000. A program named “Reformat” changed the format of the files to that of GenBank from the GCG format, creating one file per sequence. A second program named “IDENT_CDR3” processed each of these files as follows. Files were tested for duplication by previous entries, duplicates were discarded. Each reading frame was tested. Most entries had a single open reading frame (ORF), none had two, and some had none. Entries with multiple stops in every reading frame were discarded because this indicates poor quality of sequencing. The sequence was written in triplets in the ORF or in all three reading frames if no ORF was found. The sequence was examined for three motifs: a) AA sequence=“YYCxx”, b) DNA sequence=“tgg ggc (=WG)”, and DNA sequence=“g gtc acc (=BstE11)”. FR3 ends with a conserved motif YYCAR or a close approximation. When writing the DNA sequence, IDENT_CDR3 prints the DNA mostly in lower case. Cysteine codons (TGT or TGC) are printed in uppercase. When the motif “tay tay tgy” is found, IDENT_CDR3 starts a new line that contains “< > xxx xxx xxx xxx xxx” where the xxx's stand for the actual five codons that encode YYC and the next two codons (most often AR or AK). The following DNA is printed in triplets on new lines. A typical processed entry appears as in Table 1P.
Following the YYC motif, IDENT_CDR3 seeks the sequence “TGG GGC” (the “WG” motif) in the correct reading frame, 5/6 bases is counted as a hit. If found, the DNA is made uppercase. Following the WG motif (if found) or the YYC motif (if no WG found), IDENT_CDR3 seeks the sequence “G GTC ACC” (the BstEII site) in the correct reading frame, 6/7 bases is counted as a hit. If found, the bases are made upper case. If either the WG or BstEII motif are not found, a note is inserted saying that the feature was not identified. The output of IDENT_CDR3 was processed by hand. In many cases, the lacking YYC motif could be seen as a closely related sequence, such as YFC, FYC, or HYC. When this was supported by an appropriately positioned WG and/or BstEII site, the effective YYC site was marked and the sequence retained for further analysis. If the YYC motif could not be identified or if the WG or BstEII sites could not be found, the entry was discarded. For example, the entry in Table 2P had no YYC motif.
The double underscored sequence encodes YHCAS and is taken as the end of FR3. Note that there is a WG motif at bases 403-408 (bold upper case) and a BstEII site at bases 420-426 (bold upper case). Using WordPerfect, I first made all occurrences of TGC and TGT bold. I then searched for “YYC not found”. If I could see the “YYC”-related sequence quickly, I edited the entry so that a YYC was shown. The entry above would be converted to that shown in Table 3P. This processing reduced the list of entries to 1669.
A third program named “New_DJ” processed the output of IDENT_CDR3. The end of the YYC motif (including the two codon following TGy=Cys) was taken as the end of FR3. The WG motif was taken as the end of the region that might contain a D segment. If WG was not observed and BstEII was, the WG site was assumed to be 17 bases upstream of BstEII. Using the WG motif for alignment, the sequence was compared to each human GLG JH segment (1-6) and the best one identified (New_DJ always assigned a JH segment). Starting from the WG motif of JH and moving toward the 5′ end, the program looked for the first codon having more than one mismatch. The region from YYCxx (SEQ ID NO:113) to this codon was taken as the region that might contain a D segment.
The region that might contain a D segment was tested against all the germ-line genes (GLGs) of human D segments and the best D segment was identified. The scoring involved matching the observed sequence to the GLG sequence in all possible ways. Starting at each base, multiply by 4 for a match and divide by 4 for a mismatch. Record the maximum value obtained for this function. The match was deemed significant if 7/7, 8/9, 9/11, etc. or more bases matched. Of the 1383 sequences examined for D segments,
“Assign_D” processes the output of New_DJ. For each sequence that had a significant match with a GLG D segment, a file was written containing the putative D segment, the DJ segment, the identified GLG D segment, the identified JH segment, the phase of the match between observed and GLG gene. For example, “D1—1-01_Phz0_hsa239356.txt” is a file recording the match of entry hsa239356 with D1-01 in phase 0. The file contains the information shown in Table 4P. The final DV of the second sequence immediately precedes the WG in JH and is ascribed to JH3. Other files that begin D1—1-01_Phz0 match the same GLG D segment and these can be aligned by sliding amino-acid sequences across each other.
Table 5P shows how sequence hs6d4xb7 is first assigned to JH4 and then to D3-22. Note that the DNA sequence TGGGGG is aligned to the TGG GGC of the GLG and that the sequence is truncated on the left to fit. The program finds that JH4 has the best fit (5 misses and 18 correct out of 23). From the right, the program sees that DYWGQ (underscored) come from JH, but then the match drops off and the rest of the sequence on the left comes either from added bases or a D segment.
The lower part of Table 5P shows that the possible D segment matches D#13 (3-23) is a very good match.
Of 1383 files accepted by Assign_D, 757 had identifiable D segments. The tally of JHs in Table 6P shows that JH4 is by far the most common
JH4 is most common, JH6 next, followed by JH3 and JH5. JH1 and JH2 are seldom used. Table 7P shows the length distributions of each JH class; they do not differ significantly class to class. These lengths count only amino-acids that are not accounted for by JH and so are shorter that the lengths given in Table 8P which cover from YYCAR (SEQ ID NO:112) to WG.
Table 8P contains the distribution of lengths for a) all the CDR3 segments, b) the CDR3 segments with identified D segments, and c) the CDR3 segments having no identifiable D segment. The CDR3s with identifiable D segments (13.9) are systematically longer than are those that lack D segments (11.2).
The identified CDR3 segments can be collated in two ways: aligned to the left (looking for a pattern following YYCAR; SEQ ID NO:112) or aligned to the right (looking for a pattern preceding WG). Table 9P shows the collation of left-aligned sequences while Table 10P shows the right-aligned sequences. For each position, I have tabulated the frequency of each AA type (A-M in the first block and N-Y in the second). The column headed “#” shows how many sequences have some AA at that position. The final column shows all of the AA types seen at that position with the most frequent first and the least frequent last. In the left-aligned sequences, we see that Gly is highly over-represented in the first seven positions while Tyr is over-represented at positions 8-16.
In Table 11P, I have tabulated the AA frequencies for the sequences having between 7 and 15 AAs between YYCAR (SEQ ID NO:112)_and WG. The last four positions can be viewed as coming from JH and so would be given lower levels of diversity than would earlier positions. From these tabulations, I conclude that most AA types are allowed at all the positions, but there is a fairly strong tendency to have Gly at the early positions and to end in Asp-Tyr (DY). We could use these tendencies in designing a pattern of variegation. I would not exclude any AA except Cys, but I might increase the frequency of Gly in the first several positions and Tyr in the last few.
There are 80 sequences (5.8%) having a pair of cysteines in CDR3. It is more surprising that 53 (3.8%) have a single Cys in CDR3.
MS-DOS was used to make a list of the files written by Assign_D. “Filter” converts the output of MS-DOS Dir into a form that can be read into WordPerfect and sorted to bring a files
belonging to the same D region together.
“Filter2” collects the sequences and produces a draft table of sequences, grouped by the D-segment used, and written so that the sequences can be aligned. The output of Filter2 were edited by hand. For each group, the translation of the GLG was inserted and the collection of observed sequences was aligned to the conserved part of the GLG. “Filter3” collated the aligned sequences. Table 12P shows an example of an alignment and the tabulation of AA types. The entries are as follows: “Entry” is the name used in the data base, “Seq1” is the sequence from the YYCAR (SEQ ID NO:112) motif to the first amino acid not assigned to JH and “L1” is the length of the segment. The segments are shown aligned to the identified D segment. Seq2 is the sequence from the YYCAR (SEQ ID NO:112) motif to the WG motif (i.e. including part of JH) and “L2” is the length of that sequence. JH is the identified JH segment for this sequence. “P” is the phase of the match. For positive values of P, P bases are found in the observed sequence that do not correspond to any from the GLG, i.e. the observed sequence has had that many bases inserted. For negative values of P, there are |P| bases in the GLG sequence for which there are no corresponding bases in the observed sequence. “Score” is approximately 1/(probability of accidental match). This is calculated by looking at all possible alignments. For each alignment, the score is first set to 1.0. Base by base, the score is multiplied by 4. if the bases match and divided by 4. if they do not. This is done for all starting points and ending points and the maximum value is recorded.
Table 13P is a summary of how often each D segment was identified and in which reading frame. I have not been consistent with Corbett et al. in assigning the phases of the GLG D segments. The MRC Web page that I took the GLGs from did not have D segments D1-14, D4-11, D5-18, or D6-25. None of these contribute to any great extent and this omission is unlikely to have any serious effect on the conclusions. The column headed “%” contains the percentage of the sequences examined here. The column headed “C %” contains the percentage reported by Corbett et al. I assume that the data used in Corbett et al. is mostly included in my collection. Nevertheless, the observed frequencies differ in detail. For example, my compilation shows that 10.7% of the collection contains a D segment encoding two cysteines while they have only 4.16% in this category. In D3 phase “0”, I see 19.4% of the collection while they report 11.8%.
The most common actual D segments were further analyzed. The GLGs are heavily edited at either end. The aligned sequences were aligned. For each D-segment having more than seven examples, Filter3 produced a table of the frequency of each amino-acid type at each position. From these tabulations, library components shown in Table 17P were designed. At each position where at least half the examples have an amino acid, I entered either the dominant AA type or “x”. An AA type was “dominant” if it occurred more than 50% of the time. L is the length and f is the number of sequences observed that have related sequences.
Table 14P shows possible library components for a library of CDR3's. “L” is the length of the insert and “f” is the frequency of the motif in the assayed collection. Table 17P shows vgDNA that embodies each of the components shown in Table 14P. In Table 17P, the oligonucleotides (ON) Ctop25, CtprmA, CBprmB, and CBot25 allow PCR amplification of each of the variegated ONs (vgDNA): C1t08, C2t10, C3t12, C4t14, C5t15, C6t17, C7t18, and c8t19. After amplification, the dsDNA can be cleaved with AflII and BstEII (or KpnI) and ligated to similarly cleaved vector that contains the remainder of the 3-23 synthetic domain. Preferably, this vector already contains diversity in CDR1 and CDR2 as disclosed herein. Preferably, the recipient vector contains a stuffer in place of CDR3 so that there will be no parental sequence that would then occur in the resulting library. Table 50P shows a version of the V3-23 gene segment with each CDR replaced by a short segment that contains both stop codons and restriction sites that will allow specific cleavage of any vector that does not have the stuffer removed. The stuffer can either be short and contain a restriction enzyme site that will not occur in the finish library, allowing removal of vectors that are not cleaved by both AflII and BstEII (or KpnI) and religated. Alternatively, the stuffer could be 200-400 bases long so that uncleaved or once cleaved vector can be readily separated from doubly cleaved vector.
In the vgDNA for HC CDR3, <1> means a mixture comprising 0.27 Y, 0.27 G, and 0.027 of each of the amino-acid codons {A, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W}; <2> means an equimolar mixture of K and R; and <3> means an equimolar mixture of S and G.
Analysis of Human Kappa Light Chains and Preferred Variegation Scheme:
A collection of 285 human kappa chains was assembled from the public data base. Table 27 shows the names of the entries used. The GLG sequences of nine bases at each end of the framework regions were used to find the FR/CDR junctions. Only in cases where all six junctions could be found was the sequences included. Table 25P shows the distribution of lengths in CDRs in human kappas. CDR1s with lengths of 11, 12, 13, 16, and 17 were observed with 11 being predominant and 12 well represented. CDR2 exhibits only length 7. CDR3 exhibits lengths of 1, 4, 6, 7, 8, 9, 10, 11, 12, 13, and 19. Essentially all examples are in the 8, 9, or 10 length groups.
Table 26P shows the distribution of V and J genes seen in the sample. A27 is the most common V and JK1 is the most common J. Thus, a suitable synthetic kappa gene comprises A27 joined to JK1. Table 30P shows a suitable synthetic kappa chain gene, including a PlacZ promoter, ribosome-binding site, and signal sequence (M13 III signal). The DNA sequence encodes the GLG amino-acid sequence, but does not comprise the GLG DNA sequence. Restriction sites are designed to fall within each framework region so that diversity can be cloned into the CDRs. XmaI and EspI are in FR1, SexAI is in FR2, RsrII is in FR3, and KpnI (or Acc65I) are in FR4. Additional sites are provided in the constant kappa chain to facilitate construction of the gene.
Table 30P also shows a suitable scheme of variegation for kappa. In CDR1, a preferred length is 11 codons. The A27 GLG has a CDR1 of 12 codons, but the sample of mature kappa chains has length 11 predominating. One could also introduce a component of kappas having length 12 in CDR1 by introducing codon 52 as <2> (i.e. a Ser-biased mixture). CDR2 of kappa is always 7 codons. Table 31P shows a tally of 285 CDR2s and a preferred variegation scheme for CDR2. The predominant length of CDR3 in kappa chains is 9 codons. Table 32P shows a tally of 166 CDR3s from human kappas and a preferred variegation scheme (which is also shown in Table 30P).
Analysis of Lambda Chains and Preferred Variegation Scheme:
A collection of 158 lambda sequences was obtained from the public data base. Of these 93 contained sequences in which the FR/CDR boundaries could be identified automatically. Table 33P shows the distribution of lengths of CDRs.
Method of Construction:
The diversity of HC, kappa, and lambda are best constructed in separate vectors. First a synthetic gene is designed to embody each of the synthetic variable domains. The light chains are bounded by restriction sites for ApaLI (positioned at the very end of the signal sequence) and AscI (positioned afer the stop codon). The heavy chain is bounded by SfiI (positioned within the Pe1B signal sequence) and NotI (positioned in the linker between CH1 and the anchor protein. The initial genes are made with “stuffer” sequences in place of the desired CDRs. A “Stuffer” is a sequence the is to be cut away and replaced by diverse DNA but which does not allow expression of a functional antibody gene. For example, the stuffer may contain several stop codons and restriction sites that will not occur in the correct finished library vector. In Table 40P, the stuffer for CDR1 of kappa A27 contains a StuI site. The vgDNA for CDR1 is introduced as a cassette from EspI, XmaI, or AflII to either SexAI or KasI. After the ligation, the DNA is cleaved with StuI; there should be no StuI sites in the desired vectors.
REFERENCES


    Corbett, S J, Tomlinson, I M, Sonnhammer, E L L, Buck, D, Winter, G. “Sequences of the Human Immunoglobulin Diversity (D) Segment Locus: A Systematic Analysis Provides No Evidence for the Use of DIR Segments, Inverted D Segments, ‘Minor’ D Segments or D-D Recombination”. J Molec Biol (1997) 270:587-597.


TABLES







TABLE 1P





Typical entry in which YYC motif is found.















++++C:\tmp\haj10335.txt








LOCUS
HAJ10335 306 bp mRNA PRI 18-AUG-1998


DEFINITION
Homo sapiens mRNA for immunoglobulin heavy chain variable region,



clone ELD16/6.


ACCESSION
AJ010335


VERSION
AJ010335.1 GI: 3445266


Ngene =
306







Stop codons in reading frame 1











   49
115
124
253
277







No stops in reading frame 2


Stop codons in reading frame 3












   12
 60
 81
147
204
213








  1
  t ttg ggg tcc ctg aga ctc tcc TGT gca gcc tct gga ttc acc


 


 44
gtc agt agc aac tac atg acc tgg gtc cgc cag gct cta ggg aag


 


 89
ggg ctg gag tgg gtc tca gtt att tat agc ggt ggt agc aca tac


 


134
tac gca gac tcc gtg aag ggc gga ttc acc atc tcc aga gac aat


 


179
tcc aag aac aca ctg tat ctt caa atg aac agc ctg aga ccc gag


 


224
gac acg gct gtg


 


<
  > TAT TAC TGT gcg aca


 


251
ggt aat cgc ctg gaa atg gct gca att aac TGG GGC caa gga acc


 


263
ctG GTC ACC aa (SEQ ID NO: 113)
















TABLE 2P





entry in which YYC motif was not automatically identified















++C:\tmp\hs202g3.txt


!!NA_SEQUENCE 1.0








LOCUS
HS202G3 522 bp mRNA PRI 03-AUG-1995


DEFINITION
H. sapiens mRNA for immunoglobulin variable region (clone 202-G3).


ACCESSION
Z47259


VERSION
Z47259.1 GI: 619470


Ngene =
522







No stops in reading frame 1


Stop codons in reading frame 2










   89
110
305
314







Stop codons in reading frame 3











   84
192
321
351
369








  1
atg gac tgg acc tgg agg ttc ctc ttt gtg gtg gca gca gct aca


 


 46
ggt gtc cag tcc cag gtg cag ctg gtg cag tct ggg gct gag gtg


 


 91
aag aag cct ggg tcc tcg gtg aag gtc tcc TGC aag gct tct gga


 


136
ggc acc ttc agc agc tat gct atc agc tgg gtg cga cag gcc cct


 


181
gga caa ggg ctt gag tgg atg gga ggg atc atc cct atc ttt ggt


 


226
aca gca aac tac gca cag aag ttc cag ggc aga gtc acg att acc


 


271
gcg gac gaa tcc acg agc aca gcc tac atg gag ctg agc agc ctg


 


316
aga tct gag gac acg gcc gtg tat cac TGT gcg agt gag gga tgg


 


361
gag agt TGT agt ggt ggt ggc TGC tac gac ggt atg gac gtc TGG


 


406
GGC caa ggg acc acG GTC ACC gtc tcc tca gct tcc acc aag ggc


 


451
cca tcg gtc ttc ccc ctg gcg ccc TGC tcc agg agc acc tct ggg


 


496
ggc aca gcg gcc ctg ggc TGC ctg (SEQ ID NO: 114)


 


YYC
not found !!!
















TABLE 3P





Entry of Table 2P after editting.















++C:\tmp\hs202g3.txt


!!NA_SEQUENCE 1.0








LOCUS
HS202G3 522 bp mRNA PRI 03-AUG-1995


DEFINITION
H. sapiens mRNA for immunoglobulin variable region (clone 202-G3).


ACCESSION
Z47259


VERSION
Z47259.1 GI: 619470


Ngene =
522







No stops in reading frame 1


Stop codons in reading frame 2










   89
110
305
314







Stop codons in reading frame 3











   84
192
321
351
369








  1
atg gac tgg acc tgg agg ttc ctc ttt gtg gtg gca gca gct aca


 


 46
ggt gtc cag tcc cag gtg cag ctg gtg cag tct ggg gct gag gtg


 


 91
aag aag cct ggg tcc tcg gtg aag gtc tcc TGC aag gct tct gga


 


136
ggc acc ttc agc agc tat gct atc agc tgg gtg cga cag gcc cct


 


181
gga caa ggg ctt gag tgg atg gga ggg atc atc cct atc ttt ggt


 


226
aca gca aac tac gca cag aag ttc cag ggc aga gtc acg att acc


 


271
gcg gac gaa tcc acg agc aca gcc tac atg gag ctg agc agc ctg


 


316
aga tct gag gac acg gcc gtg


 


<YHCAS>
tat cac TGT gcg agt







(SEQ ID NO: 116)









gag gga tgg


 


361
gag agt TGT agt ggt ggt ggc TGC tac gac ggt atg gac gtc TGG


 


406
GGC caa ggg acc acG GTC ACC gtc tcc tca gct tcc acc aag ggc


 


451
cca tcg gtc ttc ccc ctg gcg ccc TGC tcc agg agc acc tct ggg


 


496
ggc aca gcg gcc ctg ggc TGC ctg (SEQ ID NO: 115)


 


YYC
not found !!!
















TABLE 4P





contents of file D1_1-01_Phz0_hsa239356.txt
















DRGGKYQLAPKGGM
(SEQ ID NO: 117)


 


DRGGKYQLAPKGGMDV
(SEQ ID NO: 118)


 


JH3 D# 1 Phase 15 Score 6.55D+04
















TABLE 5P





alignment of a CDR3::JH segment to GLG JHs and D-segments.















+c:\tmp\hs6d4xb7.txt









         1    1    2    2    3    3   3



1234567890    5    0    5    0    5   9


Observed
tatgatagtagtgggtcatactccgactacTGGGGGcag (SEQ ID NO: 119)


JH1
------------gctgaatacttccagcactggggccagggcaccctggtcaccgtctcctcag--(SEQ ID NO: 120) 



Miss=  9 Nt= 27


JH2
-----------ctactggtacttcgatctctggggccgtggcaccctggtcactgtctcctcag--(SEQ ID NO: 121) 



Miss= 13 Nt= 28


JH3
--------------tgatgcttttgatatctggggccaagggacaatggtcaccgtctcttcag--(SEQ ID NO: 122) 



Miss= 14 Nt= 25


JH4
----------------actactttgactactggggccagggaaccctggtcaccgtctcctcag--(SEQ ID NO: 123) 



Miss=  5 Nt= 23


JH5
-------------acaactggttcgacccctggggccagggaaccctggtcaccgtctcctcag--(SEQ ID NO: 124) 



Miss= 11 Nt= 26


JH6
-attactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcag--(SEQ ID NO: 125) 



Miss= 23 Nt= 38


 


4
tat gat agt agt ggg tca TAC Tcc GAC TAC TGG GGg CAG (SEQ ID NO: 126)



 Y   D   S   S   G   S   Y   S   D   Y   W   G   Q  (SEQ ID NO: 127)


 


JH4
--- --- --- --- --- -ac tac ttt gac tac tgg ggc cag gga acc ctg gtc acc gtc tcc tca g-- 



(SEQ ID NO: 128)



 -   -   -   -   -   -   Y   F   D   Y   W   G   Q   G   T   L   V   T   V   S   S   -



(SEQ ID NO: 129)


 







Fract = 0.783 = 18/23


Matching the rest to D segments:








D#13
--------gtattactatgatagtagtggttattactac  GLG      (SEQ ID NO: 130)



gatcgccacaattactatgatagtagtgggtcatactcc  Observed (SEQ ID NO: 131)



--------gt...................t.at....a.  . = match


D#13
Phase=   9 Score=    4.3980E+12
















TABLE 6P





Number of sequences identified as having JH derived from GLG JHn





















JH
1
2
3
4
5
6


# sequences
17
40
198
707
160
261
















TABLE 7P





Distribution of CDR3 fragments that might contain D segments.







