# Patent

## Title
Libraries of genetic packages comprising novel HC CDR3 designs

## Abstract

Provided are compositions and methods for preparing and identifying antibodies having CDR3s that vary in sequence and in length from very short to very long which in certain embodiments may bind to a carbohydrate moiety or the active site of an enzyme. Libraries coding for antibodies with the CDR3s are also provided. The libraries can be provided by modifying a pre-existing nucleic acid library.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a US national phase entry under 35 U.S.C. § 371 of PCT/US2009/037174 filed Mar. 13, 2009, which claims priority to U.S. Application Ser. No. 61/036,219, filed on Mar. 13, 2008, and which also claims priority to U.S. Application Ser. No. 61/047,529 filed on Apr. 24, 2008. The disclosure of both of the prior applications are considered part of (and are incorporated by reference in) the disclosure of this application.


BACKGROUND
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. See, e.g., Knappik et al., J. Mol. Biol., 296, pp. 57-86 (2000), which is incorporated herein by reference. 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 a combination of the first two. Typically, the diversity produced by these methods is limited to sequence diversity, i.e., each member of the library has the same length but 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. D segments are more common in antibodies having long HC CDR3s. The following also may occur during joining of antibody gene segments: (i) the end of the V gene may have zero to several bases 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 such 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 and least likely to be immunogenic. Rather, the libraries, typically, attempt to include as much diversity or variegation as possible at every amino acid residue. This makes library construction time-consuming and less efficient than necessary. 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.
In addition to the labor of constructing synthetic libraries is the question of immunogenicity. For example, there are libraries in which all CDR residues are either Tyr (Y) or Ser (S). Although antibodies (Abs) selected from these libraries show high affinity and specificity, their very unusual composition may make them immunogenic. The present invention is directed toward making Abs that could well have come from the human immune system and so are less likely to be immunogenic. The libraries of the present invention retain as many residues from V-D-J or V-J fusions as possible.
SUMMARY
Provided are libraries of vectors or packages that encode members of a diverse family of human antibodies comprising heavy chain (HC) CDR3s that are between about 3 amino acids in length to about 35 amino acids in length. The HC CDR3s may also, in certain embodiments, may be rich in Tyr (Y) and Ser (S) and/or comprise diversified D regions and/or comprise extended JH regions. For example, the HC CDR3s may contain greater than about 40% (e.g., between about 43% and about 80%; e.g., greater than about 40% but less than about 100%) Y and/or S residues, e.g., as provided in the examples herein. Also provided are focused libraries comprising such HC CDR3s.
A diversified D region is a D region into which one or more amino acid changes have been introduced (e.g., as compared to the sequence of a naturally occurring D region; for example, a stop codon can be changed to a Tyr residue).
An extended JH region is a JH region that has one or more amino acid residues present at the amino terminus of the framework sequence of the JH region (e.g., amino terminal to FR4 sequences, e.g., which commence with WGQ . . . ). For example, JH1 is an extended JH region. As other examples, JH2, JH3, JH4, JH5, and JH6 are extended JH regions.
Provided also are methods of making and screening the above libraries and the HC CDR3s and antibodies obtained in such screening. Compositions and kits for the practice of these methods are also described herein.
In some aspects, the disclosure features 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 (e.g., a diverse family of antibodies) and collectively display, display and express, or comprise at least a portion of the diversity of the family, wherein the vectors or genetic packages comprise variegated DNA sequences that encode a heavy chain (HC) CDR3 selected from the group consisting of:

    
    
        (a) a HC CDR3 that is about 3 or about 4 or about 5 amino acids in length;
        (b) a HC CDR3 that is about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, about 31, about 32, about 33, about 34 or about 35 amino acids in length (e.g., about 23 to about 35 amino acids in length); and
        c) a HC CDR3 that is from about 6 to about 20 amino acids in length (e.g., about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, or about 20 amino acids in length);
    
    


wherein the HC CDR3 comprises amino acids from a D region (e.g., a diversified D region) (or fragment thereof (e.g., 3 or more amino acids of the D region, e.g., diversified D region)) or a JH region (e.g., an extended JH region).
In some embodiments, the HC CDR3 is enriched in Tyr (Y) and Ser (S) (e.g., greater than 40% of the residues of the HC CDR3 are Y and/or S).