For JH1





















0
1
2
3
4
5
6
7
8
9
10
11
12
13



0
0
1
1
3
1
1
2
0
3
1
1
1
2








Total = 17 Median = 8.0


For JH2





















0
1
2
3
4
5
6
7
8
9
10
11
12
13
14


0
0
0
0
0
2
4
6
2
6
3
4
5
2
3


15
16
17
18













2
0
0
1


















Total = 40 Median = 9.0


For JH3





















0
1
2
3
4
5
6
7
8
9
10
11
12
13
14


0
0
2
6
16
12
17
17
15
22
20
20
18
13
4


15
16
17
18
19












8
3
2
1
2

















Total = 198 Median = 8.6


For JH4





















0
1
2
3
4
5
6
7
8
9
10
11
12
13
14


0
0
7
15
19
40
63
82
81
77
81
53
57
44
30


15
16
17
18
19
20
21
22
23
24
25
26
27
28
29


15
23
8
3
5
2
0
1
0
0
0
0
0
0
0


30
31
32
33
34
35











0
0
0
0
0
1
















Total = 707 Median = 8.6


For JH5





















0
1
2
3
4
5
6
7
8
9
10
11
12
13
14


0
0
0
3
4
6
13
19
12
14
22
18
10
18
10


15
16
17
18
19
20
21
22
23
24
25
26
27
28
29


5
1
1
0
0
1
1
0
0
0
0
0
0
0
0


30
31
32
33
34
35
36
37
38
39
40
41
42
43
44


0
0
0
0
0
0
0
0
0
0
0
0
1
0
0


45
46















0
1




















Total = 160 Median = 9.4


For JH6





















0
1
2
3
4
5
6
7
8
9
10
11
12
13
14


2
0
1
2
5
15
20
18
22
29
29
28
23
16
10


15
16
17
18
19
20











14
9
9
4
2
3
















Total = 261 Median = 9.6
















TABLE 8P





Lengths of CDR3 segments from YYCAR to WG.







Distribution of lengths from end of FR3 to WG motif all sequences.












L


















0
1
2
3
4
5
6
7
8
9





N
6
0
0
4
2
9
13
38
61
88


Sum(N)
6
6
6
10
12
21
34
72
133
221


f
.004
.004
.004
.007
.009
.015
.025
.052
.096
.160












L


















10
11
12
13
14
15
16
17
18
19





N
101
118
154
150
118
125
105
84
61
46


SN
322
440
594
744
862
987
1092
1176
1237
1283


f
.233
.318
.430
.538
.623
.714
.790
.850
.894
.928












L


















20
21
22
23
24
25
26
27
28
29





N
42
16
17
7
9
2
1
0
2
1


SN
1325
1341
1358
1365
1374
1376
1377
1377
1379
1380


f
.958
.970
.982
.987
.993
.995
.996
.996
.997
.998












L


















30
31
32
33
34
35
36
37
38
39





N
0
0
0
0
0
0
0
1
0
0


SN
1380
1380
1380
1380
1380
1380
1380
1381
1381
1381


f
.998
.998
.998
.998
.998
.998
.998
.999
.999
.999













L

















40
41
42
43
44
45
46






N
0
0
1
0
0
0
1



SN
1381
1381
1382
1382
1382
1382
1383



f
.999
.999
.999
.999
.999
.999
1.0
Median = 12.65










Distribution of lengths from end of FR3 to WG motif with assigned D.












L


















0
1
2
3
4
5
6
7
8
9





N
3
0
0
0
0
0
3
9
21
15


SN
3
3
3
3
3
3
6
15
36
51


f
.004
.004
.004
.004
.004
.004
.008
.019
.046
.065












L


















10
11
12
13
14
15
16
17
18
19





N
39
64
77
97
72
77
75
63
45
35


SN
90
154
231
328
400
477
552
615
660
695


f
.115
.196
.294
.418
.510
.608
.703
.783
.841
.885












L


















20
21
22
23
24
25
26
27
28
29





N
38
15
15
6
9
2
1
0
1
1


SN
733
748
763
769
778
780
781
781
782
783


f
.934
.953
.972
.980
.991
.994
.995
.995
.996
.997












L


















30
31
32
33
34
35
36
37
38
39





N
0
0
0
0
0
0
0
1
0
0


SN
783
783
783
783
783
783
783
784
784
784


f
.997
.997
.997
.997
.997
.997
.997
.999
.999
.999













L

















40
41
42
43
44
45
46






N
0
0
0
0
0
0
1



SN
784
784
784
784
784
784
785



f
.999
.999
.999
.999
.999
.999
1.0
Median = 13.90










Distribution of lengths from end of FR3 to WG motif with no assigned D.












L


















0
1
2
3
4
5
6
7
8
9





N
3
0
0
4
2
9
10
29
40
73


SN
3
3
3
7
9
18
28
57
97
170


f
.005
.005
.005
.012
.015
.030
.047
.095
.162
.284












L


















10
11
12
13
14
15
16
17
18
19





N
62
54
77
53
46
48
30
21
16
11


SN
232
286
363
416
462
510
540
561
577
588


f
.388
.478
.607
.696
.773
.853
.903
.938
.965
.983












L


















20
21
22
23
24
25
26
27
28
29





N
4
1
2
1
0
0
0
0
1
0


SN
592
593
595
596
596
596
596
596
597
597


f
.990
.992
.995
.997
.997
.997
.997
.997
.998
.998












L


















30
31
32
33
34
35
36
37
38
39





N
0
0
0
0
0
0
0
0
0
0


SN
597
597
597
597
597
597
597
597
597
597


f
.998
.998
.998
.998
.998
.998
.998
.998
.998
.998













L













40
41
42






N
0
0
1



SN
597
597
598



f
.998
.998
1.0
Median = 11.17





L is the length


N is the number of examples


Sum(N) = SN is the sum of the Ns


f is the cumulative fraction seen













TABLE 9P





Tally of left-aligned CDR3 sequences





























A
C
D
E
F
G
H
I
K
L
M
#






1
74
6
278
109
11
319
50
18
11
60
8
1383
GDERVASLHTNQPIWYFKMCX


 


2
50
9
64
32
29
249
43
42
41
109
22
1377
GRPSLDVYTANHIQKEFMWCX


 


3
81
18
74
39
25
214
29
42
16
83
19
1377
GSYRTVLADPIWEQHNFMCK|


 


4
70
23
92
49
50
228
23
58
21
70
16
1373
GSYDRVALTIPFEWNCHQKMX


 


5
86
28
106
32
59
217
21
41
16
72
19
1371
GYSDAVTLRFIPWNECHMQK|X


 


6
88
17
104
28
94
171
17
48
12
50
17
1362
GYSDFATVRWPLINEQCHMK|


 


7
69
15
110
21
89
176
22
50
15
81
12
1349
GSYDFVLTAPRWINHEQCKM|X


 


8
53
19
141
17
90
150
18
47
17
68
11
1311
YSGDFLTVWAPIRNCHEKQM|


 


9
44
21
120
24
102
174
24
36
20
71
11
1250
YGSDFLNVRTAWPIEHCKQM|


 


10
39
31
129
23
124
116
23
42
9
58
32
1162
YDFGSLIARPTVWNMCEHQK


 


11
36
12
158
17
137
83
13
18
10
40
21
1061
YDFGSPLVANWMTRIEHCKQX


 


12
34
11
164
10
82
74
34
30
1
31
20
943
YDFGPSVAHLINMRTWCEQKX


 


13
32
2
121
6
84
56
10
26
7
43
32
789
YDFGLSPVAMIWRTHNKQEC


 


14
23

131
5
59
65
10
16
4
25
34
639
YDGFMVLAPISWNRHTQEKX


 


15
15
4
107
5
43
42
1
23

20
34
521
YDFGVMILWAPRSENCQTH|


 


16
4
2
80
3
33
26
4
5
1
10
29
396
YDVFMGPSLNTRIWAHECQ|K


 


17
3
1
63

19
19
9
13

12
21
291
DYVMFGILHPSTWAQRCNX


 


18
3

47

16
13
1
4

7
23
207
DYVMFGPSLTIAHN


 


19
5
1
39
1
4
13
3
3

1
14
146
DYVMGAFHINRSCELPQW


 


20
2

17

4
5

3

4
12
100
VYDMGFLIPSARWQ


 


21


17

3
8
1
1


4
58
DVGYMFHINTW


 


22
1

7

6
1

1


5
42
VDFMYSAGITW


 


23


9


1

1

1
1
25
DVYGILMPS


 


24
1

2



1


1
1
18
VYDAHLMPT


 


25


1


3





9
GVDPSY


 


26





2




2
7
GMSTV


 


27


2





1

1
6
DKMST


 


28
1

1


1





6
VADGS


 


29


1








4
DPSV


 


30




1






3
FST


 


31








1
1

3
KLV


 


32




1
1





3
FGP


 


33





1





3
PG


 


34






1


1

3
HLS


 


35
1










3
AVW


 


36


1

1






3
DFP


 


37











3
PSY


 


38









1

2
LS


 


39
1







1


2
AK


 


40











2
PS


 


41











2
ST


 


42











2
S


 


43








1


1
K


 


44











1
S


 


45











1
T


 


46











1
S


 



816
220
2186
421
1166
2428
358
568
205
920
421






N
P
Q
R
S
T
V
W
Y
|
X
#






1
35
23
31
108
63
50
94
16
13

6
1383
GDERVASLHTNQPIWYFKMCX


 


2
44
114
42
169
114
59
62
21
60

2
1377
GRPSLDVYTANHIQKEFMWCX


 


3
26
73
37
110
140
97
89
42
122
1

1377
GSYRTVLADPIWEQHNFMCK|


 


4
48
51
22
79
141
65
77
49
139

2
1373
GSYDRVALTIPFEWNCHQKMX


 


5
37
41
18
61
157
75
85
38
158
2
2
1371
GYSDAVTLRFIPWNECHMQK|X


 


6
32
54
23
67
152
80
78
64
165
1

1362
GYSDFATVRWPLINEQCHMK|


 


7
44
59
18
58
157
73
85
54
139
1
1
1349
GSYDFVLTAPRWINHEQCKM|X


 


8
38
48
14
41
167
68
59
59
185
1

1311
YSGDFLTVWAPIRNCHEKQM|


 


9
52
40
14
47
123
45
48
41
192
1

1250
YGSDFLNVRTAWPIEHCKQM|


 


10
33
37
12
39
73
36
36
35
235


1162
YDFGSLIARPTVWNMCEHQK


 


11
33
49
7
20
68
21
37
29
251

1
1061
YDFGSPLVANWMTRIEHCKQX


 


12
30
53
10
19
45
19
42
18
215

1
943
YDFGPSVAHLINMRTWCEQKX


 


13
10
34
7
22
40
15
33
25
184


789
YDFGLSPVAMIWRTHNKQEC


 


14
13
22
6
12
15
10
26
14
148

1
639
YDGFMVLAPISWNRHTQEKX


 


15
5
12
3
12
12
3
40
20
119
1

521
YDFGVMILWAPRSENCQTH|


 


16
10
24
2
6
12
7
49
5
82
2

396
YDVFMGPSLNTRIWAHECQ|K


 


17
1
8
2
2
8
5
42
4
58

1
291
DYVMFGILHPSTWAQRCNX


 


18
1
13


8
5
31

35


207
DYVMFGPSLTIAHN


 


19
2
1
1
2
2

24
1
29


146
DYVMGAFHINRSCELPQW


 


20

3
1
2
3

23
2
19


100
VYDMGFLIPSARWQ


 


21
1




1
14
1
7


58
DVGYMFHINTW


 


22




2
1
12
1
5


42
VDFMYSAGITW


 


23

1


1

5

5


25
DVYGILMPS


 


24

1



1
5

5


18
VYDAHLMPT


 


25

1


1

2

1


9
GVDPSY


 


26




1
1
1




7
GMSTV


 


27




1
1





6
DKMST


 


28




1

2




6
VADGS


 


29

1


1

1




4
DPSV


 


30




1
1





3
FST


 


31






1




3
KLV


 


32

1









3
FGP


 


33

2









3
PG


 


34




1






3
HLS


 


35






1
1



3
AVW


 


36

1









3
DFP


 


37

1


1



1


3
PSY


 


38




1






2
LS


 


39











2
AK


 


40

1


1






2
PS


 


41




1
1





2
ST


 


42




2






2
S


 


43











1
K


 


44




1






1
S


 


45





1





1
T


 


46




1






1
S


 



495
769
270
876
1518
741
1104
540
2572
10
17
18621
















TABLE 10P





Tally of right-aligned sequences





























A
C
D
E
F
G
H
I
K
L
M
#






5





1





1
G


 


6











1
S


 


7





1





1
G


 


8





1





1
G


 


9











2
RV


 


10











2
RV


 


11





1

1



2
GI


 


12











2
V


 


13











2
TY


 


14


1


1





3
DGN


 


15







1



3
ISY


 


16


1








3
DSY


 


17
1










3
APY


 


18


1

1





1
3
DFM


 


19


2


1





3
DG


 


20







1

1

3
ILV


 


21











3
WP


 


22





3





4
GS


 


23





2
1




6
GHQSV


 


24
1




3



1

6
GALR


 


25
1

2




1



7
DTAIS


 


26
1
1
1


1


1
1
1
9
ACDGKLMST


 


27
2

5
1

2

1

1

18
DAGVEILNQRS


 


28


2
2

3

1

2

25
TGQSDELPRIV


 


29
3

5
6

7


1
1
1
42
GEDVAPQRSKLMTY|


 


30
2

9

1
9
1
4

5
2
58
DGRLSIVPAMQTFHNY


 


31
4
2
19
9
2
18
1
2
1
3

100
DGSERVYALPTCFINHKW


 


32
10
5
18
5
3
16
3
3
2
14
1
146
DGLRVAPYSTCEQFHINWKM


 


33
20

18
10
7
34
7
8
2
6
1
207
GARDPSYTEVIFHLQWKM


 


34
13
4
31
18
9
37
8
16
4
14
4
291
GDRYPVEILASTFHQWCKMNX|


 


35
17
5
32
23
10
70
12
10
6
25
1
396
GRSDYLEVTPAHNFIWKCQM|


 


36
23
6
51
21
9
79
19
15
14
36
9
521
GDSYRLTVPAEHIKNFMWCQ|


 


37
35
12
56
23
15
110
14
17
5
24
4
639
GYDVRSTAPLEIFHNCWQKMX


 


38
28
19
68
27
29
133
26
31
12
43
7
789
GSYDVRLPTIFAEHCNWKQM


 


39
51
25
80
27
33
162
16
30
18
55
15
943
GSDRYVLATPFWIECKHMQNX


 


40
44
14
73
36
46
161
27
32
17
59
8
1061
GSRDYVTLPFAEIWHQNKCM


 


41
54
21
74
25
23
178
23
52
15
57
11
1162
GSYTDRVLPAIWNQEFHCKMX|


 


42
57
13
82
40
42
190
14
39
15
82
15
1250
GSYDLVRTANPFEIWQKMHC|


 


43
75
18
54
25
35
242
13
29
18
49
12
1311
GYSTARVPDLWNFIQECKHM|


 


44
63
17
79
15
43
197
20
38
14
76
8
1349
YGSTDLRAPVWNFIQHCEKM


 


45
59
16
69
35
55
165
26
23
23
75
9
1362
YGSLRTDNAFPVWEHIKCQM


 


46
41
19
125
26
27
208
31
14
16
38
8
1371
YGDSNRWATLPHFEVQCKIM


 


47
160
10
24
13
53
332
36
16
11
40
10
1373
GYAWPSFRLHTVNDIEKCMQX


 


48
21
4
8
5
680
27
4
44
5
145
288
1377
FMLISGVYPAWTDNQREKCHX


 


49
23
2
1181
29
1
30
15
4
2
8
1
1377
DGEAHNQSYVLPTIRCKW|FMX


 


50
7
7
15

42
3
41
135
3
59
4
1383
YVIPSLFHNDTACXMGKQRW|


 



816
220
2186
421
1166
2428
358
568
205
920
421






N
P
Q
R
S
T
V
W
Y
|
X
#






5











1
G


 


6




1






1
S


 


7











1
G


 


8











1
G


 


9



1


1




2
RV


 


10



1


1




2
RV


 


11











2
GI


 


12






2




2
V


 


13





1


1


2
TY


 


14
1










3
DGN


 


15




1



1


3
ISY


 


16




1



1


3
DSY


 


17

1






1


3
APY


 


18











3
DFM


 


19











3
DG


 


20






1




3
ILV


 


21

1





2



3
WP


 


22




1






4
GS


 


23


1

1

1




6
GHQSV


 


24



1







6
GALR


 


25




1
2





7
DTAIS


 


26




1
1





9
ACDGKLMST


 


27
1

1
1
1

2




18
DAGVEILNQRS


 


28

2
3
2
3
4
1




25
TGQSDELPRIV


 


29

3
3
2
2
1
5

1
1

42
GEDVAPQRSKLMTY|


 


30
1
3
2
7
5
2
4

1


58
DGRLSIVPAMQTFHNY


 


31
2
3

7
10
3
7
1
6


100
DGSERVYALPTCFINHKW


 


32
3
9
4
12
8
6
12
3
9


146
DGLRVAPYSTCEQFHINWKM


 


33

16
6
19
15
12
10
3
13


207
GARDPSYTEVIFHLQWKM


 


34
2
20
5
31
12
12
20
5
23
1
2
291
GDRYPVEILASTFHQWCKMNX|


 


35
12
18
5
39
35
19
23
7
26
1

396
GRSDYLEVTPAHNFIWKCQM|


 


36
11
24
6
42
47
29
28
7
44
1

521
GDSYRLTVPAEHIKNFMWCQ|


 


37
14
33
9
54
52
37
55
11
58

1
639
GYDVRSTAPLEIFHNCWQKMX


 


38
18
33
12
46
77
32
58
17
73


789
GSYDVRLPTIFAEHCNWKQM


 


39
11
38
12
70
94
42
61
33
68

2
943
GSDRYVLATPFWIECKHMQNX


 


40
24
52
27
74
140
61
66
29
71


1061
GSRDYVTLPFAEIWHQNKCM


 


41
31
55
29
70
156
76
61
51
97
1
2
1162
GSYTDRVLPAIWNQEFHCKMX|


 


42
48
47
24
68
171
68
70
39
125
1

1250
GSYDLVRTANPFEIWQKMHC|


 


43
38
58
28
73
164
76
66
43
194
1

1311
GYSTARVPDLWNFIQECKHM|


 


44
48
60
24
69
131
86
57
52
252


1349
YGSTDLRAPVWNFIQHCEKM


 


45
62
51
16
75
116
74
50
39
324


1362
YGSLRTDNAFPVWEHIKCQM


 


46
97
38
21
55
110
39
26
55
377


1371
YGDSNRWATLPHFEVQCKIM


 


47
25
54
9
44
54
34
32
122
292

2
1373
GYAWPSFRLHTVNDIEKCMQX


 


48
8
22
7
6
28
10
25
16
23

1
1377
FMLISGVYPAWTDNQREKCHX


 


49
15
6
13
4
13
5
9
2
11
2
1
1377
DGEAHNQSYVLPTIRCKW|FMX


 


50
23
122
3
3
67
9
350
3
480
1
6
1383
YVIPSLFHNDTACXMGKQRW|


 


50
495
769
270
876
1518
741
1104
540
2572
10
17

18621
















TABLE 11P





Tallies of AA frequencies in all CDR3 by length







Tally of sequences of length 7 # = 38





















A
C
D
E
F
G
H
I
K
L
M
#






1
1

8
1
1
14
1

1
5

38
GDLRWAEFHKS


 


2
1

1

2
6
3

2
1
1
38
RGNHVFKTYADLMW


 


3
1

4

1
5
1
2

2

38
GSDWYPVILTAFHN


 


4
3

1

1
12
1
1

1

38
GYSANRVDFHILPT


 


5
2


1
14
3

4
1
3
3
38
FIGLMARVYEKP


 


6


26



1
1



38
DVPTHISWY


 


7
1

2



2
3

1

38
YVINDHSALR


 



9

42
2
19
40
9
11
4
13
4






N
P
Q
R
S
T
V
W
Y
|
X
#






1



3
1


2



38
GDLRWAEFHKS


 


2
6


7

2
3
1
2


38
RGNHVFKTYADLMW


 


3
1
3


5
2
3
4
4


38
GSDWYPVILTAFHN


 


4
2
1

2
4
1
2

6


38
GYSANRVDFHILPT


 


5

1

2


2

2


38
FIGLMARVYEKP


 


6

2


1
2
3
1
1


38
DVPTHISWY


 


7
3


1
2

7

16


38
YVINDHSALR


 



12
7

15
13
7
20
8
31


266










Tally of sequences of length 8 # = 61





















A
C
D
E
F
G
H
I
K
L
M
#






1
3

7
3

14
2
2

5

61
GDLTVRSAEHINWPQY


 


2
1

9
1
1
15

1
2
1

61
GDTNRSVKWYAEFILPQ


 


3
2

3

1
10
1
1

7
1
61
GLSTYVDPRAFHIMNQW


 


4
4
1
3
1
1
15
1


4

61
GYRALQDSWVCEFHNPT


 


5
10

2
1

9
5

1
5
1
61
AGYHLTPRVDSEKMW


 


6
5
1


24
2

7

5
2
61
FIALPSVYGMCQRW


 


7
5

37
2


4
1

2

61
DAHSELNVIP|


 


8
1

2

3

1
12

3

61
YISFLVDNAHPRT


 



31
2
63
8
30
65
14
24
3
32
4






N
P
Q
R
S
T
V
W
Y
|
X
#






1
2
1
1
4
4
5
5
2
1


61
GDLTVRSAEHINWPQY


 


2
6
1
1
4
3
8
3
2
2


61
GDTNRSVKWYAEFILPQ


 


3
1
3
1
3
7
7
5
1
7


61
GLSTYVDPRAFHIMNQW


 


4
1
1
4
5
3
1
2
3
11


61
GYRALQDSWVCEFHNPT


 


5

4

4
2
5
4
1
7


61
AGYHLTPRVDSEKMW


 


6

3
1
1
3

3
1
3


61
FIALPSVYGMCQRW


 


7
2
1


4

2


1

61
DAHSELNVIP|


 


8
2
1

1
7
1
3

24


61
YISFLVDNAHPRT


 



14
15
8
22
33
27
27
10
55
1

488










Tally of sequences of length 9 # = 88





















A
C
D
E
F
G
H
I
K
L
M
#






1
9

12
4

21
1
1
2
5

88
GDARNVLEQTKWHIPSY


 


2
2

2
3
3
13
4

3
7
2
88
GPSRLNTHEFKYADMQW


 


3
4
2
3
3
3
15



1
1
88
GTPSQNRVWYADEFCLM


 


4
5
1
6
3
6
22
2
4
1
6
1
88
GSDFLARITYENPWHVCKM


 


5
7
1
4
3
4
14
2


7
2
88
GSYALNDFVERWHMQTCP


 


6
13

2
1
3
13
6
2
1
4
1
88
YAGHNLPSVFTWDIEKMQR


 


7
4

2

41
2

3
1
14
5
88
FLMAPWIDGSVKNQTY


 


8
1
1
73
2

2
1


2

88
DEGLSACHNQRV


 


9

1
1

4
1
3
8

2

88
YVISFHPLNTCDGR


 



45
6
105
19
64
103
19
18
8
48
12






N
P
Q
R
S
T
V
W
Y
|
X
#






1
7
1
3
8
1
3
7
2
1


88
GDARNVLEQTKWHIPSY


 


2
5
11
2
10
11
5

2
3


88
GPSRLNTHEFKYADMQW


 


3
5
7
6
5
7
11
5
5
5


88
GTPSQNRVWYADEFCLM


 


4
3
3

5
7
4
2
3
4


88
GSDFLARITYENPWHVCKM


 


5
6
1
2
3
12
2
4
3
11


88
GSYALNDFVERWHMQTCP


 


6
5
4
1
1
4
3
4
3
17


88
YAGHNLPSVFTWDIEKMQR


 


7
1
4
1

2
1
2
4
1


88
FLMAPWIDGSVKNQTY


 


8
1

1
1
2

1




88
DEGLSACHNQRV


 


9
2
3

1
8
2
9

43


88
YVISFHPLNTCDGR


 



35
34
16
34
54
31
34
22
85


792










Tally of sequences of length 10 # = 101





















A
C
D
E
F
G
H
I
K
L
M
#






1
8
1
19
7
1
16
3

2
3
2
101
DGNAERTSQVHLWKMYCF


 


2
3

8
3
5
13

5

15
2
101
LGRDSPVFINTAEQYMW


 


3
6

9

1
26
1
3
1
4
1
101
GSYDAVTLNRIPWFHKMQ


 


4
7

6

1
25
1
5

4
1
101
GSYARDINPLTVWQFHM


 


5
6

5
9
4
16
1

3
4

101
GYTESANDPRFLVKQWH


 


6
6
1
6
5
4
23
2
4
3
3
1
101
GYRSWADEFINKLTHCMQV


 


7
13

3
1
5
9
3
1

4
1
101
YASGPRWFTVLDHNEIMQ


 


8
2
1

1
57
3

4

15
4
101
FLIMSGWANPVCEY


 


9
3

78
2

6

1
1
1

101
DGAQENIKLPRSW


 


10


3

4

4
13

1

101
YIPSVFHNDL


 



54
3
137
28
82
137
15
36
10
54
12






N
P
Q
R
S
T
V
W
Y
|
X
#






1
9

4
6
5
6
4
3
2


101
DGNAERTSQVHLWKMYCF


 


2
5
6
3
11
8
4
6
1
3


101
LGRDSPVFINTAEQYMW


 


3
4
3
1
4
14
5
6
2
10


101
GSYDAVTLNRIPWFHKMQ


 


4
5
5
3
7
11
4
4
4
8


101
GSYARDINPLTVWQFHM


 


5
6
5
2
5
8
10
4
2
11


101
GYTESANDPRFLVKQWH


 


6
4

1
8
7
3
1
7
12


101
GYRSWADEFINKLTHCMQV


 


7
2
7
1
7
11
5
5
6
17


101
YASGPRWFTVLDHNEIMQ


 


8
2
2


4

2
3
1


101
FLIMSGWANPVCEY


 


9
2
1
3
1
1


1



101
DGAQENIKLPRSW


 


10
4
8


7

5

52


101
YIPSVFHNDL


 



43
37
18
49
76
37
37
29
116


1010










Tally of sequences of length 11 # = 118





















A
C
D
E
F
G
H
I
K
L
M
#






1
7
1
21
11

23
5
2

7

118
GDEVRALQHSPTINCWY


 


2
1
2
9
1
1
24
5
6
2
7
3
118
GSRDYLPIVHQTMNCKWAEFX


 


3
4

4
2
4
13
2
3
1
7
2
118
SGTVRLYWADFNQIEHMKP


 


4
10

3
3
2
25
1
2

4
3
118
SGARTWYLVDEMQFINPH


 


5
5
2
10
1
4
24
2

1
5
1
118
GSVYDTNALRFWCHQEKM


 


6
6

4
2
7
19
2
3
1
5
1
118
GSYWTFAVLRDINEHQKMP


 


7
4
1
8
5
2
20
4
1

2
1
118
GYSNRDWTEPAHFLQVCIM


 


8
13
2
6
1
8
12
4

2
7

118
YAGWFLDPRSTHCKVE


 


9
2

2

68
2

5

14
7
118
FLMYVITADGP


 


10
2
1
100
5

3
2


1
1
118
DEGAHCLMNPQ


 


11


2

6

1
7
1
6
1
118
YPVISFLNDHKM


 



54
9
169
31
102
165
28
29
8
65
20






N
P
Q
R
S
T
V
W
Y
|
X
#






1
2
4
7
8
5
3
10
1
1


118
GDEVRALQHSPTINCWY


 


2
3
7
4
10
11
4
6
2
9

1
118
GSRDYLPIVHQTMNCKWAEFX


 


3
4
1
4
8
25
12
9
6
7


118
SGTVRLYWADFNQIEHMKP


 


4
2
2
3
9
26
8
4
6
5


118
SGARTWYLVDEMQFINPH


 


5
6

2
5
15
9
11
4
11


118
GSVYDTNALRFWCHQEKM


 


6
3
1
2
5
16
9
6
11
15


118
GSYWTFAVLRDINEHQKMP


 


7
9
5
2
9
11
6
2
7
19


118
GYSNRDWTEPAHFLQVCIM


 


8

6

5
5
5
2
11
29


118
YAGWFLDPRSTHCKVE


 


9

1



4
6

7


118
FLMYVITADGP


 


10
1
1
1








118
DEGAHCLMNPQ


 


11
3
13


7

11

60


118
YPVISFLNDHKM


 



33
41
25
59
121
60
67
48
163

1
1298










Tally of sequences of length 12 # = 154





















A
C
D
E
F
G
H
I
K
L
M
#






1
5

31
12

37
6
1
1
7
3
154
GDRESVLHAPMNQTWYIK


 


2
5
1
7
6
1
25
3
7
3
13
2
154
GSRLPDIQEAVYHKNTMWCF


 


3
10
2
7
5
1
19

5
4
12
2
154
GRSYLATVPDQEIKWCMNF


 


4
8

9
6
8
27

6
5
6
1
154
GVSDNAFRTYEILKWPQM


 


5
18
1
8
5
6
42
1
9
1
7
3
154
GSAIDYLFPTEQVMNWCHK


 


6
13

12
4
10
23
1
7

8
1
154
GAVDSFYTLPRWINEQHM


 


7
11
2
4
3
10
15
1
4

12

154
YGSPLRAFWTNVDIECQH


 


8
3
2
18
3
3
25
4
2
5
6

154
YGDSNLTKRWHPAEFCIQV


 


9
15
1
2

8
33
4
7
1
5
1
154
GYWARFISPLHTDQCKMN


 


10
1
1
2
1
79
1
2
5
1
19
26
154
FMLIPYDHVWACEGKNQRST


 


11
2

135
2

4
2




154
DGYAEHSVNR


 


12

1
1

6
1
9
16

4

154
YVPIHFSLNCDGW


 



91
11
236
47
132
252
33
69
21
99
39






N
P
Q
R
S
T
V
W
Y
|
X
#






1
3
4
3
14
10
3
10
2
2


154
GDRESVLHAPMNQTWYIK


 


2
3
11
7
22
24
3
5
2
4


154
GSRLPDIQEAVYHKNTMWCF


 


3
2
8
6
17
17
9
9
4
15


154
GRSYLATVPDQEIKWCMNF


 


4
9
4
4
7
17
7
18
5
7


154
GVSDNAFRTYEILKWPQM


 


5
3
6
4

20
6
4
2
8


154
GSAIDYLFPTEQVMNWCHK


 


6
5
8
3
8
11
9
13
8
10


154
GAVDSFYTLPRWINEQHM


 


7
5
14
2
12
15
6
5
9
24


154
YGSPLRAFWTNVDIECQH


 


8
10
4
2
5
15
6
2
5
34


154
YGDSNLTKRWHPAEFCIQV


 


9
1
6
2
10
7
3

18
30


154
GYWARFISPLHTDQCKMN


 


10
1
4
1
1
1
1
2
2
3


154
FMLIPYDHVWACEGKNQRST


 


11
1


1
2

2

3


154
DGYAEHSVNR


 


12
2
18


5

32
1
58


154
YVPIHFSLNCDGW


 



45
87
34
97
144
53
102
58
198


1848










Tally of sequences of length 13 # = 150





















A
C
D
E
F
G
H
I
K
L
M
#






1
4
2
28
9
3
37
8
3
3
5

150
GDTESHRVLPAQFIKCNW


 


2
11
4
4
1
2
32
3
1
5
11
3
150
GRSPALTKVCDYHMQWFEIN


 


3
7
2
8
4
4
23
11
1
4
6
2
150
GSYHQTDPRAVLEFKNCMWI


 


4
6
2
6
4
6
30
1
8

6
1
150
GSWYTIADFLPVEQRCHMNX


 


5
8

10
4
2
28
1
2

22
3
150
GLSYDATWPREQMNVFIH


 


6
10
2
11
1
6
21

2
2
5
1
150
GYSPTDAQVFRLNWCIKEM


 


7
5
1
8
1
4
19
1
6
5
21
2
150
LGYSTDPIRVAKFNWMQCEH


 


8
7
5
22
5
3
12
3
3
3
8
1
150
YDSGLARTCEQVNPFHIKWM


 


9
1
2
12
3
1
26
7
2
4
7
2
150
NGYDSWHLPRKETVCIMAFQ


 


10
19
1
2
2
17
24
5
2

5
1
150
YGAFWHLPTNSVDEIQRCM


 


11
1


1
105
2

2
1
13
14
150
FMLYGIVAEKPQRSWX


 


12


130
3

5
1




150
DGYEQNHT


 


13
1

2

5

5
14

18
1
150
YVLIPSFHTDAMN


 



80
21
243
38
158
259
46
46
27
127
31






N
P
Q
R
S
T
V
W
Y
|
X
#






1
2
5
4
8
9
11
8
1



150
GDTESHRVLPAQFIKCNW


 


2
1
13
3
20
17
7
5
3
4


150
GRSPALTKVCDYHMQWFEIN


 


3
3
8
11
8
16
11
7
2
12


150
GSYHQTDPRAVLEFKNCMWI


 


4
1
6
4
4
18
10
6
16
14

1
150
GSWYTIADFLPVEQRCHMNX


 


5
3
6
4
5
19
8
3
7
15


150
GLSYDATWPREQMNVFIH


 


6
3
15
8
6
16
13
8
3
17


150
GYSPTDAQVFRLNWCIKEM


 


7
4
7
2
6
15
14
6
4
19


150
LGYSTDPIRVAKFNWMQCEH


 


8
4
4
5
7
15
7
5
2
29


150
YDSGLARTCEQVNPFHIKWM


 


9
31
5
1
5
10
3
3
9
16


150
NGYDSWHLPRKETVCIMAFQ


 


10
3
5
2
2
3
4
3
15
35


150
YGAFWHLPTNSVDEIQRCM


 


11

1
1
1
1

2
1
3

1
150
FMLYGIVAEKPQRSWX


 


12
2

3


1


5


150
DGYEQNHT


 


13
1
14


13
4
21

51


150
YVLIPSFHTDAMN


 



58
89
48
72
152
93
77
63
220

2
1950










Tally of sequences of length 14 # = 118





















A
C
D
E
F
G
H
I
K
L
M
#






1
6

29
7
2
32
8
1
1
2

118
GDVHERTAFLPSIKNQ


 


2
4

10
1
5
22
7
3
4
7

118
GPDRYSVHLFAKIQTENW


 


3
11
2
7
2
3
25

5
1
9
2
118
GVARYLSDITFWCEMPK


 


4
5
2
7
7
3
12
4
4
3
6

118
SGVYPDELRTANHIFKWC


 


5
6
5
12

2
18
2
2
2
4
1
118
GYSDTVARCLPFHIKNWMQ


 


6
6

10
5
4
16

5
3
2
1
118
YGSTDRAEIFVKWLPQMN


 


7
4

4
1
4
32
2
2
2

1
118
GSVTYNADFHIKPQRWEM


 


8
6
1
5
1
4
18
2
5

3
2
118
GSYTWAPRDIFNVLHMCE


 


9
5
2
4
1
2
11
2
1
5
9
1
118
YSGTLVAKNRDWCFHPEIM


 


10
2
5
9
2
3
21

2
2
4

118
YGSDNTCQLRFWAEIKPV


 


11
12

1
3
5
25
2


2
1
118
YGWAPVFNEHLTDMQR


 


12
1



64
5
1
5

12
16
118
FMLGIPSVAHQTY


 


13
3

97
4

5
1
1
1
1

118
DGEANQHIKLV


 


14
2



3

4
12

6

118
YVPILHFANS


 



73
17
195
34
104
242
35
48
24
67
25






N
P
Q
R
S
T
V
W
Y
|
X
#






1
1
2
1
7
2
7
10




118
GDVHERTAFLPSIKNQ


 


2
1
13
2
10
8
2
8
1
10


118
GPDRYSVHLFAKIQTENW


 


3

2

11
8
4
13
3
10


118
GVARYLSDITFWCEMPK


 


4
5
8

6
13
6
12
3
12


118
SGVYPDELRTANHIFKWC


 


5
2
3
1
6
15
10
7
2
18


118
GYSDTVARCLPFHIKNWMQ


 


6
1
2
2
7
16
12
4
3
19


118
YGSTDRAEIFVKWLPQMN


 


7
5
2
2
2
18
12
13
2
10


118
GSVTYNADFHIKPQRWEM


 


8
4
6

6
16
12
4
9
14


118
GSYTWAPRDIFNVLHMCE


 


9
5
2

5
14
10
8
4
27


118
YSGTLVAKNRDWCFHPEIM


 


10
6
2
5
4
13
6
2
3
27


118
YGSDNTCQLRFWAEIKPV


 


11
4
7
1
1

2
6
14
32


118
YGWAPVFNEHLTDMQR


 


12

4
1

4
1
3

1


118
FMLGIPSVAHQTY


 


13
2

2



1




118
DGEANQHIKLV


 


14
2
14


2

20

53


118
YVPILHFANS


 



38
67
17
65
129
84
111
44
233


1652










Tally of sequences of length 15 # = 125





















A
C
D
E
F
G
H
I
K
L
M
#






1
7

26
8
3
29
1
3

10

125
GDLREASTVNFIPYH


 


2
6

2
3

22
3
4
1
9

125
RGPLNSTYAVIQEHWDK


 


3
4
4
5
7
2
19
2
6
2
9
2
125
GRYLSVEPIDTACQWFHKMN


 


4
7
4
14
6
6
15
2
7
5
7
4
125
GDYAILVEFRKSTCMNPWHQ


 


5
6
3
10
2
5
18

4
2
3
2
125
GSYVDRWAFTICLNEKMP


 


6
6
2
7
2
5
10
1
5

7
1
125
SRYGTDLWAPFIVNCEQHM


 


7
8
4
14
2
2
22
3
3
1
9
1
125
GSDLAVRPYCTHIWEFNKM


 


8
6
2
4


22

2
2
3

125
GYSVWRATDNPLCIKQ


 


9
4
3
8

4
20
4
3
1
6

125
YGSDLPTRVAFHQCINKW


 


10
3
4
5
8
8
17
1
3

7

125
YGEFNTLSRDVCPAIWH


 


11
4
2
15
3
3
17
1
1
1


125
YGDSNPAWEFRTCQHIKV


 


12
22
3


2
31
3
1

3
3
125
GYAWPSNCHLMFQRVITX


 


13




71
1

4

6
30
125
FMLISQTVGPRY


 


14


115
2
1
1
1




125
DNEFGHPQ


 


15

3


5
1
1
20

7
1
125
YVILPFSCNGHMQ


 



83
34
225
43
117
245
23
66
15
86
44






N
P
Q
R
S
T
V
W
Y
|
X
#






1
4
3

10
7
6
6

2


125
GDLREASTVNFIPYH


 


2
8
11
4
23
7
7
5
3
7


125
RGPLNSTYAVIQEHWDK


 


3
2
7
3
13
9
5
8
3
13


125
GRYLSVEPIDTACQWFHKMN


 


4
4
4
1
6
5
5
7
3
13


125
GDYAILVEFRKSTCMNPWHQ


 


5
3
2

8
18
5
11
8
15


125
GSYVDRWAFTICLNEKMP


 


6
3
6
2
12
24
9
4
7
12


125
SRYGTDLWAPFIVNCEQHM


 


7
2
6

7
21
4
8
3
5


125
GSDLAVRPYCTHIWEFNKM


 


8
4
4
2
7
19
5
12
10
21


125
GYSVWRATDNPLCIKQ


 


9
3
6
4
5
19
6
5
1
23


125
YGSDLPTRVAFHQCINKW


 


10
8
4

6
7
8
5
2
29


125
YGEFNTLSRDVCPAIWH


 


11
7
5
2
3
14
3
1
4
39


125
YGDSNPAWEFRTCQHIKV


 


12
4
7
2
2
6
1
2
8
24

1
125
GYAWPSNCHLMFQRVITX


 


13

1
2
1
4
2
2

1


125
FMLISQTVGPRY


 


14
3
1
1








125
DNEFGHPQ


 


15
2
7
1

5

33

39


125
YVILPFSCNGHMQ


 



57
74
24
103
165
66
109
52
243

1
1875










Distribution of D-JH with number of cys's












0
1
2
3
4






1248
53
80
1
1











Tally of AAs in the YYCar motif





















A
C
D
E
F
G
H
I
K
L
M
#






1


1
1
14

1




1383
YFDEH


 


2

4
1

92

11


4

1383
YFHCLSWDR


 


3

1379









1383
CRS


 


4
1207

3

2
12

2

2

1383
AVTSGNDFILRQX


 


5
14


1
4
18
17
9
187
4
1
1383
RKTSGHAIVNFLQYPEM|


 



1221
1383
5
2
112
30
29
11
187
10
1






N
P
Q
R
S
T
V
W
Y
|
X
#






1








1366


1383
YFDEH


 


2



1
3


2
1265


1383
YFHCLSWDR


 


3



2
2






1383
CRS


 


4
4

1
2
17
51
79



1
1383
AVTSGNDFILRQX


 


5
7
2
3
992
55
56
9

3
1

1383
RKTSGHAIVNFLQYPEM|


 



11
2
4
997
77
107
88
2
2634
1
1
6915
















TABLE 12P







Alignment and tabulation of sequences having 3-22 D segments


D3:3-22_Phz0 YYYDSSGYYY (SEQ ID NO: 448) = GLG
















Entry
Seq1
L1
Seq2
L2
JH
P
Score





1
hs3d6hcv
GRDYYDSGGYFT
12
GRDYYDSGGYFTVAFDI
17
3
6
1.76D+13




(SEQ ID NO: 334)

(SEQ ID NO: 335)






 


2
hs6d4xb7
DRHNYYDSSGSYS
13
DRHNYYDSSGSYSDY
15
4
9
4.40D+12




(SEQ ID NO: 336)

(SEQ ID NO: 337)






 


3
hs6d4xg3
DCPAPAKMYYYGSGICT
17
DCPAPAKMYYYGSGICTFDY
20
4
3
6.55D+04




(SEQ ID NO: 338)

(SEQ ID NO: 339)






 


4
hs83x6f2
AFYDSAD
7
AFYDSADDY
9
4
−4
2.62D+05




(SEQ ID NO: 340)

(SEQ ID NO: 341)






 


5
hsa230644
RDYYDSSGPEAG
12
RDYYDSSGPEAGFDI
15
3
3
6.87D+10




(SEQ ID NO: 342)

(SEQ ID NO: 343)






 


6
hsa239386
DGTLIDTSAYYYL
13
DGTLIDTSAYYYLY
14
4
6
6.87D+10




(SEQ ID NO: 344)

(SEQ ID NO: 345)






 


7
hsa234232
NSSDSS
6
NSSDSSVLDV
10
6
−4
6.55D+04




(SEQ ID NO: 346)

(SEQ ID NO: 347)






 


8
hsa239378
DQVFDSGGYNHR
12
DQVFDSGGYNHRFDS
15
4
3
1.07D+09




(SEQ ID NO: 348)

(SEQ ID NO: 349)






 


9
hsa239367
DLEYYYDSGGHYSP
14
DLEYYYDSGGHYSPFHY
17
4
9
1.10D+12




(SEQ ID NO: 350)

(SEQ ID NO: 351)






 


10
hsa239339
DDSSGY
6
DDSSGYYYIDY
11
4
−10
1.72D+10




(SEQ ID NO: 352)

(SEQ ID NO: 353)






 


11
hsa245311
GHYYDSPGQYSYS
13
GHYYDSPGQYSYSEY
15
4
3
1.07D+09




(SEQ ID NO: 354)

(SEQ ID NO: 355)






 


12
hsa240578
GGFRPPPYDYESSAYRTYR
19
GGFRPPPYDYESSAYRTYRLDF
22
4
21
2.75D+11




(SEQ ID NO: 356)

(SEQ ID NO: 357)






 


13
hsa245359
DSDTRAY
7
DSDTRAYYWYFDL
13
2
−7
1.68D+07




(SEQ ID NO: 358)

(SEQ ID NO: 359)






 


14
hsa245028
GRHYYDSSGYYSTPE
15
GRHYYDSSGYYSTPENYFDY
20
4
6
1.80D+16




(SEQ ID NO: 360)

(SEQ ID NO: 361)






 


15
hsa245019
DPSYYYDSSGLPL
13
DPSYYYDSSGLPLHGMDV
18
6
9
4.40D+12




(SEQ ID NO: 362)

(SEQ ID NO: 363)






 


16
hsa244991
TYYYDSSGYLLTR
13
TYYYDSSGYLLTRYFQH
17
1
3
4.50D+15




(SEQ ID NO: 364)

(SEQ ID NO: 365)






 


17
hsa244945
NAPHYDSSGYYQT
13
NAPHYDSSGYYQTFDY
16
4
6
7.04D+13




(SEQ ID NO: 366)

(SEQ ID NO: 367)






 


18
hsa244943
GYHSSSYA
8
GYHSSSYADAFDI
13
3
−7
6.71D+07




(SEQ ID NO: 368)

(SEQ ID NO: 369)






 


19
hsa245289
PIGYCSGGSC
10
PIGYCSGGSCYSFDY
15
4
−4
2.62D+05




(SEQ ID NO: 370)

(SEQ ID NO: 371)






 


20
hsa240554
THGTYVTSGYYPKI
14
THGTYVTSGYYPKI
14
4
6
2.68D+08




(SEQ ID NO: 372)

(SEQ ID NO: 373)






 


21
hsa279533
GATYYYESSGNYP
13
GATYYYESSGNYPDY
15
4
9
7.04D+13




(SEQ ID NO: 374)

(SEQ ID NO: 375)






 


22
hsa389177
AFYHYDSTGYPNRRY
15
AFYHYDSTGYPNRRYYFDY
19
4
6
4.29D+09




(SEQ ID NO: 376)

(SEQ ID NO: 377)






 


23
hsa7321
SYSYYYDSSGYWGG
14
SYSYYYDSSGYWGGYFDY
18
4
9
4.50D+15




(SEQ ID NO: 378)

(SEQ ID NO: 379)






 


24
hsaj2772
LSPYYYDSSSYH
12
LSPYYYDSSSYHDAFDI
17
3
6
2.62D+05




(SEQ ID NO: 380)

(SEQ ID NO: 381)






 


25
hsb7g4f08
EEDYYDSSGQAS
12
EEDYYDSSGQASYNWFXP
18
5
6
2.75D+11




(SEQ ID NO: 382)

(SEQ ID NO: 383)






 


26
hsb7g3b02
ETNYYDSGGYPG
12
ETNYYDSGGYPGFDF
15
4
6
4.40D+12




(SEQ ID NO: 384)

(SEQ ID NO: 385)






 


27
hsb7g3c12
GDHYYDRSGYRH
12
GDHYYDRSGYRHSYYYYAMDV
21
6
6
2.75D+11




(SEQ ID NO: 386)