In some embodiments, the library (e.g., the vectors or genetic packages thereof) comprises a D region or a fragment of a D region (e.g., wherein the D region is adjacent to a JH region).
In some embodiments, the library comprises a JH region, e.g., an extended JH region.
In some embodiments, the HC CDR3 comprises amino acids from a D region or a fragment of a D region (e.g., wherein the D region is adjacent to a JH region).
In some embodiments, the D region is selected from the group consisting of D2-2 (RF 2), D2-8(RF 2), D2-15(RF 2), D2-21(RF 2), D3-16(RF 2), D3-22 (RF 2), D3-3 (RF-2), D3-9 (RF 2), D3-10 (RF 2), D1-26 (RF 3), D4-11 (RF 2), D4-4 (RF 2), D5-5 (RF 3), D5-12 (RF 3), D5-18 (RF 3), D6-6 (RF1), D6-13 (RF 1), and D6-19 (RF 1).
In some embodiments, the HC CDR3 comprises amino acids from a JH region. The JH region may be an extended JH region. In some embodiments, the extended JH region is selected from the group consisting of JH1, JH2, JH3, JH4, JH5, and JH6. In some embodiments, the JH region may be enriched in Y and/or S residues, for example, it may contain greater than about 40% (e.g., between about 43% and about 80%; e.g., greater than about 40% but less than about 100%) Y and/or S residues.
In some embodiments, the D region comprises one or more cysteine (Cys) residues and in some embodiments, the one or more Cys residues are held constant (e.g., are not varied).
In some embodiments, the HC CDR3 (e.g., the DNA encoding the HC CDR3) comprises one or more filling codons between FR3 and the D region and each filling codon is individually NNK, TMY, TMT, or TMC (TMY, TMT, or TMC encode S or Y).
In some embodiments, the HC CDR3 (e.g., the DNA encoding the HC CDR3) comprises one or more filling codons between the D region and JH and each filling codon is individually NNK, TMY, TMT, or TMC.
In some embodiments, the library (e.g., the vectors or genetic packages of the library) further comprises a HC CDR1, HC CDR2, and/or a light chain and also comprises diversity in the HC CDR1, HC CDR2, or light chain comprises diversity in HC CDR1 and/or HC CDR2, and/or a light chain (e.g., kappa or lambda light chain) (respectively). For example, HC CDR3 diversity can be constructed in the background of diversity in HC CDR1, HC CDR2, and/or light chains. For example, the light-chain diversity may be encoded in the same DNA molecule as the HC diversity or the LC and HC diversities may be encoded in separate DNA molecules.
In some aspects, the disclosure features a library comprising a HC CDR3 that is 3, 4, or 5 amino acids in length, wherein the CDR3 comprises amino acids from a JH region (e.g., extended JH region) or from a D region (e.g., a diversified D region) (or fragment thereof (e.g., 3 or more amino acids of the D region, e.g., diversified D region)) joined to the FR4 portion of a JH region.
In some embodiments, the HC CDR3 is from a D region joined to the FR4 portion of a JH region and comprises a trimer, a tetramer, or a pentamer, wherein the trimer, tetramer, or pentamer does not comprise a cysteine residue.
In some embodiments, the HC CDR3 is from a D region joined to the FR4 portion of a JH region and comprises a trimer, a tetramer, or a pentamer, wherein the trimer, tetramer, or pentamer does not comprise a stop codon.
In some embodiments, the D region (e.g., the DNA encoding the D region) comprises a TAG codon and the TAG codon is replaced by a codon selected from the group consisting of TCG, TTG, TGG, CAG, AAG, TAT, and GAG.
In some embodiments, the D region (e.g., the DNA encoding the D region) comprises a TAA codon and the TAA codon is replaced by a codon selected from the group consisting of TCA, TTA, CAA, AAA, TAT, and GAA.
In some embodiments, the D region (e.g., the DNA encoding the D region) comprises a TGA codon and the TGA codon is replaced by a codon selected from the group consisting of TGG, TCA, TTA, AGA, and GGA.
In some embodiments, the library further comprises diversity in HC CDR1 and/or HC CDR2, and/or a light chain (e.g., kappa or lambda light chain). For example, HC CDR3 diversity can be constructed in the background of diversity in HC CDR1, HC CDR2, and/or light chains. For example, the light-chain diversity may be encoded in the same DNA molecule as the HC diversity or the LC and HC diversities may be encoded in separate DNA molecules.