(SEQ ID NO: 387)






 


28
hsb8g3b07
DRSSGN
6
DRSSGNYFDGMDV
13
6
−10
6.55D+04




(SEQ ID NO: 388)

(SEQ ID NO: 389)






 


29
hsfog1h
GRSRYSGYG
9
GRSRYSGYGFYSGMDV
16
6
−4
2.62D+05




(SEQ ID NO: 390)

(SEQ ID NO: 391)






 


30
hsgvh0209
DDTSGYGP
8
DDTSGYGPYYFYYGMDV
17
6
−10
2.68D+08




(SEQ ID NO: 392)

(SEQ ID NO: 393)






 


31
hsgvh55
RAYYDTSFYFEY
12
RAYYDTSFYFEYY
13
4
3
1.72D+10




(SEQ ID NO: 394)

(SEQ ID NO: 395)






 


32
hsgvh0304
DRIDYYKSGYYLGSA
15
DRIDYYKSGYYLGSADS
17
4
6
1.68D+07




(SEQ ID NO: 396)

(SEQ ID NO: 397)






 


33
hsgvh0332
DTDSSSHYG
9
DTDSSSHYGRFDP
13
5
−7
1.68D+07




(SEQ ID NO: 398)

(SEQ ID NO: 399)






 


34
hsgvh0328
VSISHYDSSGRPQRVF
16
VSISHYDSSGRPQRVFYGMDV
21
6
9
1.07D+09




(SEQ ID NO: 400)

(SEQ ID NO: 401)






 


35
hsgvh536
QARENVFYDSSGPTAP
16
QARENVFYDSSGPTAPFDH
19
4
15
1.72D+10




(SEQ ID NO: 402)

(SEQ ID NO: 403)






 


36
hshcmg42
VPAGNYYDTSGPDN
14
VPAGNYYDTSGPDNAD
16
4
12
1.72D+10




(SEQ ID NO: 404)

(SEQ ID NO: 405)






 


37
hsig001vh
WYYFDTSGYYPRNFYYMDV
19
WYYFDTSGYYPRNFYYMDV
19
4
3
2.81D+14




(SEQ ID NO: 406)

(SEQ ID NO: 407)






 


38
hsig13g10
GYYYDSGGNYNG
12
GYYYDSGGNYNGDY
14
4
3
1.10D+12




(SEQ ID NO: 408)

(SEQ ID NO: 409)






 


39
hsighpat3
DLRSYDPSGYYN
12
DLRSYDPSGYYNDGFDI
17
3
6
2.75D+11




(SEQ ID NO: 410)

(SEQ ID NO: 411)






 


40
hsigh13g7
GYYYDRGGNCNG
12
GYYYDRGGNCNGDY
14
4
3
6.87D+10




(SEQ ID NO: 412)

(SEQ ID NO: 413)






 


41
hsigh13g1
GYYYDRGGNYNG
12
GYYYDRGGNYNGDY
14
4
3
1.10D+12




(SEQ ID NO: 414)

(SEQ ID NO: 415)






 


42
hsighxx20
THYDSSGL
8
THYDSSGLDAFDI
13
3
−4
1.72D+10




(SEQ ID NO: 416)

(SEQ ID NO: 417)






 


43
hsihr9
DDSSGS
6
DDSSGSYYFDY
11
4
−10
1.07D+09




(SEQ ID NO: 418)

(SEQ ID NO: 419)






 


44
hsihv11
LSGGYYS
7
LSGGYYSDFDY
11
4
−13
2.68D+08




(SEQ ID NO: 420)

(SEQ ID NO: 421)






 


45
hs ej1f
GDYSDSSDSYI
11
GDYSDSSDSYIDAFDV
16
3
3
1.10D+12




(SEQ ID NO: 422)

(SEQ ID NO: 423)






 


46
hsmvh51
GETYYYDSRGYA
12
GETYYYDSRGYAFDH
15
4
6
2.62D+05




(SEQ ID NO: 424)

(SEQ ID NO: 425)






 


47
hsmvh517
PTRDSSGY
8
PTRDSSGYYVGY
12
4
−4
1.07D+09




(SEQ ID NO: 426)

(SEQ ID NO: 427)






 


48
hsmvh0406
GSFYYDSSGYPP
12
GSFYYDSSGYPPFDC
15
4
6
6.87D+10




(SEQ ID NO: 428)

(SEQ ID NO: 429)






 


49
hst14x14
GPYYYDSSGYYL
12
GPYYYDSSGYYLLDY
15
4
6
1.80D+16




(SEQ ID NO: 430)

(SEQ ID NO: 431)






 


50
hsvhig2
EEGYYDSSGYYSLGA
15
EEGYYDSSGYYSLGASDY
18
4
6
4.50D+15




(SEQ ID NO: 432)

(SEQ ID NO: 433)






 


51
hsvhia2
RPDSSGSRW
9
RPDSSGSRWYFDY
13
4
−7
6.71D+07




(SEQ ID NO: 434)

(SEQ ID NO: 435)






 


52
hsy14936
GYYDISGYYF
10
GYYDISGYYFDAFNI
15
3
−4
2.81D+14




(SEQ ID NO: 436)

(SEQ ID NO: 437)






 


53
hsy14934
DRGYDSSGYYGN
12
DRGYDSSGYYGNLDC
15
4
3
1.76D+13




(SEQ ID NO: 438)

(SEQ ID NO: 439)






 


54
hsy14935
DRGYDSIGYYGN
12
DRGYDSIGYYGNLDC
15
4
3
1.10D+12




(SEQ ID NO: 440)

(SEQ ID NO: 441)






 


55
hsz80519
AEDLTYYYDRSGWGVHGLL
19
AEDLTYYYDRSGWGVHGLLYYFDY
24
4
15
4.40D+12




(SEQ ID NO: 442)

(SEQ ID NO: 443)






 


56
hsz80429
LYPHYDSSGYYYV
13
LYPHYDSSGYYYVLDY
16
4
6
4.50D+15




(SEQ ID NO: 444)

(SEQ ID NO: 445)






 


57
hsz80461
DRVGYYDSSGYPPGSP
16
DRVGYYDSSGYPPGSPLDY
19
4
9
1.76D+13




(SEQ ID NO: 446)

(SEQ ID NO: 447)










Frequency of each AA type at each position in 57 Sequences


having D3-22 segments































Pos
A
C
D
E
F
G
H
I
K
L
M
N
P
Q
R
S
T
V
W
Y
|
X
#






1





1
















1



 


2





1
















1



 


3
1



1








1








3



 


4
1


1










1


1




4



 


5


5


1



1


2

1
1

1




12



 


6
3

3
4

6



3

1
2

2
2
1


1


28
x


 


7
1

5
4
1
7
2
1

1

1
3

5
3
4
1
1
1


41
x


 


8
2
1
4

1
5
3
1



4
4
1
3
1
3
1

14


48
x


 


9


4

2
3
5
1

1


1

2
2
2
1

28


52
Y


 


10
1

4

2
1

1




1

1
4
1


40


56
Y


 


11


46
2


1


1


1

2


1

3


57
D


 


12
1
1
1




1
1



1

4
39
7


1


57
S


 


13
1




8

1
1



1

1
43
1





57
S


 


14
3

2

1
45




1



1
3






56
G


 


15





2
2


2

5
3
2
1
4


1
33


55
Y


 


16
2
1
1
1
2
3
1


1

1
6

3
1
1

1
24


49
x


 


17
3
1

1
1
5
2
1

4

6
6
2

7
2
1
1
3


46
x


 


18





8
1

1
2

2
2

4

3
1

3


27



 


19





2

1



1
1

3
4

1




13



 


20
2


1
2
1



1


1






1


9



 


21







1

1









1


3



 


22

1

















1


2



 


23










1





1





2



 


24


1



















1



 


25

















1




1





Average Dseg = 11.9 Average DJ = 15.7


Median D = 12 12 Shortest 6 Longest 19


Median DJ = 15 15 Shortest 9 Longest 24













TABLE 13P







Frequency of D-segments. “|” stands for a stop codon.



















D seg
“0”
%
C %
GLG
“1”
%
C %
GLG
“2”
%
C %
GLG






















1-01
1
0.13
0
VQLERX
4
0.53
0.22
GTTGTX
5
0.66
0.34
YNWND






(SEQ ID NO: 132)



(SEQ ID NO: 133)



(SEQ ID NO: 134)


 


1-07
0
0
0
V|LELX
3
0.4
0.11
GITGTX
9
1.19
0.34
YNWNY






(SEQ ID NO: 135)



(SEQ ID NO: 136)



(SEQ ID NO: 137)


 


1-20
0
0
0
V|LERX
1
0.13
0.22
GITGTX
4
0.53
0.45
YNWND






(SEQ ID NO: 138)



(SEQ ID NO: 139)



(SEQ ID NO: 140)


 


1-26
4
0.53
0
V|WELLX
13
1.72
0.90
GIVGATX
36
4.76
0.78
YSGSYY






(SEQ ID NO: 141)



(SEQ ID NO: 142)



(SEQ ID NO: 143)


 


2-02
31
4.1
2.47
GYCSSTSCYT
4
0.53
0.22
RIL||YQLLYX
9
1.19
2.47
DIVVVPAAIX






(SEQ ID NO: 144)



(SEQ ID NO: 145)



(SEQ ID NO: 146)


 


2-08
5
0.66
0.56
GYCTNGVCYT
0
0
0
RILY|WCMLYX
3
0.4
0.56
DIVLMVYAIX






(SEQ ID NO: 147)



(SEQ ID NO: 148)



(SEQ ID NO: 149)


 


2-15
29
3.83
1.57
GYCSGGSCYS
2
0.26
0.11
RIL|WW|LLLX
7
0.92
1.57
DIVVVVAATX






(SEQ ID NO: 150)



(SEQ ID NO: 151)



(SEQ ID NO: 152)


 


2-21
16
2.11
0.67
AYCGGDCYS
0
0
0
SILWW|LLFX
7
0.92
0.67
HIVVVTAIX






(SEQ ID NO: 153)



(SEQ ID NO: 154)



(SEQ ID NO: 155)


 


3-03
32
4.23
2.80
YYDFWSGYYT
7
0.92
0.90
VLRFLEWLLYX
27
3.57
1.12
ITIFGVVIIX






(SEQ ID NO: 156)



(SEQ ID NO: 157)



(SEQ ID NO: 158)


 


3-09
13
1.72
1.35
YYDILTGYYN
5
0.66
0.78
VLRYFDWLL|X
0
0
0
ITIF|LVIIX






(SEQ ID NO: 159)



(SEQ ID NO: 160)



(SEQ ID NO: 161)


 


3-10
42
5.55
4.26
YYYGSGSYYN
13
1.72
0.89
VLLWFGELL|X
11
1.45
2.91
ITMVRGVIIX






(SEQ ID NO: 162)



(SEQ ID NO: 163)



(SEQ ID NO: 164)


 


3-16
18
2.38
0.67
YYDYVWGSYRYT
8
1.06
0
VL|LRLGELSLYX
5
0.66
0.34
IMITFGGVIVIX






(SEQ ID NO: 165)



(SEQ ID NO: 166)



(SEQ ID NO: 167)


 


3-22
57
7.53
3.36
YYYDSSGYYY
1
0.13
0.11
VLL|||WLLLX
6
0.79
0.34
ITMIVVVITX






(SEQ ID NO: 168)



(SEQ ID NO: 169)



(SEQ ID NO: 170)


 


4-04
5
0.66
0.28
DYSNY
2
0.26
0
|LQ|LX
2
0.26
0.06
TTVTX






(SEQ ID NO: 171)



(SEQ ID NO: 172)



(SEQ ID NO: 173)


 


4-17
29
3.83
1.45
DYGDY
0
0
0
|LR|LX
20
2.64
0.90
TTVTX






(SEQ ID NO: 174)



(SEQ ID NO: 175)



(SEQ ID NO: 176)


 


4-23
10
1.32
0.56
DYGGNS
1
0.13
0
|LRW|LX
4
0.53
0.56
TTVVTX






(SEQ ID NO: 177)



(SEQ ID NO: 178)



(SEQ ID NO: 179)


 


5-05
3
0.4
0.06
WIQLWLX
10
1.32
0.39
VDTAMVX
31
4.1
0.73
GYSYGY






(SEQ ID NO: 180)



(SEQ ID NO: 181)



(SEQ ID NO: 182)


 


5-12
0
0
0
WI|WLRLX
8
1.06
0.45
VDIVATIX
14
1.85
1.12
GYSGYDY






(SEQ ID NO: 183)



(SEQ ID NO: 184)



(SEQ ID NO: 185)


 


5-24
11
1.45
0
|RWLQLX
5
0.66
0.34
VEMATIX
13
1.72
0.44
RDGYNY






(SEQ ID NO: 186)



(SEQ ID NO: 187)



(SEQ ID NO: 188)


 


6-06
11
1.45
0.78
SIAARX
9
1.19
0.48
EYSSSS
1
0.13
0.11
V|QLVX






(SEQ ID NO: 189)



(SEQ ID NO: 190)



(SEQ ID NO: 191)


 


6-13
19
2.51
1.01
GIAAAGX
35
4.62
2.13
GYSSSWY
2
0.26
0.31
V|QQLVX






(SEQ ID NO: 192)



(SEQ ID NO: 193)



(SEQ ID NO: 194)


 


6-19
14
1.85
2.12
GIAVAGX
48
6.34
2.02
GYSSGWY
4
0.53
0.56
V|QWLVX






(SEQ ID NO: 195)



(SEQ ID NO: 196)



(SEQ ID NO: 197)


 


D7: 7-27
1
0.13
0
|LGX
2
0.26
0.68
LTGX
2
0.26
0.22
NWG










(SEQ ID NO: 198)





Total = 757













TABLE 14P







Possible library components.












Component
L
f






D2_2-02_Phz0
xxxYCSSTSCxxx
13,
31,
(SEQ ID NO: 199)


 


D3_3-16_Phz0
xxxxYVWGSYxxx
13,
18,
(SEQ ID NO: 200)


 


D5_5-12_Phz2
xxxxxxxSGYxxx
13,
14,
(SEQ ID NO: 201)


 


D3_3-09_Phz0
xxxYDILTGYYxx
13,
13,
(SEQ ID NO: 202)


 


D2_2-02_Phz2
xxxVVVPAAxxxx
13,
 9,
(SEQ ID NO: 203)


 


D3_3-22_Phz0
xxxYYDSSGYxx
12,
57,
(SEQ ID NO: 204)


 


D3_3-03_Phz0
xxxDFWSGxxxx
12,
32,
(SEQ ID NO: 205)


 


D3_3-03_Phz2
xxxTIFGVxxxx
12,
27,
(SEQ ID NO: 206)


 


D5_5-12_Phz1
xxxxIVATxxxx
12,
 8,
(SEQ ID NO: 207)


 


D3_3-10_Phz0
xxxYGSGSYYx
11,
42,
! could add one x at either end (SEQ ID NO: 208)


 


D5_5-05_Phz2
xxxxYSYGxxx
11,
31,
(SEQ ID NO: 209)


 


D2_2-15_Phz0
xxxCSGxxCYx
11,
29,
(SEQ ID NO: 210)


 


D6_6-13_Phz0
xxxxAAAGxxx
11,
19,
(SEQ ID NO: 211)


 


D4_4-23_Phz0
xGxxxGGNxxx
11,
10,
(SEQ ID NO: 212)


 


D1_1-26_Phz2
xxxSGSYxxx
10,
35,
(SEQ ID NO: 213)


 


D6_6-13_Phz1
xxxSSSWxxx
10,
35,
(SEQ ID NO: 214)


 


D4_4-17_Phz2
xxxxTTVTTx
10,
20,
(SEQ ID NO: 215)


 


D2_2-21_Phz0
xxxC(SG)GDxCx
10,
16,
(SEQ ID NO: 216)


 


D6_6-19_Phz0
xxx(IV)AVAGxx
10,
14,
(SEQ ID NO: 217)


 


D3_3-10_Phz1
xxLWFGELxx
10,
13,
(SEQ ID NO: 218)


 


D5_5-24_Phz0
GxxWLxxxxF
10,
11,
(SEQ ID NO: 219)


 


D5_5-05_Phz1
xxxDTxMVxx
10,
10,
(SEQ ID NO: 220)


 


D3_3-16_Phz1
xxxxxGExxx
10,
 8,
(SEQ ID NO: 221)


 


D6_6-19_Phz1
xxxxSGWxx
 9,
48,
(SEQ ID NO: 222)


 


D5_5-24_Phz2
xxxxGYNxx
 9,
13,
(SEQ ID NO: 223)


 


D3_3-10_Phz2
xxxVRGVxx
 9,
11,
(SEQ ID NO: 224)


 


D6_6-06_Phz0
xxxIAAxxx
 9,
11,
(SEQ ID NO: 225)


 


D1_1-07_Phz2
xxYxWNxxx
 9,
 9,
(SEQ ID NO: 226)


 


D4_4-17_Phz0
xxxYGDxx
 8,
29,
(SEQ ID NO: 227)


 


D1_1-26_Phz1
xxVGATxx
 8,
13,
(SEQ ID NO: 228)


 


D6_6-06_Phz1
xxxYSSSx
 8,
 9,
(SEQ ID NO: 229)
















TABLE 15P





Lengths of CDRs: 1095 actual VH domains and 51 VH GLGs.

















Length


























0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17





CDR1
0
0
10
0
1
820
38
175
1
1
5
1
11
0
23
1
7
0


GLG
0
0
0
0
0
38
3
10
0
0 . . .










CDR2
0
0
0
0
0
2
0
0
0
0
0
0
0
0
0
0
464
579


GLG
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
17
28


CDR3
0
0
0
4
2
8
6
28
40
65 
77
90
117
117
88
105
86
81












Length
























18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
(33 or more)





CDR2
9
31
1
3
3
1
0
0
0
0
2
0
0 . . .





GLG
1
4
0
0 . . .














CDR3
45
36
36
16 
16
8
8
2
3
0
2
1
0
0
1
5
















TABLE 16P







Library of HC CDR3













Component
Fraction of
Length
#X
Complexity
library
Adjusted
















1:
YYCA21111YFDYWG.
8
4
2.6 E  5
.10 (0-8)
.02



(2 = KR; SEQ ID NO: 6)







 


2:
YYCA2111111YFDYWG.
10
6
9.4 E  7
.14 (9-10)
.14



(2 = KR; SEQ ID NO: 7)







 


3:
YYCA211111111YFDYTG.
12
8
3.4 E 10
.25 (11 + 12 + 13/2)
.25



(2 = KR; SEQ ID NO: 8)







 


4:
YYCAR111S2S3111YFDYWG.
14
6
1.9 e  8
.13 (14 + 13/2)
.14



(2 = SG 3 = YW; SEQ ID NO: 9)







 


5:
YYCA2111CSG11CY1YFDYWG.
15
6
9.4 E  7
.13 (15 + 16/2)
.14



(2 = KR; SEQ ID NO: 10)







 


6:
YYCA211S1TIFG11111YFDYWG.
17
8
1.7 E 10
.11 (17 + 16/2)
.12



(2 = KR; SEQ ID NO: 11)







 


7:
YYCAR111YY2S33YY111YFDYWG.
18
6
3.8 E  8
.04 (18)
.08



(2 = D|G; 3 = S|G; SEQ ID NO: 12)







 


8:
YYCAR1111YC2231CY111YFDYWG.
19
8
2.0 E 11
.10 (19 on)
.11



(2 = S|G; 3 = T|D|G; SEQ ID NO: 13)





Allowed lengths: 8, 10, 12, 14, 15, 17, 18, & 19













TABLE 17P







vgDNA encoding the CDR3 elements of the library





! CDR3 library components








(Ctop25)
5′-gctctggtcaa C|TTA|AGg|gct|gag|g-3′ (SEQ ID NO: 40)


 


(CtprmA)
5′-gctctggtcaa C|TTA|AGg|gct|gag|gac-


!
              AflII...



  |acc|gct|gtc|tac|tac|tgc|gcc-3′ (SEQ ID NO: 41)


!



(CBprmB)
[RC] 5′-|tac|ttc|gat|tac|ttg|ggc|caa|GGT|ACC|ctG|GTC|ACC|tcgctccacc-3′ (SEQ ID NO: 42)


!
                                               BstEII...


(CBot25)
[RC]                             5′-|GGT|ACC|ctG|GTC|ACC|tcgctccacc-3′ (SEQ ID NO: 43)


!








!N.B. [RC] means the the actual oligonucleotide is the reverse complement


!     of the one shown.


!N.B. The 20 bases at 3′ end of CtprmA are identical to the most 5′ 20 bases


!     of each of the vgDNA molecules.


!N.B. Ctop25 is identical to the most 5′ 25 bases of CtprmA.


!N.B. The 23 most 3′ bases of CBprmB are the reverse complement of the


!     most 3′ 23 bases of each of the vgDNA molecules.


!N.B. CBot25 is identical to the 25 bases at the 5′ end of CBprmB.


!








(C1t08)
5′-cc|gct|gtc|tac|tac|tgc|gcc|-



       <2>|<1>|<1>|<1>|<1>-



     |tac|ttc|gat|tac|ttg|ggc|caa|GG-3′ (SEQ ID NO: 44)







!2 = KR, 1 = 0.27Y + 0.27G + 0.027{ADEFHIKLMNPQRSTVW} no C


!








(C2t10)
5′-cc|gct|gtc|tac|tac|tgc|gcc|-



       <2>|<1>|<1>|<1>|<1>|<1>|<1>|-



     tac|ttc|gat|tac|ttg|ggc|caa|GG-3′ (SEQ ID NO: 45)







!2 = KR, 1 = 0.27Y + 0.27G + 0.027{ADEFHIKLMNPQRSTVW} no C


!








(C3t12)
5′-cc|gct|gtc|tac|tac|tgc|gcc|-



       <2>|<1>|<1>|<1>|<1>|<1>|<1>|<1>|<1>|-



     tac|ttc|gat|tac|ttg|ggc|caa|GG-3′ (SEQ ID NO: 46)







!2 = KR, 1 = 0.27Y + 0.27G + 0.027{ADEFHIKLMNPQRSTVW} no C


!








(C4t14)
5′-cc|gct|gtc|tac|tac|tgc|gcc|cgt|-



     |<1>|<1>|<1>|tct|<2>|tct|<3>|<1>|<1>|<1>|-



   tac|ttc|gat|tac|ttg|ggc|caa|GG-3′ (SEQ ID NO: 47)







!2 = SG, 1 = 0.27Y + 0.27G + 0.027{ADEFHIKLMNPQRSTVW} no C, 3 = YW


!








(C5t15)
5′-cc|gct|gtc|tac|tac|tgc|gcc|-



        <2>|<1>|<1>|<1>|tgc|tct|ggt|<1>|<1>|tgc|tat|<1>|-



     tac|ttc|gat|tac|ttg|ggc|caa|GG-3′ (SEQ ID NO: 48)







!2 = KR, 1 = 0.27Y + 0.27G + 0.027{ADEFHIKLMNPQRSTVW} no C


!