In some aspects, the disclosure provides a method of diversifying a library, the method comprising mutagenizing a library described herein.
In some embodiments, the mutagenizing comprises error-prone PCR.
In some embodiments, the mutagenizing comprises wobbling.
In some embodiments, the mutagenizing comprises dobbling.
In some embodiments, the mutagenizing introduces on average about 1 to about 10 mutations (e.g., about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10 mutations; e.g., base changes) per HC CDR3.
These embodiments of the present invention, other embodiments, and their features and characteristics will be apparent from the description, drawings, and claims that follow.


DETAILED DESCRIPTION
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 encode members of a diverse family of human antibodies comprising heavy chain (HC) CDR3s that are between about 3 to about 35 amino acids in length may be prepared and used. The HC CDR3s may also, in certain embodiments, may be rich in Y and S and/or comprise diversified D regions. Also provided are focused libraries comprising such HC CDR3s.
Definitions
For convenience, before further description of the present invention, certain terms employed in the specification, examples and appended claims are defined here.
The singular forms “a”, “an”, and “the” include plural references unless the context clearly dictates otherwise.
The term “affinity” or “binding affinity” refers to the apparent association constant or Ka. The Ka is the reciprocal of the dissociation constant (Kd). A binding protein may, for example, have a binding affinity of at least 105, 106, 107, 108, 109, 1010 and 1011 M−1 for a particular target molecule. Higher affinity binding of a binding protein to a first target relative to a second target can be indicated by a higher KA (or a smaller numerical value KD) for binding the first target than the KA (or numerical value KD) for binding the second target. In such cases, the binding protein has specificity for the first target (e.g., a protein in a first conformation or mimic thereof) relative to the second target (e.g., the same protein in a second conformation or mimic thereof; or a second protein). Differences in binding affinity (e.g., for specificity or other comparisons) can be at least 1.5, 2, 3, 4, 5, 10, 15, 20, 37.5, 50, 70, 80, 91, 100, 500, 1000, or 105 fold.
Binding affinity can be determined by a variety of methods including equilibrium dialysis, equilibrium binding, gel filtration, ELISA, surface plasmon resonance, or spectroscopy (e.g., using a fluorescence assay). Exemplary conditions for evaluating binding affinity are in TRIS-buffer (50 mM TRIS, 150 mM NaCl, 5 mM CaCl2 at pH7.5). These techniques can be used to measure the concentration of bound and free binding protein as a function of binding protein (or target) concentration. The concentration of bound binding protein ([Bound]) is related to the concentration of free binding protein ([Free]) and the concentration of binding sites for the binding protein on the target where (N) is the number of binding sites per target molecule by the following equation:

[Bound]=N·[Free]/((1/KA)+[Free]).

It is not always necessary to make an exact determination of KA, though, since sometimes it is sufficient to obtain a quantitative measurement of affinity, e.g., determined using a method such as ELISA or FACS analysis, is proportional to KA, and thus can be used for comparisons, such as determining whether a higher affinity is, e.g., 2-fold higher, to obtain a qualitative measurement of affinity, or to obtain an inference of affinity, e.g., by activity in a functional assay, e.g., an in vitro or in vivo assay.
The term “antibody” refers to a protein that includes at least one immunoglobulin variable domain or immunoglobulin variable domain sequence. For example, an antibody can include a heavy (H) chain variable region (abbreviated herein as VH), and a light (L) chain variable region (abbreviated herein as VL). In another example, an antibody includes two heavy (H) chain variable regions and two light (L) chain variable regions. Heavy chain and light chain may also be abbreviated as HC and LC, respectively. The term “antibody” encompasses antigen-binding fragments of antibodies (e.g., single chain antibodies, Fab and sFab fragments, F(ab′)2, Fd fragments, Fv fragments, scFv, and domain antibodies (dAb) fragments (de Wildt et al., Eur J. Immunol. 1996; 26(3):629-39.)) as well as complete antibodies. An antibody can have the structural features of IgA, IgG, IgE, IgD, IgM (as well as subtypes thereof). Antibodies may be from any source, but primate (human and non-human primate) and primatized are preferred.
The VH and VL regions can be further subdivided into regions of hypervariability, termed “complementarity determining regions” (“CDR”), interspersed with regions that are more conserved, termed “framework regions” (“FR”). The extent of the framework region and CDRs has been precisely defined (see, Kabat, E. A., et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242, and Chothia, C. et al. (1987) J. Mol. Biol. 196:901-917, see also www.hgmp.mrc.ac.uk). Kabat definitions are used herein. Each VH and VL is typically composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4.
The VH or VL chain of the antibody can further include all or part of a heavy or light chain constant region, to thereby form a heavy or light immunoglobulin chain, respectively. In one embodiment, the antibody is a tetramer of two heavy immunoglobulin chains and two light immunoglobulin chains, wherein the heavy and light immunoglobulin chains are inter-connected by, e.g., disulfide bonds. In IgGs, the heavy chain constant region includes three immunoglobulin domains, CH1, CH2 and CH3. The light chain constant region includes a CL domain. The variable region of the heavy and light chains contains a binding domain that interacts with an antigen. The constant regions of the antibodies typically mediate the binding of the antibody to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (Clq) of the classical complement system. The light chains of the immunoglobulin may be of types, kappa or lambda. In one embodiment, the antibody is glycosylated. An antibody can be functional for antibody-dependent cytotoxicity and/or complement-mediated cytotoxicity.
One or more regions of an antibody can be human or effectively human. For example, one or more of the variable regions can be human or effectively human. For example, one or more of the CDRs can be human, e.g., HC CDR1, HC CDR2, HC CDR3, LC CDR1, LC CDR2, and LC CDR3. Each of the light chain CDRs can be human. HC CDR3 can be human. One or more of the framework regions can be human, e.g., FR1, FR2, FR3, and FR4 of the HC or LC. For example, the Fc region can be human. In one embodiment, all the framework regions are human, e.g., derived from a human somatic cell, e.g., a hematopoietic cell that produces immunoglobulins or a non-hematopoietic cell. In one embodiment, the human sequences are germline sequences, e.g., encoded by a germline nucleic acid. In one embodiment, the framework (FR) residues of a selected Fab can be converted to the amino-acid type of the corresponding residue in the most similar primate germline gene, especially the human germline gene. One or more of the constant regions can be human or effectively human. For example, at least 70, 75, 80, 85, 90, 92, 95, 98, or 100% of an immunoglobulin variable domain, the constant region, the constant domains (CH1, CH2, CH3, CL), or the entire antibody can be human or effectively human.
All or part of an antibody can be encoded by an immunoglobulin gene or a segment thereof. Exemplary human immunoglobulin genes include the kappa, lambda, alpha (IgA1 and IgA2), gamma (IgG1, IgG2, IgG3, IgG4), delta, epsilon and mu constant region genes, as well as the many immunoglobulin variable region genes. Full-length immunoglobulin “light chains” (about 25 KDa or about 214 amino acids) are encoded by a variable region gene at the NH2-terminus (about 110 amino acids) and a kappa or lambda constant region gene at the COOH— terminus Full-length immunoglobulin “heavy chains” (about 50 KDa or about 446 amino acids), are similarly encoded by a variable region gene (about 116 amino acids) and one of the other aforementioned constant region genes, e.g., gamma (encoding about 330 amino acids). The length of human HC varies considerably because HC CDR3 varies from about 3 amino-acid residues to over 35 amino-acid residues.
Herein, the terms “D segment” and “D region” are used interchangeably and are identical. It is to be understood that these items have both DNA and amino-acid representations and that which is meant is clear from the context.
A “library” or “display library” refers to a collection of nucleotide, e.g., DNA, sequences within clones; or a genetically diverse collection of polypeptides displayed on replicable display packages capable of selection or screening to provide an individual polypeptide or a mixed population of polypeptides.
The term “package” as used herein refers to a replicable genetic display package in which the particle is displaying a polypeptide at its surface. The package may be a bacteriophage which displays an antigen binding domain at its surface. This type of package has been called a phage antibody (pAb).
A “pre-determined target” refers to a target molecule whose identity is known prior to using it in any of the disclosed methods.