(C6t17)
5′-cc|gct|gtc|tac|tac|tgc|gcc|-



      <2>|<1>|<1>|tct|<1>|act|atc|ttc|ggt|<1>|<1>|<1>|<1>|<1>|-



     tac|ttc|gat|tac|ttg|ggc|caa|GG-3′ (SEQ ID NO: 49)







!2 = KR, 1 = 0.27Y + 0.27G + 0.027{ADEFHIKLMNPQRSTVW} no C


!








(C7t18)
5′-cc|gct|gtc|tac|tac|tgc|gcc|cgt|-







    |<1>|<1>|<1>|tat|tac|<2>|tct|<3>|<3>|tac|tat|<1>|<1>|<1>|-









     tac|ttc|gat|tac|ttg|ggc|caa|GG-3′ (SEQ ID NO: 50)







!2 = DG, 1 = 0.27Y + 0.27G + 0.027{ADEFHIKLMNPQRSTVW} no C, 3 = SG


!








(c8t19)
5′-cc|gct|gtc|tac|tac|tgc|gcc|cgt|-







    |<1>|<1>|<1>|<1>|tat|tgc|<2>|<2>|<3>|<1>|tgc|tat|<1>|<1>|<1>|-









     tac|ttc|gat|tac|ttg|ggc|caa|GG-3′ (SEQ ID NO: 51)







!2 = SG, 1 = 0.27Y + 0.27G + 0.027{ADEFHIKLMNPQRSTVW} no C, 3 = TDG


!
















TABLE 19





Names of 1398 GeneBank entries examined





















haj10335
hsa006167
hsa234193
hsa234294
hsa239370
hsa241345
hsa244970


hs201e3
hsa006169
hsa234194
hsa234296
hsa239371
hsa241346
hsa244971


hs201g1
hsa006171
hsa234196
hsa234298
hsa239372
hsa241347
hsa244972


hs201m2
hsa006173
hsa234197
hsa235649
hsa239373
hsa241348
hsa244973


hs202e2
hsa131921
hsa234199
hsa235658
hsa239375
hsa241349
hsa244974


hs202g3
hsa132847
hsa234202
hsa235662
hsa239376
hsa241350
hsa244975


hs202g9
hsa132849
hsa234203
hsa235664
hsa239377
hsa241351
hsa244976


hs202m3
hsa132850
hsa234205
hsa235665
hsa239378
hsa241353
hsa244977


hs203e1
hsa132851
hsa234206
hsa235667
hsa239379
hsa241354
hsa244978


hs203g1
hsa132852
hsa234207
hsa235671
hsa239380
hsa241355
hsa244979


hs203m5
hsa224746
hsa234208
hsa235675
hsa239381
hsa241356
hsa244980


hs204e1
hsa225092
hsa234209
hsa235677
hsa239382
hsa241357
hsa244981


hs204g1
hsa225093
hsa234211
hsa238036
hsa239383
hsa241420
hsa244982


hs3d6hcv
hsa230634
hsa234212
hsa238037
hsa239384
hsa241421
hsa244983


hs6d4xa7
hsa230635
hsa234214
hsa238038
hsa239385
hsa242555
hsa244984


hs6d4xb7
hsa230636
hsa234217
hsa238039
hsa239386
hsa242556
hsa244985


hs6d4xf1
hsa230637
hsa234221
hsa238040
hsa239387
hsa243108
hsa244986


hs6d4xf2
hsa230638
hsa234224
hsa238326
hsa239388
hsa243110
hsa244987


hs6d4xg3
hsa230639
hsa234227
hsa238327
hsa239390
hsa244928
hsa244988


hs6d4xh5
hsa230640
hsa234229
hsa238328
hsa239391
hsa244929
hsa244989


hs83x6b2
hsa230641
hsa234230
hsa239330
hsa240553
hsa244930
hsa244990


hs83x6b5
hsa230643
hsa234232
hsa239331
hsa240554
hsa244931
hsa244991


hs83x6c3
hsa230644
hsa234235
hsa239332
hsa240555
hsa244932
hsa244992


hs83x6c4
hsa230645
hsa234238
hsa239333
hsa240556
hsa244933
hsa244993


hs83x6c5
hsa230646
hsa234239
hsa239334
hsa240557
hsa244934
hsa244994


hs83x6d4
hsa230647
hsa234242
hsa239335
hsa240558
hsa244935
hsa244995


hs83x6f1
hsa230648
hsa234245
hsa239336
hsa240559
hsa244936
hsa244996


hs83x6f2
hsa230649
hsa234248
hsa239337
hsa240560
hsa244937
hsa244997


hs83x6f3
hsa230650
hsa234249
hsa239338
hsa240561
hsa244938
hsa244998


hs83x6f5
hsa230651
hsa234251
hsa239339
hsa240562
hsa244939
hsa244999


hs83x6h3
hsa230652
hsa234252
hsa239340
hsa240563
hsa244940
hsa245000


hs83x9a6
hsa230653
hsa234255
hsa239341
hsa240564
hsa244941
hsa245001


hs83x9b6
hsa230654
hsa234256
hsa239342
hsa240565
hsa244942
hsa245002


hs83x9b9
hsa230655
hsa234257
hsa239343
hsa240566
hsa244943
hsa245003


hs83x9c8
hsa230656
hsa234258
hsa239344
hsa240567
hsa244944
hsa245004


hs83x9d6
hsa230657
hsa234259
hsa239345
hsa240568
hsa244945
hsa245005


hs83x9d7
hsa230658
hsa234260
hsa239346
hsa240569
hsa244946
hsa245006


hs83x9e6
hsa234156
hsa234262
hsa239347
hsa240570
hsa244947
hsa245007


hs83x9e8
hsa234158
hsa234263
hsa239348
hsa240571
hsa244948
hsa245008


hs83x9e9
hsa234160
hsa234264
hsa239349
hsa240572
hsa244949
hsa245009


hs83x9f6
hsa234161
hsa234266
hsa239350
hsa240573
hsa244950
hsa245010


hs83x9g6
hsa234163
hsa234268
hsa239351
hsa240575
hsa244951
hsa245011


hs9d4x10
hsa234164
hsa234269
hsa239353
hsa240576
hsa244952
hsa245012


hs9d4x7
hsa234166
hsa234270
hsa239354
hsa240578
hsa244953
hsa245013


hs9d4x8
hsa234168
hsa234272
hsa239355
hsa240580
hsa244954
hsa245014


hs9d4x9
hsa234169
hsa234273
hsa239356
hsa240581
hsa244955
hsa245015


hs9d4xa6
hsa234171
hsa234274
hsa239357
hsa240582
hsa244956
hsa245016


hs9d4xa7
hsa234172
hsa234276
hsa239358
hsa240585
hsa244957
hsa245017


hs9d4xb6
hsa234175
hsa234277
hsa239359
hsa240586
hsa244958
hsa245018


hs9d4xc2
hsa234178
hsa234279
hsa239360
hsa240588
hsa244959
hsa245019


hs9d4xd6
hsa234180
hsa234281
hsa239361
hsa240589
hsa244960
hsa245020


hs9d4xe6
hsa234181
hsa234282
hsa239362
hsa240590
hsa244961
hsa245021


hs9d4xf3
hsa234183
hsa234283
hsa239363
hsa240592
hsa244962
hsa245022


hs9d4xh4
hsa234184
hsa234284
hsa239364
hsa240593
hsa244963
hsa245023


hs9d4xh5
hsa234186
hsa234286
hsa239365
hsa240594
hsa244965
hsa245024


hsa005975
hsa234187
hsa234287
hsa239366
hsa240595
hsa244966
hsa245025


hsa005977
hsa234189
hsa234288
hsa239367
hsa240599
hsa244967
hsa245026


hsa006161
hsa234190
hsa234290
hsa239368
hsa240604
hsa244968
hsa245027


hsa006165
hsa234191
hsa234291
hsa239369
hsa241344
hsa244969
hsa245028


hsa245029
hsa245225
hsa245319
hsa279536
hsasighc
hsb8g3g01
hsfs11hc


hsa245030
hsa245226
hsa245320
hsa279537
hsavh510
hsb8g3g03
hsfs9whc


hsa245031
hsa245228
hsa245321
hsa279543
hsavh512
hsb8g3g05
hsgad2h


hsa245032
hsa245229
hsa245322
hsa279544
hsavh513
hsb8g3g10
hsgvh0117


hsa245033
hsa245230
hsa245323
hsa279545
hsavh514
hsb8g3h01
hsgvh0118


hsa245034
hsa245231
hsa245325
hsa279552
hsavh515
hsb8g4c02
hsgvh0119


hsa245035
hsa245232
hsa245326
hsa389169
hsavh516
hsb8g4e01
hsgvh0120


hsa245036
hsa245233
hsa245338
hsa389170
hsavh517
hsb8g4e05
hsgvh0121


hsa245037
hsa245234
hsa245342
hsa389171
hsavh519
hsb8g4f11
hsgvh0122


hsa245039
hsa245235
hsa245343
hsa389172
hsavh520
hsb8g4h09
hsgvh0123


hsa245040
hsa245236
hsa245345
hsa389173
hsavh523
hsb8g4h10
hsgvh0124


hsa245041
hsa245237
hsa245346
hsa389174
hsavh524
hsb8g5d10
hsgvh0201


hsa245042
hsa245238
hsa245347
hsa389175
hsavh526
hsb8g5h08
hsgvh0202


hsa245043
hsa245239
hsa245348
hsa389176
hsavh529
hsbel1
hsgvh0203


hsa245044
hsa245240
hsa245349
hsa389177
hsavh53
hsbel14
hsgvh0204


hsa245045
hsa245241
hsa245350
hsa389178
hsavh56
hsbel28
hsgvh0205


hsa245046
hsa245246
hsa245352
hsa389179
hsb3g4a07
hsbel29
hsgvh0206


hsa245047
hsa245251
hsa245353
hsa389180
hsb73g04n
hsbel3
hsgvh0207


hsa245048
hsa245255
hsa245355
hsa389181
hsb74a08n
hsbel34
hsgvh0208


hsa245049
hsa245258
hsa245356
hsa389182
hsb7g1a11
hsbel43
hsgvh0209


hsa245050
hsa245260
hsa245357
hsa389183
hsb7g2b01
hsbel45
hsgvh0210


hsa245051
hsa245261
hsa245358
hsa389184
hsb7g3a01
hsbel5
hsgvh0211


hsa245052
hsa245262
hsa245359
hsa389185
hsb7g3a05
hsbel54
hsgvh0213


hsa245053
hsa245263
hsa249378
hsa389186
hsb7g3a10
hsbel69
hsgvh0214


hsa245054
hsa245265
hsa249628
hsa389187
hsb7g3b02
hsbo1vhig
hsgvh0215


hsa245055
hsa245266
hsa249629
hsa389188
hsb7g3b03
hsbo3vhig
hsgvh0216


hsa245056
hsa245268
hsa249630
hsa389190
hsb7g3b05
hsbr1vhig
hsgvh0217


hsa245057
hsa245272
hsa249631
hsa389191
hsb7g3c03
hsbradh3
hsgvh0218


hsa245058
hsa245273
hsa249632
hsa389192
hsb7g3c12
hscal4ghc
hsgvh0219


hsa245059
hsa245275
hsa249633
hsa389193
hsb7g3d07
hsd4xd10
hsgvh0220


hsa245060
hsa245277
hsa249634
hsa389194
hsb7g3e01
hsd4xf21
hsgvh0221


hsa245061
hsa245278
hsa249635
hsa389195
hsb7g3f02
hsd4xg2
hsgvh0222


hsa245062
hsa245279
hsa249636
hsa389927
hsb7g3f10
hsd4xi10
hsgvh0223


hsa245063
hsa245280
hsa249637
hsa389929
hsb7g3g02
hsd4xi4
hsgvh0224


hsa245064
hsa245281
hsa271600
hsa6351
hsb7g3g04
hsd4xk9
hsgvh0302


hsa245065
hsa245282
hsa271601
hsa7321
hsb7g4a08
hsd4xl3
hsgvh0304


hsa245066
hsa245283
hsa271602
hsa7322
hsb7g4c05
hsd5hc
hsgvh0306


hsa245067
hsa245284
hsa271603
hsa7323
hsb7g4d09
hsdo1vhig
hsgvh0307


hsa245068
hsa245285
hsa271604
hsa7325
hsb7g4f08
hseliepa1
hsgvh0308


hsa245069
hsa245286
hsa279513
hsa7326
hsb7g4g07
hseliepa3
hsgvh0309


hsa245071
hsa245287
hsa279514
hsa7328
hsb7g5g03
hseliepa4
hsgvh0310


hsa245072
hsa245288
hsa279515
hsa7438
hsb8g1c04
hseliepb2
hsgvh0311


hsa245073
hsa245289
hsa279516
hsa7440
hsb8g1e04
hseliepd2
hsgvh0312


hsa245201
hsa245290
hsa279517
hsa7441
hsb8g1f03
hselilpb1
hsgvh0314


hsa245203
hsa245291
hsa279519
hsa7442
hsb8g1g04
hsevh51a1
hsgvh0315


hsa245204
hsa245292
hsa279520
hsa7443
hsb8g1h02
hsevh51b1
hsgvh0318


hsa245208
hsa245294
hsa279521
hsa7444
hsb8g2f09
hsevh52a1
hsgvh0320


hsa245209
hsa245298
hsa279522
hsaarma1
hsb8g2g08
hsevh52a2
hsgvh0321


hsa245210
hsa245299
hsa279523
hsabhiv8
hsb8g3b07
hsevh52a3
hsgvh0322


hsa245214
hsa245301
hsa279524
hsadeigvh
hsb8g3c07
hsevh52a4
hsgvh0323


hsa245215
hsa245305
hsa279526
hsaj2768
hsb8g3c08
hsevh52a5
hsgvh0324


hsa245217
hsa245307
hsa279527
hsaj2769
hsb8g3c12
hsevh52b1
hsgvh0325


hsa245218
hsa245309
hsa279528
hsaj2771
hsb8g3d03
hsevh53a1
hsgvh0326


hsa245219
hsa245311
hsa279529
hsaj2772
hsb8g3d04
hsevh53a2
hsgvh0327


hsa245220
hsa245312
hsa279530
hsaj2773
hsb8g3d07
hsfog1h
hsgvh0328


hsa245221
hsa245313
hsa279531
hsaj2776
hsb8g3d08
hsfog3h
hsgvh0329


hsa245222
hsa245315
hsa279532
hsaj2777
hsb8g3e02
hsfogbh
hsgvh0330


hsa245223
hsa245317
hsa279533
hsaj4083
hsb8g3e03
hsfom1h
hsgvh0331


hsa245224
hsa245318
hsa279535
hsaj4899
hsb8g3f03
hsfs10hc
hsgvh0332


hsgvh0333
hsigathc
hsighxx10
hsigvhc26
hsld1117
hsmvh51
hst14x23


hsgvh0334
hsigdvrhc
hsighxx11
hsigvhc27
hsld152
hsmvh510
hst14x24


hsgvh0335
hsigg1kh
hsighxx12
hsigvhc28
hsld21
hsmvh511
hst14x25


hsgvh0336
hsigg1kl
hsighxx14
hsigvhc29
hsld217
hsmvh512
hst14x3


hsgvh0419
hsigg1lh
hsighxx16
hsigvhc30
hsld218
hsmvh515
hst14x6


hsgvh0420
hsigghc85
hsighxx18
hsigvhc31
hsld25
hsmvh516
hst14x7


hsgvh0421
hsigghcv3
hsighxx2
hsigvhc32
hsmad2h
hsmvh517
hst14x8


hsgvh0422
hsigghevr
hsighxx20
hsigvhc33
hsmbcl5h4
hsmvh53
hst14x9


hsgvh0423
hsiggvdj1
hsighxx21
hsigvhc35
hsmica1h
hsmvh54
hst22x1


hsgvh0424
hsiggvdj2
hsighxx22
hsigvhc36
hsmica3h
hsmvh55
hst22x11


hsgvh0428
hsiggvhb
hsighxx23
hsigvhc37
hsmica4h
hsmvh56
hst22x12


hsgvh0429
hsiggvhc
hsighxx25
hsigvhc38
hsmica5h
hsmvh57
hst22x13


hsgvh0430
hsigh10g1
hsighxx26
hsigvhc39
hsmica6h
hsmvh58
hst22x14


hsgvh0517
hsigh10g2
hsighxx28
hsigvhc40
hsmica7h
hsmvh59
hst22x15


hsgvh0519
hsigh10g3
hsighxx29
hsigvhc41
hsmt11ige
hsnamembo
hst22x18


hsgvh0522
hsigh10g4
hsighxx3
hsigvhc42
hsmt12ige
hsnpb346e
hst22x20


hsgvh0523
hsigh10g5
hsighxx30
hsigvhc43
hsmt13ige
hsoak3h
hst22x21


hsgvh0526
hsigh10g7
hsighxx31
hsigvhls
hsmt14ige
hsog31h
hst22x22


hsgvh0527
hsigh10g8
hsighxx32
hsigvhttd
hsmt15ige
hspag1h
hst22x23


hsgvh0531
hsigh10g9
hsighxx34
hsigvp151
hsmt16ige
hsrael
hst22x25


hsgvh511
hsigh13g1
hsighxx36
hsigvp152
hsmt17ige
hsregah
hst22x26


hsgvh512
hsigh13g7
hsighxx37
hsigvp153
hsmt21ige
hsrfabh37
hst22x27


hsgvh513
hsigh14g1
hsighxx38
hsigvp154
hsmt22ige
hsrighvja
hst22x28


hsgvh515
hsigh14g2
hsighxx5
hsigvp155
hsmt23ige
hsrighvjb
hst22x30


hsgvh519
hsigh2f2
hsighxx6
hsigvp156
hsmt24ige
hsrou10
hst22x9


hsgvh521
hsigh3135
hsighxx7
hsigvp157
hsmt25ige
hsrou11
hsu24687


hsgvh526
hsigh35
hsighxx8
hsigvp158
hsmt26ige
hsrou111
hsu24688


hsgvh530
hsigh44
hsighxx9
hsigvp251
hsmt27ige
hsrou112
hsu24690


hsgvh533
hsigh4c2
hsigkrf
hsigvp255
hsmutuiem
hsrou119
hsu24691


hsgvh534
hsigh9e1
hsigmhavh
hsigvp256
hsmvh0001
hsrou122
hsv52a512


hsgvh535
hsighadi2
hsigrhe15
hsigvp257
hsmvh0002
hsrou126
hsvdj10h


hsgvh536
hsighadi3
hsigtgk1h
hsigvp360
hsmvh0003
hsrou127
hsvdj12h


hsgvh55
hsighcvr
hsigtgk4h
hsigvp363
hsmvh0004
hsrou129
hsvgcg1


hsh217e
hsighcza
hsigtgl9h
hsigvp369
hsmvh0005
hsrou13
hsvgcm1


hsh241e
hsighczb
hsigvarh1
hsigvp39
hsmvh0006
hsrou131
hsvgcm1


hsh28e
hsighczc
hsigvhc
hsihr8
hsmvh0007
hsrou18
hsvh1djh6


hsha3d1ig
hsighczd
hsigvhc01
hsihr9
hsmvh0009
hsrou219
hsvh3djh4


hshambh
hsighczf
hsigvhc02
hsihv1
hsmvh0010
hsrou221
hsvh4dj


hshcmg42
hsighczg
hsigvhc03
hsihv11
hsmvh0011
hsrou222
hsvh4djh6


hshcmg43
hsigheavy
hsigvhc04
hsihv18
hsmvh0012
hsrou233
hsvh4r


hshcmg44
hsighpat2
hsigvhc05
hsim9vch
hsmvh0401
hsrt792hc
hsvh52a43


hshcmg46
hsighpat3
hsigvhc06
hsimghc1
hsmvh0403
hsrt79hc
hsvh52a55


hshcmt42
hsighpat4
hsigvhc07
hsimghc2
hsmvh0404
hssm1vhig
hsvh5dj


hshcmt47
hsighpat5
hsigvhc08
hsimghc3
hsmvh0405
hssp46a
hsvh5djh5


hsig001vh
hsighpat6
hsigvhc09
hsimghc4
hsmvh0406
hst14vh
hsvh710p1


hsig030vh
hsighpat7
hsigvhc10
hsimghc5
hsmvh0501
hst14x1
hsvheg7


hsig033vh
hsighpat8
hsigvhc11
hsin42p5
hsmvh0502
hst14x10
hsvhfa2


hsig039vh
hsighpat9
hsigvhc12
hsin51p7
hsmvh0503
hst14x11
hsvhfa7


hsig040vh
hsighpt11
hsigvhc14
hsin51p8
hsmvh0504
hst14x12
hsvhfb5


hsig055vh
hsighpt12
hsigvhc16
hsin78
hsmvh0505
hst14x13
hsvhfc2


hsig057vh
hsighpta1
hsigvhc17
hsin87
hsmvh0506
hst14x14
hsvhfd7


hsig1059
hsighvb5
hsigvhc18
hsin89p2
hsmvh0507
hst14x15
hsvhfe5


hsig10610
hsighvca
hsigvhc19
hsin92
hsmvh0508
hst14x16
hsvhfg9


hsig13g10
hsighvcb
hsigvhc20
hsin98p1
hsmvh0509
hst14x17
hsvhgd8


hsig473
hsighvcc
hsigvhc21
hsjac10h
hsmvh0510
hst14x18
hsvhgd9


hsig7sa11
hsighvcd
hsigvhc22
hsjhba1f
hsmvh0511
hst14x19
hsvhgh7


hsigaehc
hsighvce
hsigvhc23
hsjhbr2f
hsmvh0513
hst14x20
hsvhha10


hsigaf2h2
hsighvm
hsigvhc24
hsjhej1f
hsmvh0515
hst14x21
hsvhia2


hsigashc
hsighxx1
hsigvhc25
hsld1110
hsmvh0529
hst14x22
hsvhia5


hsvhib12
hsvhp46
hsx98948
hsz74671
hsz80393
hsz80438
hsz80489


hsvhib6
hsvhp48
hsx98950
hsz74672
hsz80394
hsz80439
hsz80492


hsvhib8
hsvhp53
hsx98951
hsz74682
hsz80397
hsz80441
hsz80495


hsvhic1
hsvhp7
hsx98952
hsz74688
hsz80400
hsz80442
hsz80496


hsvhic10
hsvigd9
hsx98953
hsz74690
hsz80403
hsz80443
hsz80499


hsvhic11
hswad35vh
hsx98954
hsz74693
hsz80406
hsz80445
hsz80500


hsvhic2
hswanembo
hsx98955
hsz74695
hsz80407
hsz80458
hsz80502


hsvhic3
hswo1vhig
hsx98956
hsz80363
hsz80409
hsz80459
hsz80504


hsvhid1
hsww1p10e
hsx98958
hsz80364
hsz80411
hsz80460
hsz80507


hsvhid5
hsx98932
hsx98963
hsz80365
hsz80412
hsz80461
hsz80509


hsvhid7
hsx98933
hsy14934
hsz80367
hsz80414
hsz80462
hsz80512


hsvhid9
hsx98934
hsy14935
hsz80368
hsz80415
hsz80463
hsz80513


hsvhie4
hsx98935
hsy14936
hsz80372
hsz80416
hsz80465
hsz80517


hsvhif10
hsx98936
hsy14937
hsz80375
hsz80417
hsz80466
hsz80519


hsvhif3
hsx98938
hsy14938
hsz80377
hsz80418
hsz80473
hsz80520


hsvhif7
hsx98939
hsy14939
hsz80378
hsz80421
hsz80474
hsz80527


hsvhig2
hsx98940
hsy14940
hsz80383
hsz80422
hsz80475
hsz80534


hsvhp2
hsx98941
hsy14943
hsz80385
hsz80424
hsz80476
hsz80538


hsvhp29
hsx98943
hsy14945
hsz80386
hsz80426
hsz80477
hsz80544


hsvhp30
hsx98944
hsy18120
hsz80388
hsz80427
hsz80480
hsz80545


hsvhp32
hsx98945
hsz74663
hsz80390
hsz80429
hsz80482



hsvhp34
hsx98946
hsz74665
hsz80391
hsz80433
hsz80483



hsvhp4
hsx98947
hsz74668
hsz80392
hsz80436
hsz80487
















TABLE 20P







Human GLG CDR1 & CDR2 AA seqs














CDR2




CDR1

         1    1   1



Name
1234567

1234567890123456789





1-02
GYY--MH
(SEQ ID NO: 230)
WINPNSGG--TNYAQKFQG
(SEQ ID NO: 231)


 


1-03
SYA--MH
(SEQ ID NO: 232)
WINAGNGN--TKYSQKFQG
(SEQ ID NO: 233)


 


1-08
SYD--IN
(SEQ ID NO: 234)
WMNPNSGN--TGYAQKFQG
(SEQ ID NO: 235)


 


1-18
SYG--IS
(SEQ ID NO: 236)
WISAYNGN--TNYAQKLQG
(SEQ ID NO: 237)


 


1-24
ELS--MH
(SEQ ID NO: 238)
GFDPEDGE--TIYAQKFQG
(SEQ ID NO: 239)


 


1-45
YRY--LH
(SEQ ID NO: 240)
WITPFNGN--TNYAQKFQD
(SEQ ID NO: 241)


 


1-46
SYY--MH
(SEQ ID NO: 242)
IINPSGGS--TSYAQKFQG
(SEQ ID NO: 243)


 


1-58
SSA--VQ
(SEQ ID NO: 244)
WIVVGSGN--TNYAQKFQE
(SEQ ID NO: 245)


 


1-69
SYA--IS
(SEQ ID NO: 246)
GIIPIFGT--ANYAQKFQG
(SEQ ID NO: 247)


 


1-e
SYA--IS
(SEQ ID NO: 248)
GIIPIFGT--ANYAQKFQG
(SEQ ID NO: 249)


 


1-f
DYY--MH
(SEQ ID NO: 250)
LVDPEDGE--TIYAEKFQG
(SEQ ID NO: 251)


 


2-05
TSGVGVG
(SEQ ID NO: 252)
LIYWNDDK---RYSPSLKS
(SEQ ID NO: 253)


 


2-26
NARMGVS
(SEQ ID NO: 254)
HIFSNDEK---SYSTSLKS
(SEQ ID NO: 255)


 


2-70
TSGMRVS
(SEQ ID NO: 256)
RIDWDDDK---FYSTSLKT
(SEQ ID NO: 257)


 


3-07
SYW--MS
(SEQ ID NO: 258)
NIKQDGSE--KYYVDSVKG
(SEQ ID NO: 259)


 


3-09
DYA--MH
(SEQ ID NO: 260)
GISWNSGS--IGYADSVKG
(SEQ ID NO: 261)


 


3-11
DYY--MS
(SEQ ID NO: 262)
YISSSGST--IYYADSVKG
(SEQ ID NO: 263)


 


3-13
SYD--MH
(SEQ ID NO: 264)
AIGTAGD---TYYPGSVKG
(SEQ ID NO: 265)


 


3-15
NAW--MS
(SEQ ID NO: 266)
RIKSKTDGGTTDYAAPVKG
(SEQ ID NO: 267)


 


3-20
DYG--MS
(SEQ ID NO: 268)
GINWNGGS--TGYADSVKG
(SEQ ID NO: 269)


 


3-21
SYS--MN
(SEQ ID NO: 270)
SISSSSSY--IYYADSVKG
(SEQ ID NO: 271)


 


3-23
SYA--MS
(SEQ ID NO: 272)
AISGSGGS--TYYADSVKG
(SEQ ID NO: 273)


 


3-30
SYG--MH
(SEQ ID NO: 274)
VISYDGSN--KYYADSVKG
(SEQ ID NO: 275)


 


3303
SYA--MH
(SEQ ID NO: 276)
VISYDGSN--KYYADSVKG
(SEQ ID NO: 277)


 


3305
SYG--MH
(SEQ ID NO: 278)
VISYDGSN--KYYADSVKG
(SEQ ID NO: 279)


 


3-33
SYG--MH
(SEQ ID NO: 280)
VIWYDGSN--KYYADSVKG
(SEQ ID NO: 281)


 


3-43
DYT--MH
(SEQ ID NO: 282)
LISWDGGS--TYYADSVKG
(SEQ ID NO: 283)


 


3-48
SYS--MN
(SEQ ID NO: 284)
YISSSSST--IYYADSVKG
(SEQ ID NO: 285)


 


3-49
DYA--MS
(SEQ ID NO: 286)
FIRSKAYGGTTEYTASVKG
(SEQ ID NO: 287)


 


3-53
SNY--MS
(SEQ ID NO: 288)
VIYSGGS---TYYADSVKG
(SEQ ID NO: 289)


 


3-64
SYA--MH
(SEQ ID NO: 290)
AISSNGGS--TYYANSVKG
(SEQ ID NO: 291)


 


3-66
SNY--MS
(SEQ ID NO: 292)
VIYSGGS---TYYADSVKG
(SEQ ID NO: 293)


 


3-72
DHY--MD
(SEQ ID NO: 294)
RTRNKANSYTTEYAASVKG
(SEQ ID NO: 295)


 


3-73
GSA--MH
(SEQ ID NO: 296)
RIRSKANSYATAYAASVKG
(SEQ ID NO: 297)


 


3-74
SYW--MH
(SEQ ID NO: 298)
RINSDGSS--TSYADSVKG
(SEQ ID NO: 299)


 


3-d
SNE--MS
(SEQ ID NO: 300)
SISGGS----TYYADSRKG
(SEQ ID NO: 301)


 


4-04
SSNW-WS
(SEQ ID NO: 302)
EIYHSGS---TNYNPSLKS
(SEQ ID NO: 303)


 


4-28
SSNW-WG
(SEQ ID NO: 304)
YIYYSGS---TYYNPSLKS
(SEQ ID NO: 305)


 


4301
SGGYYWS
(SEQ ID NO: 306)
YIYYSGS---TYYNPSLKS
(SEQ ID NO: 307)


 


4302
SGGYSWS
(SEQ ID NO: 308)
YIYHSGS---TYYNPSLKS
(SEQ ID NO: 309)


 


4304
SGDYYWS
(SEQ ID NO: 310)
YIYYSGS---TYYNPSLKS
(SEQ ID NO: 311)


 


4-31
SGGYYWS
(SEQ ID NO: 312)
YIYYSGS---TYYNPSLKS
(SEQ ID NO: 313)


 


4-34
GYY--WS
(SEQ ID NO: 314)
EINHSGS---TNYNPSLKS
(SEQ ID NO: 315)


 


4-39
SSSYYWG
(SEQ ID NO: 316)
SIYYSGS---TYYNPSLKS
(SEQ ID NO: 317)


 


4-59
SYY--WS
(SEQ ID NO: 318)
YIYYSGS---TNYNPSLKS
(SEQ ID NO: 319)


 


4-61
SGSYYWS
(SEQ ID NO: 320)
YIYYSGS---TNYNPSLKS
(SEQ ID NO: 321)


 


4-b
SGYY-WG
(SEQ ID NO: 322)
SIYHSGS---TYYNPSLKS
(SEQ ID NO: 323)


 


5-51
SYW--IG
(SEQ ID NO: 324)
IIYPGDSD--TRYSPSFQG
(SEQ ID NO: 325)


 


5-a
SYW--IS
(SEQ ID NO: 326)
RIDPSDSY--TNYSPSFQG
(SEQ ID NO: 327)


 


6-1
SNSAAWN
(SEQ ID NO: 328)
RTYYRSKWY-NDYAVSVKS
(SEQ ID NO: 329)


 


74.1
SYA--MN
(SEQ ID NO: 330)
WINTNTGN--PTYAQGFTG
(SEQ ID NO: 331)











CDR1 of human GLGs































A
C
D
E
F
G
H
I
K
L
M
N
P
Q
R
S
T
V
W
Y
-
Consens.





1


7
1

3





2



35
2


1

Sd x


2
2




6
1


1

4


1
7



29

Ysg x


3
11

3
1

10





2


1
6
1

5
11

YAGS x


4
1









2






1
2
7
38
—


5
1




2








1
1



5
41
—


6







6

1
28






4
12


Mwi


7


1


5
16




5

1

23





SHng










CDR2 of human GLGs






























A
C
D
E
F
G
H
I
K
L
M
N
P
Q
R
S
T
V
W
Y
-
Consens.





1
3


2
1
5
1
2

3

1


7
4

6
7
9

X


2




1


46


1





2
1



I


3


4

1
1

2 
2


8


3
12
1
1
1
15

ysn x


4
2




2
4




1
10
1

11
2
1
5
12

ysp x


5
1

8
2
1
6

2 
4


8


1
17



1

sd x


6
3

7

2
26





3



8
2




Gsd x


7


4
1

17


1


2



24



1
1
SG x


8


1
3

3


3


10



9
4

1
2
15
— ns


9





2













3
46
—


10
1















3



47
—


11
2






4
5


1
1



35



3
T


12
1

2
2
1
3

2
1


11


2
3
1


22

Yn x


13



















51

Y


14
31










11
1


6
1
1



An x


15
4

16
1

1





1
14
11


2
1



dpq x


16





1


11



1


38





Sk


17




13




15




1


22



Vlf


18








37




13


1




Kq


19


1
1

34









14
1




GS
















TABLE 21P





Tallies of Amino-acid frequencies in mature CDR1 and CDR2






































A
C
D
E
F
G
H
I
K
L
M
N
P
Q
R
S
T
V
W
Y
|
X










Tally of 23 examples with length 14




























1

8







2







13





2
3














15
3
2





3
2


1

14









1

5





4


2

2
11









5



3



5





7





1
1


13



1



6
1



4
3

12

2







1





7





3

1
1


2
1

5
10







8




6
1



1

2


1
6
4
2





9




1
5

1



3
1

4
7
1






10
1

8


3





1
2

1
4
1


2



11
1



1

1
1







2

1

16



12
1

2
1

1
1




1



1


1
14



13










4






2
17




14
4

1


5





4



5
4











Tally of 11 examples with length 12




























1





4











7





2




1
4









4



2



3





7









4







4
1

1

1
5

2









1





5














1
9
1






6




2
1

3

2





3







7





3

1



3


1
3







8
1

3


2
1








2
2






9


1






1









9



10




1














10



11


















11




12





2





1



7
1











Tally of 175 examples with length 7




























1
2


1
1
2



1

3


2
153
10






2
3

2

1
87




1
10
1

5
61
2


2



3
3

26
1

54

1



5
1

2
76
3
1

2



4
6
1
1

6

1



2
1





11
1
145



5
5
2



13
2


2

3



6
2


140



6







1

1
1






13
159




7
2

1


67
1




10



88
5
1










Tally of 38 examples with length 6




























1











2



34
2






2
1

2

1
8





4



22







3






3




26







9



4




1

1











29
7



5


















38




6





10





3



22
3










Tally of 820 examples with length 5






























A
C
D
E
F
G
H
I
K
L
M
N
P
Q
R
S
T
V
W
Y

Seen





1
8

81
10

151
4
8
5
3

100

4
15
364
55
8

 4
SGNDT
15























x



2
7
5
12

24
1
30
1
1
5

26

1
1
23
2


681
Y
15


3
202
4
24
13
13
133
10


2

7
5
2
3
32
14
13
112
231
YAGW
17























x



4




6


172
2
7
409





3
16
205

MWI
8


5
8

6
1
1
49
241
2



79
1
3

367
56
2

 4
SHNT
14























x










CDR2























A
C
D
E
F
G
H
I
K
L
M
N










Tally of 31 examples with CDR2 of length 19



















 1




11 




1

1


 2
1






28 






 3








9
1




 4





 1


2


6


 5


 1
1

 1


22 

1



 6
16 

 1


 1

1
1





 7
1

 9








7


 8





23





1


 9
2




18








10
4




 1

1
1


1


11
1






3

1




12
2

11
9

 1
1

1
1




13






1

1





14
29 













15
25 

 3
1










16








1





17









1
1



18



1




27 





19


 1


30













Tally of 579 (n > 50, bold; over 400, underscored) examples with length 17



















 1
44 
1
 1
2
11 
81
5
69 
1
14 
6
41 


 2




7


522 
1
10 
17 
1


 3
3
1
22

5
 7
6
51 
25 
1

76 


 4
39 
2
 8
6
16 
64
9
3
2
3

15 


 5
3

194 
6
1
70
6
44 
6
4
1
55 


 6
3
1
75
4
45 
326 
1


6

43 


 7
8

24
5

226 
3
3
3
4

24 


 8
4
2
57
37 
5
22
4
18 
18 
2
2
161 


 9
56 


11 

 2

63 
157 
1
3
3


10
1

14
2
13 
30
23 
6
29 
2
3
110 


11

1
 2

7

5

1
4

3


12
405 


2

18

1

6

2


13
7

323 
22 

 7
4


1

4


14
2


5
6
 3


123 

1
4


15
1


1
188 
 2

1

22 
3



16
1


13 

 1
1

332 
3
2
1


17


11
1

565 













Tally of 464 (over 50, bold; over 400, underscored)



















 1
5

13
184 
8
 1
7
1
2
15 

6


 2




6


429 

3
4



 3

1
13

13 
 4
10 
5



154 


 4
1

12
2
6

199 
2

1

3


 5
5

20
1
1
18

4



9


 6


13
8

439 





1


 7


20
2

14
2
4
2


26 


 8
13 




 2

4
8
1
2



 9


10

4
 1
10 
1
8
1

245 


10

6


2

2




2


11
14 

 3



1
1
8


408 


12
4

13


 4



2

1


13
2



2









14




2


2

441 




15



18




413 

3
5


16
1

 1


31

2



2





















P
Q
R
S
T
V
W
Y
X













Tally of 31 examples with CDR2 of length 19



















 1

1
15
1
1




RF x



 2




2




I



 3


18
1
1


1

Rk



 4



21 
1




S



 5

1
 1
1
1


1

K x



 6
3


1
6
1



A x



 7



3
1


10 

y x



 8

1

5
1




G



 9


 1
1

1

7
1
G



10



1
21 


1

T



11




26 




T



12



2
1


2

x



13







29 

Y



14
1



1




A



15

1


1




A



16
10


20 





Sp



17





29 



V



18

1
 2






K



19









G









Tally of 579 (n > 50, bold; over 400, underscored) examples with length 17



















 1
1
4
34
30 
19 
118 
66 
31 

VGIW x



 2



3
8
10 



I



 3


 8
262 
19 
1
46 
46 

SNI x



 4
178 
23 
 6
50 
11 
8
16 
120 

PYG x



 5

4
 8
133 
9
7
1
27 

DSGN x



 6


 1
63 
8
1

2

GDS x



 7

2
11
245 
14 
6

1

SG x



 8
1
4
11
106 
90 
2
1
32 

NST X



 9
11 
5
13
4
242 
8



TKIA x



10

3
52
20 
10 
1
1
259 

YNR x



11



5



551 

Y



12
3

 1
89 
8
44 



A



13
66 
138 
 3


1

3

DQP x



14

2
 7
421 
1
2

2

SK x



15



1

357 

2
1
VF



16
1
199 
21

4




KQ x



17







1
1
G









Tally of 464 (over 50, bold; over 400, underscored)



















 1

3
26
65 
9
14 

105 

EYSL x



 2



1
2
19 



I



 3


 1
12 
1


250 

YN x



 4
4
5
 2
19 
28 

15 
165 

YH x



 5
1

22
365 
16 
1

1

S x



 6




1
1
1


G



 7
1

12
357 
20 
1

2
1
S x



 8
4

 3
6
420 



1
T



 9


13
9
3
1
1
157 

NY x



10

1

7



444 

Y



11
4


21 
2


2

N



12
418 


14 
7
1



P



13
6


452 
1


1

S



14


 1


18 



L



15

11 
10
1
2
1



K



16


 3
419 
5




S
















TABLE 22P





Tally of VH types
























1-02
16
1-03
16
1-08
13
1-18
27
1-24
5


1-45
0
1-46 
14
1-58
1
1-69
37
1-e
16


1-f
1
2-05
13
2-26
1
2-70
2
3-07
33


3-09
13
3-11
15
3-13
4
3-15
10
3-20
4


3-21
25
3-23
85
3-30
55
3303
59
3305
0


3-33
42
3-43
1
3-48
24
3-49
11
3-53
12


3-64
4
3-66
4
3-72
3
3-73
3
3-74 
12


3-d
0
4-04
29
4-28
3
4301
46
4302
7


4304
37
4-31
0
4-34
184 
4-39
65
4-59 
45


4-61
9
4-b
11
5-51
55
5-a
13
6-1
7


 74.1
3
















TABLE 23P 





Oligonucleotides used to variegate CDR1 and CDR2 of human HC















!(name) 5′-....DNA sequence....-3′


!everything to right of an exclamation point is commentary


![RC] means “reverse complement” of sequence shown


! If last non-comment and non-blank character is “-”, then continue


! on next line.


! Ignore case, “a” = “A”, “c” = “C”, etc.


! Ignore “|” and blanks.


! <number> means incorporate trinucleotide mixtue of given number.


!------------------------------------------------------------------------


!


! CDR1


(ON-R1V1vg)5′-    ct|TCC|GGA|ttc|act|ttc|tct|-


       <1>|tac|<1>|atg|<1>|-          ! CDR1 of length 5, ON = 55 bases


                  tgg|gtt|cgC|CAa|gct|ccT|GG-3′ (SEQ ID NO: 27)


! <1> = ADEFGHIKLMNPQRSTVWY        no C


!


(ON-R1top) 5′-cctactgtct |TCC|GGA|ttc|act|ttc|tct-3′ (SEQ ID NO: 28)


(ON-R1bot)[RC] 5′-tgg|gtt|cgC|CAa|gct|ccT|GG ttgctcactc-3′ (SEQ ID NO: 29)


(ON-R1V2vg) 5′-       ct|TCC|GGA|ttc|act|ttc|tct|-


       <6>|<7>|<7>|tac|tac|tgg|<7>|-      ! CDR1 of length 7, ON = 61 bases









tgg|gtt|cgC|CAa|gct|ccT|GG-3′ (SEQ ID NO: 30)







! <6> = ST, 1:1


! <7> = 0.2025(SG) + 0.035(ADEFHIKLMNPQRTVWY)  no C


(ON-R1V3vg) 5′-ct|TCC|GGA|ttc|act|ttc|tct|-


      |atc|agc|ggt|ggt|tct|atc|tcc|<1>|<1>|<1>|tac|tac|tgg|<1>|- ! CDR1, 1-L=14









tgg|gtt|cgC|CAa|gct|ccT|GG-3′ (SEQ ID NO: 31)! ON = 82 bases







!


! CDR2








(ON-R2V1vg)
5′-ggt|ttg|gag|tgg|gtt|tct|-







          <2>|atc|<2>|<3>|tct|ggt|ggc|<1>|act|<1>|- 









tat|gct|gac|tcc|gtt|aaa|gg-3′ (SEQ ID NO: 32) ! ON = 68  







bases, CDR2 = 17 AA


(ON-R2top) 5′-ct|tgg|gtt|cgC|CAa|gct|ccT|GGt|aaa|ggt|ttg|qag|tgg|gtt|tct-3′


           (SEQ ID NO: 33)


(ON-R2bot)(RC] 5′-tat|gct|gac|tcc|gtt|aaa|ggt|-


           cgc|ttc|act|atc|TCT|AGA|ttcctgtcac-3′ (SEQ ID NO: 34) ! XbaI plus 10 


bases of scab








(ON-R2V2vg)
5′-ggt|ttg|gag|tgg|gtt|tct|-







          <1>|atc|<4>|<1>|<1>|ggt|<5>|<1>|<1>|<1>|-









tat|gct|gac|tcc|gtt|aaa|gg-3′ (SEQ ID NO: 35) ! ON = 68 







bases, CDR2 = 17 AA


! <4> = DINSWY, equimolar ! <5> = SGDN, equimolar








(ON-R2V3vg)
5′-ggt|ttg|gag|tgg|gtt|tct|-







          <1>|atc|<4>|<1>|<1>|ggt|<5>|<1>|<1>|-









tat|aac|cct|tcc|ctt|aag|gg-3′ (SEQ ID NO: 36) ! ON = 65 



bases, CDR2 = 16 AA







(ON-R2bo3)[RC] 5′-tat|aac|cct|tcc|ctt|aag|ggt|-


           cgc|ttc|act|atc|TCT|AGA|ttcctgtcac-3′ (SEQ ID NO: 37) ! XbaI plus 10 


bases of scab








(ON-R2V4vg)
5′-ggt|ttg|gag|tgg|gtt|tct|-







          <1>|atc|<8>|agt|<1>|<1>|<1>|ggt|ggt|act|act|<1>









tat|gcc|gcc|tcc|gtt|aag|gg-3′ (SEQ ID NO: 38) ! ON = 74 



bases, CDR2 = 19 AA







(ON-R2bo4)[RC] 5′-tat|gcc|gcc|tcc|gtt|aag|ggt|-


           cgc|ttc|act|atc|TCT|AGA|ttcctgtcac-3′ (SEQ ID NO: 39) ! XbaI plus 


10 bases of scab
















TABLE 25P







Lengths of CDRs in 285 human kappa chains




























0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19






























CDR1
0
0
0
0
0
0
0
0
0
0
0
154
73
3
0
0
28
27
0
0


CDR2
0
0
0
0
0
0
0
285
0
0
0
0
0
0
0
0
0
0
0
0


CDR3
0
5
0
0
1
0
3
2
28
166
63
12
1
1
0
0
0
0
0
1
















TABLE 26P







Tally of kappa types: V and J


V genes:



