The term “replicable display package” as used herein refers to a biological particle which has genetic information providing the particle with the ability to replicate. The particle can display on its surface at least part of a polypeptide. The polypeptide can be encoded by genetic information native to the particle and/or artificially placed into the particle or an ancestor of it. The displayed polypeptide may be any member of a specific binding pair e.g., heavy or light chain domains based on an immunoglobulin molecule, an enzyme or a receptor etc. The particle may be, for example, a virus e.g., a bacteriophage such as fd or M13.
The term “vector” refers to a DNA molecule, capable of replication in a host organism, into which a gene is inserted to construct a recombinant DNA molecule. A “phage vector” is a vector derived by modification of a phage genome, containing an origin of replication for a bacteriophage, but not one for a plasmid. A “phagemid vector” is a vector derived by modification of a plasmid genome, containing an origin of replication for a bacteriophage as well as the plasmid origin of replication.
In discussing oligonucleotides, the notation “[RC]” indicates that the Reverse Complement of the oligonucleotide shown is the one to be used.
Human Antibody Heavy Chain CDR3s
The heavy chain (“HC”) Germ-Line Gene (GLG) 3-23 (also known as VP-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:1)) 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:2)), JH6 (YYYYYGMDVWGQGTTVTVSS (SEQ ID NO:3)), JH1, JH2, or JH5 could as well be used. If present, the double underscored portions of the JHs are considered to be part of CDR3. In Table 3, the FR4 parts of the JHs are underscored.
Naturally, 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 that are essentially random, D is a D segment, often with heavy editing at both ends, ny is a series of bases that are essentially random, and JHn 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 V with D and of D with JH.
Human D segments have some very strong biases. The tally of the 522 amino-acids in human D segments is Y 70 (13.4%), L 63 (12.1%), V 52 (10%), G 49 (9.4%), 141 (7.9%), T 40 (7.7%), S 33 (6.3%), W 27 (5.2%), D 21 (4%), A 19 (3.6%), R 16 (3.1%), TAG 15 (2.9%), N 14 2.7%), Q 11 (2.1%), C 9 (1.7%), E 9 (1.7%), F 8 (1.5%), M 8 (1.5%), TGA 8 (1.5%), TAA 7 (1.3%), P 1 (0.2%), H1 (0.2%), and K 0 (0%). There is one D (2-8 RF 1) that has an unpaired Cys but also a TGA stop codon, so it is little used. Thus, D segments are primarily hydrophobic.
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 (n=1,6) 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.
Provided herein are HC CDR3s that are between about 3 to a about 35 amino acids in length. The HC CDR3s may also, in certain embodiments, be rich in Y and S and/or comprise diversified D regions, where a D region is present. For example, the HC CDR3s may contain between about 43% and about 80% Y and/or S residues, e.g., about 43%, about 48%, about 69%, about 63%, about 71%, about 62%, about 58%, about 68%, about 80%, about 77%, or greater than about 40%, or about 40% to less than about 100%, of the residues are Y and/or S. For example, not all of the residues in the CDR3 are Y and/or S. The HC CDR3s may, in certain embodiments, comprise an extended JH region. Exemplary HC CDR3 component designs of the preferred libraries of this invention are shown and described in Examples 1, 2, and 3.
In some embodiments, diversity (e.g., in a CDR, e.g., HC CDR3, or framework region (e.g., framework region near or adjacent to a CDR, e.g., CDR3, e.g., HC CDR3) is generated to create on average about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, or about 1 to about 10 mutations (e.g., base change), e.g., per CDR (e.g., HC CDR3) or framework region (e.g., framework region near or adjacent to a CDR, e.g., CDR3, e.g., HC CDR3). In some implementations, the mutagenesis is targeted to regions known or likely to be at the binding interface. Further, mutagenesis can be directed to framework regions near or adjacent to the CDRs. In the case of antibodies, mutagenesis can also be limited to one or a few of the CDRs, e.g., to make precise step-wise improvements. Likewise, if the identified ligands are enzymes, mutagenesis can provide antibodies that are able to bind to the active site and vicinity. The CDR or framework region (e.g., an HC CDR3 described herein) may be, in certain embodiments, subjected to error-prone PCR to generate the diversity. This approach uses a “sloppy” version of PCR, in which the polymerase has a fairly high error rate (up to 2%), to amplify the wild-type sequence, and is generally described in Pritchard, et al. (2005) J. Theor. Biol. 234: 497-509 and Leung et al. (1989) Technique 1:11-15. Other exemplary mutagenesis techniques include DNA shuffling using random cleavage (Stemmer (1994) Nature 389-391; termed “nucleic acid shuffling”), RACHITTTM (Coco et al. (2001) Nature Biotech. 19:354), site-directed mutagenesis (Zoller et al. (1987) Nucl Acids Res 10:6487-6504), cassette mutagenesis (Reidhaar-Olson (1991) Methods Enzymol. 208:564-586) and incorporation of degenerate oligonucleotides (Griffiths et al. (1994) EMBO J. 13:3245).