O12
59
O2
0
O18
0
O8
0
A20
0


A30
0
L14
0
L1
2
L15
0
L4
2


L18
0
L5
4
L19
0
L8
4
L23
0


L9
1
L24
0
L11
4
L12
8
O11
10


O1
0
A17
5
A1
0
A18
3
A2
0


A19
13
A3
0
A23
4
A27
79
A11
26


L2
28
L16
0
L6
11
L20
0
L25
0


B3
22
B2
0
A26
0
A10
0
A14
0










JH#













1
2
3
4
5





tally
105
64
29
78
9
















TABLE 27P





Names of Kappa chains analyzed



















AB022651
HSA388657
hsigklv37
hsikcvjp1
humigkx


AB022653
hsew1vk
hsigklv38
hsikcvjp2
huimigky1


AB022654
hsew3vk
hsigklv39
hsikcvjp3
huimigky2


AB022656
hsew4vk
hsigklv40
hsikcvjp6
huimigky4


AF007572
hsigdpk13
hsigklv41
hsikcvjp7
humigky5


AF021036
hsigg1k1
hsigklv42
hsld110v1
humigky6


AF103499
HSIGGVKA
hsigklv43
hsld117v1
humigl3ac


AF103500
hsigk123
hsigklv44
hsld128v1
humikc


AF103527
hsigk319
hsigklv45
hsld140v1
humikca


AF103873
hsigklc14
hsigklv46
hsld152v1
humikcad


AF107244
hsigklc28
hsigklv49
hsld184v1
humikcaf


AF107245
hsigklc5
hsigklv50
hsld198v1
humikcag


AF107246
hsigklg31
hsigklv51
hsld24v1
humikcah


AF107247
hsigklv01
hsigklv52
hsmbcl1k1
humikcai


AF115361
hsigklv02
hsigklv53
hsmbcl1k2
humikcaj


AF165099
hsigklv03
hsigklv54a
hsmbcl2k2
humikcal


AF165101
hsigklv04
hsigklv56
hsmbcl5k4
humikcam


AF165103
hsigklv05
hsigklv57
hss10av1
humikcan


AF165108
hsigklv06
hsigklv58
hss17bv1
humikcas


AF165110
hsigklv07
hsigklv59
hss1a15v1
humikcau


AF165111
hsigklv09
hsigklv60
HSU44792
humikcav


AF184763
hsigklv10
hsigklv61
HSU44794
humikcaw


AF184767
hsigklv12
hsigklv62
HSU94422
humikcax


hsa004955
hsigklv13
hsigklv63
hsz84852
humikcay


hsa004956
hsigklv14
hsigklv65
hsz84853
humikcaz


hsa011133
hsigklv15
hsigklv66
humigk1dm
humikcb


HSA241367
hsigklv16
hsigklv68
humigk3am
humikcba


HSA241375
hsigklv17
hsigklv69
humigk3bm
humikcbb


HSA388639
hsigklv18
hsigklv71
humigk3cm
humikcbc


HSA388640
hsigklv19
hsigkvba
humigkacoa
humikcbd


HSA388641
hsigklv20
hsigkvbb
humigkacob
humikcbe


HSA388642
hsigklv21
hsigkvbc
humigkacoc
humikcbf


HSA388643
hsigklv22
hsigkvbd
humigkacoe
humikcbg


HSA388644
hsigklv23
hsigkvbe
humigkacof
humikcbh


HSA388645
hsigklv24
hsigkvbf
humigkb1aa
humikcbi


HSA388646
hsigklv25
hsigkvc01
humigkb1ab
humikcbj


HSA388647
hsigklv27
hsigkvc03
humigkb1ac
humikcbl


HSA388648
hsigklv28
hsigkvc06
humigkvra
humikcbm


HSA388650
hsigklv29
hsigkvc11
humigkvrb
humikcbn


HSA388651
hsigklv31
hsigkvc12
humigkvrc
humikcbo


HSA388652
hsigklv32
hsigkvc20
humigkvrd
humikcbp


HSA388653
hsigklv33
hsigkvc23
humigkvre
humikcbq


HSA388654
hsigklv34
hsigkvc27
humigkvrg
humikcbs


HSA388655
hsigklv35
hsigkvc29
humigkvrh
humikcbt


HSA388656
hsigklv36
hsigrklc
humigkvri
humikcbu


humikcbv
humikcvg





humikcbw
humikcvh





humikcbx
humikcvi





humikcbz
humikcvj





humikcc
humikcw





humikcca
humikcx





humikccb
humikcy





humikccc
humikcz





humikccd
S46248





humikcce
S82746





humikccf
S82747





humikccg
SU96396





humikcch
SU96397





humikcci






humikccj






humikcck






humikcco






humikccp






humikccq






humikccr






humikccs






humikcct






humikccu






humikccv






humikccw






humikcd






humikcf






humikcg






humikch






humikci






humikck






humikcm






humikcn






humikco






humikcp






humikcq






humikcr






humikcs






humikct






humikcu






humikcv






humikcva






humikcvb






humikcvc






humikcvd






humikcve






humikcvf
















TABLE 28P







AA types seen in 154 kappa sequences having CDR1 of length 11


Tally





























A
C
D
E
F
G
H
I
K
L
M
N
P
Q
R
S
T
V
W
Y
































1













11
143





R


2
148











1


2
2
1


A


3















152
2



S


4


1
3


3






147






Q


5


12
1

27





7


3
99
4
1


S


6
1






81

1







71


V


7
2

4


18

5
1
2

9


12
97
3


1
S


8


3


5
1
2
1


31
1

10
87
12


1
S


9
2

7

10
1
6




29


1
8


13
77
Y


10




2




150





1

1


L


11
96




4
2




46



2
1
3


A
















TABLE 30P





Synthetic Kappa light chain gene















!


!


!A27::JH1 with all CDRs replaced by stuffers.


!Each stuffer contains at least one stop codon and a 


!restriction site that will be unique within the diversity vector.


!








   1
GAGGACCATt GGGCCCC                 ctccgagact


!
Scab...... EcoO109I


!
           ApaI.







!-----------------------------------


!








  28
CTCGAG    cgca


!
XhoI..







!-----------------------------------


!








  38
acgcaatTAA TGTgagttag ctcactcatt aggcacccca ggcTTTACAc tttatgcttc


!
       ..-35..         Plac                    ..-10.







!-----------------------------------


!








  98
cggctcgtat gttgtgtgga attgtgagcg gataacaatt tc







!-----------------------------------


!








 140
acacagga aacagctatgac







!-----------------------------------


!








 160
catgatta cgCCAAGCTT TGGagccttt tttttggaga ttttcaac  (SEQ ID NO: 54)


!
           PflMI.......


!
             Hind3.







!-----------------------------------


!








!
M13 III signal sequence (AA seq)--------------------------->


!
  1   2   3   4   5   6   7   8   9  10  11  12  13  14  15


!
  M   K   K   L   L   F   A   I   P   L   V   V   P   F   Y


 206
gtg aag aag ctc cta ttt gct atc ccg ctt gtc gtt ccg ttt tac







!-----------------------------------


!








!
--Signal--> FR1------------------------------------------->


!
 16  17  18  19  20  21  22  23  24  25  26  27  28  29  30


!
  S   H   S   A   Q   S   V   L   T   Q   S   P   G   T   L


 251
|agc|cat|aGT|GCA|Caa|tcc|gtc|ctt|act|caa|tct|cct|ggc|act|ctt|


!
          ApaLI...







!-----------------------------------


!








!
----- FR1 ------------------------------------->| CDR1------>


!
 31  32  33  34  35  36  37  38  39  40  41  42  43  44  45


!
  S   L   S   P   G   E   R   A   T   L   S   C   R   A   S   (SEQ ID NO: 55)



|tcG|CTA|AGC|CCG|GGt|gaa|cgt|gct|acC|TTA|AGt|tgc|cgt|gct|tcc| (SEQ ID NO: 54; Cont'd)


!
   EspI.....                       AflII...


!
           XmaI....







!


!-----------------------------------








!
For CDR1:


!<1>
ADEFGHIKLMNPQRSTVWY equimolar


!<2>
S(0.2) ADEFGHIKLMNPQRTVWY (0.044 each)


!<3>
Y(0.2) ADEFGHIKLMNPQRSTVW (0.044 each)







!In a preferred embodiment, we omit codon 52 in vgDNA for CDR1.


!








!
------- CDR1 --------------------->|--- FR2 ---------------->


!
    <1>     <2> <2> xxx <3>


!
46  47  48  49  50  51  52  53  54  55  56  57  58  59  60


!
 Q   S   V   S   S   S   Y   L   A   W   Y   Q   Q   K   P



|cag|tct|gtt|tcc|tct|tct|tat|ctt|gct|tgg|tat|caa|cag|aaA|CCT|


!
                                                                SexAI...







!


!-----------------------------------








!
For CDR2:


!<1>
ADEFGHIKLMNPQRSTVWY equimolar


!<2>
S(0.2) ADEFGHIKLMNPQRTVWY (0.044 each)


!<4>
A(0.2) DEFGHIKLMNPQRSTVWY (0.044 each)


!
----- FR2 ------------------------->|------- CDR2 ---------->


!
                                     <1>         <2>     <4>


!
 61  62  63  64  65  66  67  68  69  70  71  72  73  74  75


!
  G   Q   A   P   R   L   L   I   Y   G   A   S   S   R   A



|GGT|caG|GCG|CCg|cgt|tta|ctt|att|tat|ggt|gct|tct|tcc|cgc|gct|


!
SexAI....   KasI.... (CDR1 installed as AflII-(SexAI or KasI) cassette.)







!


!-----------------------------------


!








!
CDR2-->|--- FR3 ----------------------------------------------->


!
 <1>


!
 76  77  78  79  80  81  82  83  84  85  86  87  88  89  90


!
  T   G   I   P   D   R   F   S   G   S   G   S   G   T   D



|act|gGG|ATC|CCG|GAC|CGt|ttc|tct|ggc|tct|ggt|tca|ggt|act|gac|


!
      BamHI...


!
             RsrII.....







!(CDR2 installed as (SexAI or KasI) to (BamHI or RsrII) cassette.)


!-----------------------------------


!








!
------ FR3 ------------------------------------------------->


!
 91  92  93  94  95  96  97  98  99 100 101 102 103 104 105


!
  F   T   L   T   I   S   R   L   E   P   E   D   F   A   V


 477
|ttt|acc|ctt|act|att|TCT|AGA|ttg|gaa|cct|gaa|gac|ttc|gct|gtt|


!
                     XbaI...







!


!-----------------------------------


!








!
----------->|----CDR3-------------------------->|-----FR4--->


!
                     <3> <1> <1> <1>     <1>


!
106 107 108 109 110 111 112 113 114 115 116 117 118 119 120


!
  Y   Y   C   Q   Q   Y   G   S   S   P   E   T   F   G   Q



|tat|tat|tgC|CAa|cag|taT|GGt|tct|tct|cct|gaa|act|ttc|ggt|caa|


!
           BstXI...........







!


!-----------------------------------


!








!
-----FR4------------------->|  <------- Ckappa ------------


!
121 122 123 124 125 126 127    128 129 130 131 132 133 134


!
   G   T   K   V   E   I   K     R   T   V   A   A   P   S


 510
|ggt|aCC|AAG|Gtt|gaa|atc|aag| |CGT|ACG|gtt|gcc|gct|cct|agt|


!
      StyI....                 BsiWI..


!








(CDR3 installed as XbaI to (StyI or BsiWI) cassette.)








!



!
  135 136 137 138 139 140 141 142 143 144 145 146 147 148 149


!
  V   F   I   F   P   P   S   D   E   Q   L   K   S   G   T


 552
|gtg|ttt|atc|ttt|cct|cct|tct|gac|gaa|CAA|TTG|aag|tca|ggt|act|


!
                                     MfeI...


!



!
 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164


!
  A   S   V   V   C   L   L   N   N   F   Y   P   R   E   A


 597
|gct|tct|gtc|gta|tgt|ttg|ctc|aac|aat|ttc|tac|cCT|CGT|Gaa|gct|


!
                                              BssSI...


!



!
 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179


!
  K   V   Q   W   K   V   D   N   A   L   Q   S   G   N   S


 642
|aaa|gtt|cag|tgg|aaa|gtc|gat|aAC|GCG|Ttg|cag|tcg|ggt|aac|agt|


!
                              MluI....


!



!
 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194


!
  Q   E   S   V   T   E   Q   D   S   K   D   S   T   Y   S


 687
|caa|gaa|tcc|gtc|act|gaa|cag|gat|agt|aag|gac|tct|acc|tac|tct|


!



!
 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209


!
  L   S   S   T   L   T   L   S   K   A   D   Y   E   K   H


 732
|ttg|tcc|tct|act|ctt|act|tta|tca|aag|gct|gat|tat|gag|aag|cat|


!



!
 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224


!
  K   V   Y   A   C   E   V   T   H   Q   G   L   S   S   P


 777
|aag|gtc|tat|GCt|TGC|gaa|gtt|acc|cac|cag|ggt|ctG|AGC|TCc|cct|


!
                                               SacI....


!



!
 225 226 227 228 229 230 231 232 233 234


!
  V   T   K   S   F   N   R   G   E   C   .   .           (SEQ ID NO: 332)


 822
|gtt|acc|aaa|agt|ttc|aaC|CGT|GGt|gaa|tgc|taa|tag GGCGCGCC


!
                       DsaI....                  AscI....


!
                                                  BssHII


!



 866
acgcatctctaa GCGGCCGC aacaggaggag                         (SEQ ID NO: 333)


!
             NotI....


!
              EagI..
















TABLE 31P







Tally of 285 CDR2s of length 7 in human kappa


Tally





























A
C
D
E
F
G
H
I
K
L
M
N
P
Q
R
S
T
V
W
Y
































1
51

62
7

95
1

11
15
2
1


2
6
6
3
22
1
x


2
225




18

5

5

2
1

1
3
16
9


A


3
2



9


1



2



267
2

1
1
S


4
2

1



5
4
9
1

77


4
93
80

2
7
Sx


5

1


2




80




200
2




R


6
162

7
36
4

4

1
3


3
63



2


Ax


7
5

1


3

1
1


2
2

1
125
144



x
















TABLE 32P







Tally of 166 CDR3s of length 9 from human kappa.


Tally





























A
C
D
E
F
G
H
I
K
L
M
N
P
Q
R
S
T
V
W
Y
































1






4


8
21


131
1


1


Q


2



1


9

2
1



153






Q


3
14
4
4

3
6
4


1

1
3

21
16
3
4

82
Yx


4
1

9
1
2
37
4
2
2
15
1
33


2
20
7
1

29
x


5
2

2
6

3
4
5
3


28

17
7
65
19
1
1
3
x


6
7

1

11
2

3

8

1
4

3
41
33
5
28
19
x


7




1
2



6


146
2
2
5

2


P


8
2
4
1
2
21
7
3
5
1
38


7
4
25
1
3
1
16
25
x


9
3





2
1



1



2
157



T
















TABLE 33P







lengths of CDRs in 93 human lambda chains



























0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18+





























CDR1
0
0
0
0
0
0
0
0
0
0
0
23
7
15
46
0
0
0
2


CDR2
5
0
0
1
0
0
0
80
2
0
0
1
4
0
0
0
0
0
1


CDR3
0
0
0
0
0
0
0
0
1
16
28
27
6
1
0
4
6
4
0
















TABLE 34P







Tally of 46 CDR1s of length 14 from human lambda chains


Tally





























A
C
D
E
F
G
H
I
K
L
M
N
P
Q
R
S
T
V
W
Y
































1
2




2









1
41



T


2





43



3










G


3
2










1


1
6
36



TGx


4











1



45




S


5





5





1



40




S


6


39




1



4



2




DNx


7







8



1





37


V


8


1


42









2

1


G


9
4

1


35








1
2
3



TGx


10
1



1
3








1
2



38
Yx


11


4




1



35







6
DNx


12


3

1

2


1




1
2



36
Yx


13







1




2




43


V


14




1

4








41




S
















TABLE 35P





Synthtic human lambda-chain gene















!  Lambda 14-7(A) 2a2 ::JH2::Clambda


!  AA sequence tested


!








  1
GAGGACCATt GGGCCCC   ttactccgtgac


!
Scab...... EcoO109I


!
           ApaI..







!-----------------------------------


!








!
        -----------FR1-------------------------------------------->


!
         1   2   3   4   5   6   7   8   9  10  11  12  13  14  15


!
 S   A   Q   S   A   L   T   Q   P   A   S   V   S   G   S   P   G


 30
aGT|GCA|Caa|tcc|gct|ctc|act|cag|cct|GCT|AGC|gtt|tcc|gGG|TcA|CCt|GGT|


!
 ApaLI...                           NheI...          BstEII...


!
                                                          SexAI....







!-----------------------------------


!


! For CDR1,








!<1> =
0.27 T, 0.27 G, 0.027 {ADEFHIKLMNPQRSVWY} no C


!<2> =
0.27 D, 0.27 N, 0.027 {AEFGHIKLMPQRSTVWY} no C


!<3> =
0.36 Y, 0.0355{ADEFGHIKLMNPQRSTVW} no C


!
                              T   G  <1>  S   S  <2>  V   G


!
------FR1------------------> |-----CDR1---------------------


!
 16  17  18  19  20  21  22  23  24  25  26  27  28  29  30


!
  Q   S   I   T   I   S   C   T   G   T   S   S   D   V   G



|caa|agt|atc|act|att|tct|TGT|ACA|ggt|act|tct|tct|gat|gtt|ggc|


!
                         BsrGI..


!



!








! a second vg scheme for CDR1 gives segments of length 11:


! G23<2><4>L<4><4><4><3><4><4> where








!<4> =
equimolar {ADEFGHIKLMNPQRSTVWY} no C







!-----------------------------------------------------


!








!
<1> <3> <2> <3>  V   S = vg Scheme #1, length = 14


!
-----CDR1------------->|--------FR2-------------------------


!
31  32  33  34  35  36  37  38  39  40  41  42  43  44  45


!
 G   Y   N   Y   V   S   W   Y   Q   Q   H   P   G   K   A



|ggt|tac|aat|tac|gtt|tct|tgg|tat|caa|caa|caC|CCG|GGc|aaG|GCG|


!
                                           XmaI....    KasI.....


!
                                           AvaI....







!------------------------------------------------------------------


!








!
                        <4> <4> <4> <2>  R   P   S


!
--FR2-----------------> |------CDR2--------------->|-----FR3--


!
46  47  48  49  50  51  52  53  54  55  56  57  58  59  60


!
 P   K   L   M   I   Y   E   V   S   N   R   P   S   G   V



|CCg|aag|ttg|atg|atc|tac|gaa|gtt|tcc|aat|cgt|cct|tct|ggt|gtt|







! KasI....


!------------------------------------------------------------------


!








!
-------FR3----------------------------------------------------


!
 61  62  63  64  65  66  67  68  69  70  71  72  73  74  75


!
  S   N   R   F   S   G   S   K   S   G   N   T   A   S   L



|agc|aat|cgt|ttc|TCC|GGA|tct|aaa|tcc|ggt|aat|acc|gcA|AGC|TTa|


!
                 BspEI..          |                HindIII.


!
                      BsaBI........(blunt)







!------------------------------------------------------------------


!








!
-------FR3--------------------------------------------------->|


!
 76  77  78  79  80  81  82  83  84  85  86  87  88  89  90


!
  T   I   S   G   L   Q   A   E   D   E   A   D   Y   Y   C



|act|atc|tct|ggt|CTG|CAG|gct|gaa|gac|gag|gct|gac|tac|tat|tgt|


!
                 PstI...







!


!------------------------------------------------------------------


!








!<5> =
0.36 S, 0.0355{ADEFGHIKLMNPQRTVWY} no C


!



!
 <4> <5> <4> <2> <4>  S  <4> <4> <4> <4>  V


!
-----CDR3---------------------------------->|---FR4---------


!
 91  92  93  94  95  96  97  98  99 100 101 102 103 104 105


!
  S   S   Y   T   S   S   S   T   L   V   V   F   G   G   G



|tct|tct|tac|act|tct|tct|agt|acc|ctt|gtt|gtc|ttc|ggc|ggt|GGT|


!
                                                         KpnI...







!


!----------------------------------------------------------------------


!








!
-------FR4-------------->


!
 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120


!
  T   K   L   T   V   L   G   Q   P   K   A   A   P   S   V


279
|ACC|aaa|ctt|act|gtc|ctc|gGT|CAA|CCT|aAG|Gct|gct|cct|tcc|gtt|







!  KpnI...                       HincII..








!
                                 Bsu36I...


!



!
 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135


!
  T   L   F   P   P   S   S   E   E   L   Q   A   N   K   A


324
|act|ctc|ttc|cct|cct|agt|tct|GAA|GAG|Ctt|caa|gct|aac|aag|gct|


!
                             SapI.....


!



!
 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150


!
  T   L   V   C   L   I   S   D   F   Y   P   G   A   V   T


369
|act|ctt|gtt|tgc|tTG|ATC|Agt|gac|ttt|tat|cct|ggt|gct|gtt|act|


!
                  BclI....


!



!
 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165


!
  V   A   W   K   A   D   S   S   P   V   K   A   G   V   E


414
|gtc|gct|tgg|aaa|gcc|gat|tct|tct|cct|gtt|aaa|gct|ggt|gtt|GAG|


!
                                                         BsmBI...


!



!
 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180


!
  T   T   T   P   S   K   Q   S   N   N   K   Y   A   A   S


459
|ACG|acc|act|cct|tct|aaa|caa|tct|aac|aat|aag|tac|gct|gcG|AGC|







! BsmBI....                                                   SacI....








!



!
 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195


!
  S   Y   L   S   L   T   P   E   Q   W   K   S   H   K   S


504
|TCt|tat|ctt|tct|ctc|acc|cct|gaa|caa|tgg|aag|tct|cat|aaa|tcc|







! SacI...








!



!
 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210


!
  Y   S   C   Q   V   T   H   E   G   S   T   V   E   K   T


549
|tat|tcc|tgt|caa|gtt|acT|CAT|GAa|ggt|tct|acc|gtt|gaa|aag|act|


!
                       BspHI...


!



!
 211 212 213 214 215 216 217 218 219


!
  V   A   P   T   E   C   S   .   .                    (SEQ ID NO: 57)


594
|gtt|gcc|cct|act|gag|tgt|tct|tag|tga|GGCGCGCC


!
                                     AscI....


!
                                      BssHII


!



629
aacgatgttc aag GCGGCCGC aacaggaggag                    (SEQ ID NO: 56)


!
               NotI.... Scab.......
















TABLE 36P







Tally of 23 CDR1s of length 11 from human lambda chains


Tally





























A
C
D
E
F
G
H
I
K
L
M
N
P
Q
R
S
T
V
W
Y
































1
1




6







10

6




x


2
1


1

21














G


3


15


1





7








DNx


4
2


1

1


3


7


1
8




X


5







7

16










L


6





11


1



2

8

1



X


7


1
1

1


2


2


1
14
1



X


8




1



10


1

1
1
2



7
X


9











2



6



15
Yx


10
11











1




11


X


11

3




7








9
2


2
X
















TABLE 37P







Tally of 80 CDR2s of length 7 from human lambda chains


Tally





























A
C
D
E
F
G
H
I
K
L
M
N
P
Q
R
S
T
V
W
Y
































1
1

14
32
1
13


3


1

4
5
1
2


3
X


2


18
2




8


16




2
34


X


3
1

2




1



31



39
4


2
X


4


6
4


1

14
1

41

8
1
1
2


1
DNx


5








1
1




78





R


6









1


77


2




P


7
2














78




S
















TABLE 38P







Tally of 27 CDR3s of length 11 from human lambda chains


Tally





























A
C
D
E
F
G
H
I
K
L
M
N
P
Q
R
S
T
V
W
Y
































1
4




5





6

5

4
3



X


2
3




1






2


14
5
2


Sx


3




1









7



13
6
X


4


19


2





1



1
4



DNx


5
1

4


2

2



2


1
13
2



X


6







1



3


1
21
1



S


7


1


7



12

1



4
2



X


8


2


1





10
1


6
6
1


X


9
3



1
8
10


3


1


1




X


10
1




4
1

1
1


3

1
1

6
5
3
X


11









2







25


V
















TABLE 40P





Synthetic Kappa light chain gene with stuffers
















!