In some embodiments of the invention, D segments in which a majority of the residues are either Ser or Tyr are picked. In some embodiments, when the DNA encoding the D region is synthesized, each Ser or Tyr residue is encoded by TMT, TMC, or TMY so that the encoded amino acid is either Ser or Tyr.
In some embodiments, the HC CDR3 sequences described herein may be subjected to selection for open reading frames by fusing the sequence encoding the HC CDR3 of interest in frame to an antibiotic resistance gene, such as KanR gene and selecting for kanamycin resistance. Cells in which the potential CDR3 has a stop codon or a frame shift will not have the antibiotic resistance and that sequence will be eliminated.
Methods of Construction of Libraries comprising Human Antibody Heavy Chain CDR3s and Libraries comprising Human Antibody Heavy Chain CDR3s
An antibody library is a collection of proteins that include proteins that have at least one immunoglobulin variable domain sequence. For example, camelized variable domains (e.g., VH domains) can be used as a scaffold for a library of proteins that include only one immunoglobulin variable domain sequence. In another example, the proteins include two variable domains sequences, e.g., a VH and VL domain, that are able to pair. An antibody library can be prepared from a nucleic acid library (an antibody-coding library) that includes antibody-coding sequences, e.g., comprising the sequences encoding the HC CDR3s provided herein.
In cases where a display library is used, each member of the antibody-coding library can be associated with the antibody that it encodes. In the case of phage display, the antibody protein is physically associated (directly or indirectly) with a phage coat protein. A typical antibody display library member displays a polypeptide that includes a VH domain and a VL domain. The display library member can display the antibody as a Fab fragment (e.g., using two polypeptide chains) or a single chain FIT (e.g., using a single polypeptide chain). Other formats can also be used.
As in the case of the Fab and other formats, the displayed antibody can include one or more constant regions as part of a light and/or heavy chain. In one embodiment, each chain includes one constant region, e.g., as in the case of a Fab. In other embodiments, additional constant regions are included. It is also possible to add one or more constant regions to a molecule after it is identified as having useful antigen binding site. See, e.g., US 2003-0224408.
Antibody libraries can be constructed by a number of processes (see, e.g., de Haard et al. (1999) J. Biol. Chem. 274:18218-30; Hoogenboom et al. (1998) Immunotechnology 4:1-20, Hoogenboom et al. (2000) Immunol Today 21:371-8, and Hoet et al. (2005) Nat. Biotechnol. 23(3):344-8.
In certain embodiments for constructing libraries, the heavy chains comprising the CDR3s described herein and the kappa and lambda light chains are best constructed in separate vectors. First, a synthetic gene is designed to embody each of the synthetic variable domains. The light chains may be 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 may be bounded by SfiI (positioned within the Pe1B signal sequence) and NotI (positioned in the linker between CH1 and the anchor protein). Signal sequences other than Pe1B may also be used, e.g., a M13 pIII signal sequence.
The initial genes may be 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. Stuffers are used to avoid have any one CDR sequence highly represented.
In another embodiment of the present invention, the 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.
Most preferably, the display is 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., pMID21 (DNA sequence shown in Table 35)) 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 still other embodiments, a method termed the Rapid Optimization of LIght Chains or “ROLIC”, described in U.S. Ser. No. 61/028,265 filed Feb. 13, 2008, U.S. Ser. No. 61/043,938 filed Apr. 10, 2008, and U.S. Ser. No. 12/371,000 filed Feb. 13, 2009, a large population of LCs is placed in a phage vector that causes them to be displayed on phage. A small population (e.g., 3, 10, or 25) of HCs are cloned into E. coli so that the HCs are secreted into the periplasm, e.g., those HCs having the CDR3s described herein. The E. coli are then infected with the phage vectors encoding the large population of LCs to produce the HC/LC protein pairings on the phage. The phage particles carry only a LC gene.