!
A27::JH1 with all CDRs replaced by stuffers.


!
Each stuffer contains at least one stop codon and a 


!
restriction site that will be unique within the diversity vector.


!



   1
GAGGACCATt GGGCCCC                ctccgagact


!
Scab...... EcoO109I


!
           ApaI.







!-----------------------------------


!








  28
CTCGAG    cgca


!
XhoI..







!-----------------------------------


!








  38
acgcaatTAA TGTgagttag ctcactcatt aggcacccca ggcTTTACAc tttatgcttc


!
       ..-35..         Plac                    ..-10.







!-----------------------------------


!








  98
cggctcgtat gttgtgtgga attgtgagcg gataacaatt tc







!-----------------------------------


!








 140
acacagga aacagctatgac







!-----------------------------------


!








 160
catgatta cgCCAAGCTT TGGagccttt tttttggaga ttttcaac


!
           PflMI.......


!
             Hind3.







!-----------------------------------


!








!
M13 III signal sequence (AA seq)--------------------------->


!
 1   2   3   4   5   6   7   8   9  10  11  12  13  14  15


!
 M   K   K   L   L   F   A   I   P   L   V   V   P   F   Y


 206
gtg aag aag ctc cta ttt gct atc ccg ctt gtc gtt ccg ttt tac







!-----------------------------------


!








!
--Signal-->  FR1------------------------------------------->


!
 16  17  18  19  20  21  22  23  24  25  26  27  28  29  30


!
  S   H   S   A   Q   S   V   L   T   Q   S   P   G   T   L


 251
|agc|cat|aGT|GCA|Caa|tcc|gtc|ctt|act|caa|tct|cct|ggc|act|ctt|


!
          ApaLI...







!-----------------------------------


!








!
----- FR1 --------------------------------->|-------Stuffer->


!
 31  32  33  34  35  36  37  38  39  40  41  42  43


!
  S   L   S   P   G   E   R   A   T   L   S   |   |


 296
|tcG|CTA|AGC|CCG|GGt|gaa|cgt|gct|acC|TTA|AGt|TAG|TAA|gct|ccc|


!
   EspI.....                AflII...


!
           XmaI....







!-----------------------------------


!








!
------- Stuffer for CDR1------------------------->|- FR2 -->


!
                                                    59  60


!
                                                     K   P


 341
|AGG|CCT|ctt|TGA|tct|                              g|aaA|CCT|


!
 StuI...                                               SexAI...







!-----------------------------------


!








!
----- FR2 ------|-----------Stuffer for CDR2---------------->


!
 61  62  63  64  65  66


!
  G   Q   A   P   R   |   |


 363
|GGT|caG|GCG|CCg|cgt|TAA|TGA|a AGCGCTaa TGGCCA aca gtg


!
SexAI....   KasI....                AfeI..    MscI..







!-----------------------------------


!








!
Stuffer-->|--- FR3 ----------------------------------------------->


!
 <1>


!
 76  77  78  79  80  81  82  83  84  85  86  87  88  89  90


!
  T   G   I   P   D   R   F   S   G   S   G   S   G   T   D


 405
|act|gGG|ATC|CCG|GAC|CGt|ttc|tct|ggc|tct|ggt|tca|ggt|act|gac|


!
      BamHI...


!
             RsrII.....







!-----------------------------------


!








!
--------- FR3 ---------------------STUFFER for CDR3------------------>


!
 91  92  93  94  95  96  97


!
  F   T   L   T   I   S   R   |   |


 450
|ttt|acc|att|act|att|TCT|AGA|TAA|TGA| GTTAAC TAG acc TACGTA acc tag


!
                     XbaI...          HpaI..         SnaBI.







!-----------------------------------


!


!








!
-----------------CDR3 stuffer------------------>|-----FR4--->


!
                                                118 119 120


!
                                                  F   G   Q


 501
                                                |ttc|ggt|caa|







!-----------------------------------


!








!
-----FR4------------------->|  <------- Ckappa ------------


!
121 122 123 124 125 126 127   128 129 130 131 132 133 134


!
  G   T   K   V   E   I   K     R   T   V   A   A   P   S


 510
|ggt|aCC|AAG|Gtt|gaa|atc|aag| |CGT|ACG|gtt|gcc|gct|cct|agt|


!
      StyI....                 BsiWI..







! (CDR3 installed as XbaI to (StyI or BsiWI) cassette.)


!








!
 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149


!
  V   F   I   F   P   P   S   D   E   Q   L   K   S   G   T


552
|gtg|ttt|atc|ttt|cct|cct|tct|gac|gaa|CAA|TTG|aag|tca|ggt|act|


!
                                   MfeI...


!



!



866
acgcatctctaa GCGGCCGC aacaggaggag                  (SEQ ID NO: 95)


!
             NotI....


!
              EagI..
















TABLE 41P





Variegated DNA for kappa chains















!--------------------------------------------------------------------


! Kappa chains


! For CDR1:








! <1>
ADEFGHIKLMNPQRSTVWY equimolar


! <2>
S(0.2) ADEFGHIKLMNPQRTVWY (0.044 each)


! <3>
Y(0.2) ADEFGHIKLMNPQRSTVW (0.044 each)


! <4>
A(0.2) DEFGHIKLMNPQRSTVWY (0.044 each)


 


(Ka1vg600)
                             5′-gct|acC|TTA|AGt|tgc|cgt|gct|tcc|cag-



|<1>|gtt|<2>|<2>|    <3>|ctt|gct|tgg|tat|caa|cag|aaA|CC-3′ (SEQ ID NO: 66)


 


(Ka2vg650)
          5′-caG|GCG|CCg|cgt|tta|ctt|att|tat|<1>|gct|tct|<2>|cgc|<4>|-



            |<1>|gGG|ATC|CCG|GAC|CGt|ttc|tct|ggt|tctcacc-3′ (SEQ ID NO: 71)


 


(Ka3vg670)
5′-                                                 gac|ttc|gct|gtt|-



|tat|tat|tgC|CAa|cag|<3>|<1>|<1>|<1>|cct|<1>|act|ttc|ggt|caa|-



|ggt|aCC|AAG|Gtt|g-3′ (SEQ ID NO: 77)
















TABLE 42P





Variegated DNA for lambda chains















!--------------------------


! For CDR1,








! <1> =
0.27 T, 0.27 G, 0.027 {ADEFHIKLMNPQRSVWY} no C


! <2> =
0.27 D, 0.27 N, 0.027 {AEFGHIKLMPQRSTVWY} no C


! <3> =
0.36 Y, 0.0355{ADEFGHIKLMNPQRSTVW} no C


! <4> =
equimolar {ADEFGHIKLMNPQRSTVWY} no C


! <5> =
0.36 S, 0.0355{ADEFGHIKLMNPQRTVWY} no C


 


(Lm1vg710)
5′-gt|atc|act|att|tct|TGT|ACA|ggt|<1>|tct|tct|<2>|gtt|ggc|-







       |<1>|<3>|<2>|<3>|gtt|tct|tgg|tat|caa|caa|caC|CC-3′ (SEQ ID NO: 83)


 








(Lm2vg750)
                                     5′-G|CCg|aag|ttg|atg|atc|tac|-



<4>|<4>|<4>|<2>|cgt|cct|tct|ggt|gtc|agc|aat|c-3′ (SEQ ID NO: 88)


 


(Lm3vg817)
5′-                              gac|gag|gct|gac|tac|tat|tgt|-



 |<4>|<5>|<4>|<2>|<4>|tct|<4>|<4>|<4>|<4>|gtc|ttc|ggc|ggt|GGT|-



|ACC|aaa|ctt|ac-3′ (SEQ ID NO: 93)







!-------------------------------------------------------------------
















TABLE 43P





Constant DNA for Synthetic Library















! CDR3 library components








(Ctop25)
5′-gctctggtcaa C|TTA|AGg|gct|gag|g-3′   (SEQ ID NO: 58)


(CtprmA)
5′-gctctggtcaa C|TTA|AGg|gct|gag|gac-


!
               AflII...



|acc|gct|gtc|tac|tac|tgc|gcc-3′         (SEQ ID NO: 59)


!



(CBprmB) [RC]
5′-|tac|ttc|gat|tac|ttg|ggc|caa|GGT|ACC|ctG|GTC|ACC|tcgctccacc-3′ (SEQ ID NO: 60)


!
                                          BstEII...


(CBot25) [RC]
                            5′-|GGT|ACC|ctG|GTC|ACC|tcgctccacc-3′ (SEQ ID NO: 61)







!----------------------------------------------------------------------


! Kappa chains








(Ka1Top610)
5′-ggtctcagtt-



G|CTA|AGC|CCG|GGt|gaa|cgt|gct|acC|TTA|AGt|tgc|cgt|gct|tcc|cag-3′  (SEQ ID NO: 62)


(Ka1STp615)
5′-ggtctcagtt-



G|CTA|AGC|CCG|GGt|g-3′ (SEQ ID NO: 63)


(Ka1Bot620) [RC]
                5′-ctt|gct|tgg|tat|caa|cag|aaA|-



        CCt|GGT|caG|GCG|CC aagtcgtgtc-3′ (SEQ ID NO: 64)


(Ka1SB625) [RC]
     5′-cct|GGT|caG|GCG|CC aagtcgtgtc-3′ (SEQ ID NO: 65)


!



(Ka2Tshort657)
5′-cacgagtcctA|CCT|GGT|-



    caG|GC-3′ (SEQ ID NO: 68)


(Ka2Tlong655)
5′-cacgagtcctA|CCT|GGT|-



    caG|GCG|CCg|cgt|tta|ctt|att|tat-3′ (SEQ ID NO: 69)


(Ka2Bshort660) [RC]
5′-|GAC|CGt|ttc|tct|ggt|tctcacc-3′







!----------------------------------------------------------------------








(Ka3Tlon672)
5′-      gacgagtcct  TCT|AGA|ttg|gaa|cct|gaa|gac|ttc|gct|gtt|-



|tat|tat|tgC|CAa|c-3′ (SEQ ID NO: 72)


(Ka3BotL682) 
                                     [RC] 5′-act|ttc|ggt|caa|-



|ggt|aCC|AAG|Gtt|gaa|atc|aag|     |CGT|ACG| tcacaggtgag-3′ (SEQ ID NO: 73)


(Ka3Bsho694) [RC]
5′-              gaa|atc|aag|     |CGT|ACG| tcacaggtgag-3′ (SEQ ID NO: 74)







!----------------------------------------------------------------------








(Lm1TPri75)
5′-gacgagtcct GG|TcA|CCt|GGT|-3′ (SEQ ID NO: 78)


(Lm1TLo715)
5′-gacgagtcct GG|TcA|CCt|GGT|-







                caa|agt|atc|act|att|tct|TGT|ACA|ggt-3′ (SEQ ID NO: 79)








(Lm1BLo724) [RC]
5′-gtt|tct|tgg|tat|caa|caa|caC|CCG|GGc|aaG|GCG|-







            AGA TCT  tcacaggtgag-3′ (SEQ ID NO: 80)








(Lm1BSh737) [RC]
5′-                                 Gc|aaG|GCG|-







            AGAp TCT  tcacaggtgag-3′ (SEQ ID NO: 81)


!------------------------------------------------------








(Lm2TSh757)
5′-gagcagagga C|CCG|GGc|aaG|GC-3′ (SEQ ID NO: 84)


(Lm2TLo753)
5′-gagcagagga C|CCG|GGc|aaG|GCG|CCg|aag|ttg|atg|atc|tac|-3′ (SEQ ID NO: 85)


(Lm2BLo762) [RC]
5′-cgt|cct|tct|ggt|gtc|agc|aat|cgt|ttc|TCC|GGA|tcacaggtgag-3′ (SEQ ID NO: 86)


(Lm2BSh765) [RC]
5′-                            cgt|ttc|TCC|GGA|tcacaggtgag-3′ (SEQ ID NO: 87)







!------------------------------------------------------








(Lm3TSh822)
5′-CTG|CAG|gct|gaa|gac|gag|gct|gac             -3′ (SEQ ID NO: 89)


(Lm3TLo819)
5′-CTG|CAG|gct|gaa|gac|gag|gct|gac|tac|tat|tgt|-3′ (SEQ ID NO: 90)


(Lm3BLo825) [RC]
                         5′-gtc|ttc|ggc|ggt|GGT|-



|ACC|aaa|ctt|act|gtc|ctc|gGT|CAA|CCT|aAG|G acacaggtgag-3′ (SEQ ID NO: 91)


(Lm3BSh832) [RC]
5′-c|gGT|CAA|CCT|aAG|G acacaggtgag-3′                     (SEQ ID NO: 92)







!---------------------------------------------------------------------------
















TABLE 48P





Synthtic human lambda-chain gene with stuffers in place of CDRs















! Lambda 14-7(A) 2a2 ::JH2::Clambda


! AA sequence tested








!



   1
GAGGACCATt GGGCCCC   ttactccgtgac


!
Scab...... EcoO109I


!
          ApaI..







!---------------------------------------------


!








!
        -----------FR1-------------------------------------------->


!
         1   2   3   4   5   6   7   8   9  10  11  12  13  14  15


!
 S   A   Q   S   A   L   T   Q   P   A   S   V   S   G   S   P   G


  30
aGT|GCA|Caa|tcc|gct|ctc|act|cag|cct|GCT|AGC|gtt|tcc|gGG|TcA|CCt|GGT|


!
 ApaLI...                           NheI...          BstEII...


!
                                                          SexAI....







!---------------------------------------------


!








!
------FR1------------------> |-----stuffer for CDR1---------


!
 16  17  18  19  20  21  22  23


!
  Q   S   I   T   I   S   C   T


  81
|caa|agt|atc|act|att|tct|TGT|ACA|tct TAG TGA ctc


!
                         BsrGI..







!---------------------------------------------


!








!
-----Stuffer--------------------------->--------------------


!
31  32  33  34  35  36  37  38  39  40  41  42  43  44  45


!
 R   S   |   |   P   |                   H   P   G   K   A


 117
AGA TCT TAA TGA ccg tag                 caC|CCG|GGc|aaG|GCG|


!
BglII                                     XmaI....    KasI.....


!
                                          AvaI....







!----------------------------------------------------------------


!








!
 --|-------------Stuffer ------------------------------------->


!
  P


 150
|CCg|TAA|TGA|atc tCG TAC G                        ct|ggt|gtt|


!
KasI....               BsiWI...







!----------------------------------------------------------------


!








!
------FR3----------------------------------------------------


!
 61  62  63  64  65  66  67  68  69  70  71  72  73  74  75


!
  S   N   R   F   S   G   S   K   S   G   N   T   A   S   L


 177
|agc|aat|cgt|ttc|TCC|GGA|tct|aaa|tcc|ggt|aat|acc|gcA|AGC|TTa|


!
                 BspEI..          |                HindIII.


!
                      BsaBI........(blunt)







!----------------------------------------------------------------


!








!
-------FR3------------->|--Stuffer------------------------->|


!
 76  77  78  79  80  81  82  83  84  85  86  87  88  89  90


!
  T   I   S   G   L   Q


 222
|act|atc|tct|ggt|CTG|CAG|gtt ctg tag ttc CAATTG ctt tag tga ccc


!
                 PstI...                 MfeI..







!----------------------------------------------------------------


!








!
-----Stuffer------------------------------->|---FR4---------


!
                                                  103 104 105


!
                                                    G   G


 270
                                                  |ggc|ggt|GGT|


!
                                                           KpnI...







!----------------------------------------------------------------


!








!
-------FR4-------------->


!
 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120


!
  T   K   L   T   V   L   G   Q   P   K   A   A   P   S   V


 279
|ACC|aaa|ctt|act|gtc|ctc|gGT|CAA|CCT|aAG|Gct|gct|cct|tcc|gtt|


!
KpnI...                      HincII..


!
                                 Bsu36I...


!



!
 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135


!
  T   L   F   P   P   S   S   E   E   L   Q   A   N   K   A


 324
|act|ctc|ttc|cct|cct|agt|tct|GAA|GAG|Ctt|caa|gct|aac|aag|gct|


!
                             SapI.....


!



!
 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150


!
  T   L   V   C   L   I   S   D   F   Y   P   G   A   V   T   (SEQ ID NO: 98)


 369
|act|ctt|gtt|tgc|tTG|ATC|Agt|gac|ttt|tat|cct|ggt|gct|gtt|act| (SEQ ID NO: 97)


!
                  BclI....
















TABLE 50P





3-23::CDR3::JH4 Stuffers in place of CDRs















                       FR1(DP47/V3-23)---------------


           20  21  22  23  24  25  26  27  28  29  30


            A   M   A   E   V   Q   L   L   E   S   G


ctgtctgaac  CC atg gcc gaa|gtt|CAA|TTG|tta|gag|tct|ggt|


Scab......  NcoI....          | MfeI  |


 


--------------FR1--------------------------------------------


 31  32  33  34  35  36  37  38  39  40  41  42  43  44  45


  G   G   L   V   Q   P   G   G   S   L   R   L   S   C   A


|ggc|ggt|ctt|gtt|cag|cct|ggt|ggt|tct|tta|cgt|ctt|tct|tgc|gct|


 


----FR1-------------------->|...CDR1 stuffer....|---FR2------


 46  47  48  49  50  51  52  53  54  55  56  57  58  59  60


  A   S   G   F   T   F   S   S   Y   A   |   |   W   V   R


|gct|TCC|GGA|ttc|act|ttc|tct|tCG|TAC|Gct|TAG|TAA|tgg|gtt|cgC|


    | BspEI |                 | BsiWI|                     |BstXI.


 


 -------FR2-------------------------------->|...CDR2 stuffer.


 61  62  63  64  65  66  67  68  69  70  71  72  73  74  75


  Q   A   P   G   K   G   L   E   W   V   S   |   p   r   |


|CAa|gct|ccT|GGt|aaa|ggt|ttg|gag|tgg|gtt|tct|TAA|CCT|AGG|TAG|


...BstXI        |                                  AvrII..


 


.....CDR2 stuffer....................................|---FR3---


--------FR3-------------------------------------------------


  91  92  93  94  95  96  97  98  99 100 101 102 103 104 105


  T   I   S   R   D   N   S   K   N   T   L   Y   L   Q   M


|act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|


        | XbaI  |


 


---FR3-----------..> Stuffer------------->|


 106 107 108 109 110


  N   S   L   R   A (SEQ ID NO: 53)


|aac|agC|TTA|AGg|gct|TAG TAA AGG cct TAA (SEQ ID NO: 52)


       |AflII |              StuI...


 


|----- FR4 ---(JH4)-----------------------------------------


  Y   F   D   Y   W   G   Q   G   T   L   V   T   V   S   S      (SEQ ID NO: 26)


|tat|ttc|gat|tat|tgg|ggt|caa|GGT|ACC|ctG|GTC|ACC|gtc|tct|agt|... (SEQ ID NO: 25)


                            | KpnI  |  | BstEII |

## Claims

1. A focused library of vectors or genetic packages, comprising variegated DNA molecules, each of which comprises a DNA sequence that encodes an antibody heavy chain variable region having a CDR1 region, a CDR2 region, and a CDR3 region, wherein the variegated DNA molecules collectively encode a plurality of antibody heavy chain variable regions comprising heavy chain CDR3 motifs of:
xxxYCSSTSCxxx (SEQ ID NO:199), wherein each x independently is any amino acid or is absent;
xxxxYVWGSYxxx (SEQ ID NO:200), wherein each x independently is any amino acid or is absent;
xxxxxxxSGYxxx (SEQ ID NO:201), wherein each x independently is any amino acid or is absent;
xxxYDILTGYYxx (SEQ ID NO:202), wherein each x independently is any amino acid or is absent;
xxxVVVPAAxxxx (SEQ ID NO:203), wherein each x independently is any amino acid or is absent;
xxxYYDSSGYxx (SEQ ID NO:204), wherein each x independently is any amino acid or is absent;
xxxDFWSGxxxx (SEQ ID NO:205), wherein each x independently is any amino acid or is absent;
xxxTIFGVxxxx (SEQ ID NO:206), wherein each x independently is any amino acid or is absent;
xxxxIVATxxxx (SEQ ID NO:207), wherein each x independently is any amino acid or is absent;
xxxYGSGSYYx (SEQ ID NO:208), wherein each x independently is any amino acid or is absent;
xxxxYSYGxxx (SEQ ID NO:209), wherein each x independently is any amino acid or is absent;
xxxCSGxxCYx (SEQ ID NO:210), wherein each x independently is any amino acid or is absent;
xxxxAAAGxxx (SEQ ID NO:211), wherein each x independently is any amino acid or is absent;
xGxxxGGNxxx (SEQ ID NO:212), wherein each x independently is any amino acid or is absent;
xxxSGSYxxx (SEQ ID NO:213), wherein each x independently is any amino acid or is absent;
xxxSSSWxxx (SEQ ID NO:214), wherein each x independently is any amino acid or is absent;
xxxxTTVTTx (SEQ ID NO:215), wherein each x independently is any amino acid or is absent;
xxxC(SG)GDxCx (SEQ ID NO:216), wherein each x independently is any amino acid or is absent;
xxx(IV)AVAGxx (SEQ ID NO:217), wherein each x independently is any amino acid or is absent;
xxLWFGELxx (SEQ ID NO:218), wherein each x independently is any amino acid or is absent;
GxxWLxxxxF (SEQ ID NO:219), wherein each x independently is any amino acid or is absent;
xxxDTxMVxx (SEQ ID NO:220), wherein each x independently is any amino acid or is absent;
xxxxxGExxx (SEQ ID NO:221), wherein each x independently is any amino acid or is absent;
xxxxSGWxx (SEQ ID NO:222), wherein each x independently is any amino acid or is absent;
xxxxGYNxx (SEQ ID NO:223), wherein each x independently is any amino acid or is absent;
xxxVRGVxx (SEQ ID NO:224), wherein each x independently is any amino acid or is absent;
xxxIAAxxx (SEQ ID NO:225), wherein each x independently is any amino acid or is absent;
xxYxWNxxx (SEQ ID NO:226), wherein each x independently is any amino acid or is absent;
xxxYGDxx (SEQ ID NO:227), wherein each x independently is any amino acid or is absent;
xxVGATxx (SEQ ID NO:228), wherein each x independently is any amino acid or is absent; and
xxxYSSSx (SEQ ID NO:229), wherein each x independently is any amino acid or is absent.

2. The focused library of claim 1, wherein the vectors are yeast vectors.

3. The focused library of claim 1, wherein the genetic packages are yeast cells.

4. The focused library of claim 3, wherein the yeast cells display the plurality of antibody heavy chain variable regions.