In another aspect, in a method termed the Economical Selection of Heavy Chains or “ESCH”, also described in U.S. Ser. No. 61/028,265 filed Feb. 13, 2008, U.S. Ser. No. 61/043,938 filed Apr. 10, 2008, and U.S. Ser. No. 12/371,000 filed Feb. 13, 2009, a small population of LCs may be placed in a vector that causes them to be secreted. A new library of HCs in phage is constructed, such as those provided herein comprising the CDR3s. The LCs and HCs can then be combined by the much more efficient method of infection. Once a small set of effective HC are selected, these can be used as is, fed into ROLIC to obtain an optimal HC/LC pairing, or cloned into a Fab library of LCs for classical selection.
In another embodiment of this invention, the diversity captured by the methods of the present invention may be displayed and/or expressed using a vector suitable for expression in a eukaryotic cell, e.g., a yeast vector, e.g., for expression in a yeast cell.
Other types of protein display include cell-based display (see, e.g., WO 03/029,456); ribosome display (see, e.g., Mattheakis et al. (1994) Proc. Natl. Acad. Sci. USA 91:9022 and Hanes et al. (2000) Nat. Biotechnol. 18:1287-92); protein-nucleic acid fusions (see, e.g., U.S. Pat. No. 6,207,446); and immobilization to a non-biological tag (see, e.g., U.S. Pat. No. 5,874,214).
Antibodies isolated from the libraries of the present disclosure may be analyzed to determine the type of the LC and the closest germline gene. In a preferred embodiment, non-germline framework residues are changed back to the germline amino acid so long as binding affinity and specificity are not adversely affected to an unacceptable extent. The substitutions may be done as a group or singly. Human germline sequences are disclosed in Tomlinson, I. A. et al., 1992, J. Mol. Biol. 227:776-798; Cook, G. P. et al., 1995, Immunol. Today 16 (5): 237-242; Chothia, D. et al., 1992, J. Mol. Bio. 227:799-817. The V BASE directory provides a comprehensive directory of human immunoglobulin variable region sequences (compiled by Tomlinson, I. A. et al. MRC Centre for Protein Engineering, Cambridge, UK). Antibodies are “germlined” by reverting one or more non-germline amino acids in framework regions to corresponding germline amino acids of the antibody, so long as binding properties are substantially retained. Similar methods can also be used in the constant region, e.g., in constant immunoglobulin domains.
For example, an antibody can include one, two, three, or more amino acid substitutions, e.g., in a framework, CDR, or constant region, to make it more similar to a reference germline sequence. One exemplary germlining method can include identifying one or more germline sequences that are similar (e.g., most similar in a particular database) to the sequence of the isolated antibody. Mutations (at the amino acid level) are then made in the isolated antibody, either incrementally or in combination with other mutations. For example, a nucleic acid library that includes sequences encoding some or all possible germline mutations is made. The mutated antibodies are then evaluated, e.g., to identify an antibody that has one or more additional germline residues relative to the isolated antibody and that is still useful (e.g., has a functional activity). In one embodiment, as many germline residues are introduced into an isolated antibody as possible.
In one embodiment, mutagenesis is used to substitute or insert one or more germline residues into a framework and/or constant region. For example, a germline framework and/or constant region residue can be from a germline sequence that is similar (e.g., most similar) to the non-variable region being modified. After mutagenesis, activity (e.g., binding or other functional activity) of the antibody can be evaluated to determine if the germline residue or residues are tolerated (i.e., do not abrogate activity). Similar mutagenesis can be performed in the framework regions.
Selecting a germline sequence can be performed in different ways. For example, a germline sequence can be selected if it meets a predetermined criteria for selectivity or similarity, e.g., at least a certain percentage identity, e.g., at least 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 99.5% identity. The selection can be performed using at least 2, 3, 5, or 10 germline sequences. In the case of CDR1 and CDR2, identifying a similar germline sequence can include selecting one such sequence. In the case of CDR3, identifying a similar germline sequence can include selecting one such sequence, but may include using two germline sequences that separately contribute to the amino-terminal portion and the carboxy-terminal portion. In other implementations, more than one or two germline sequences are used, e.g., to form a consensus sequence.
CDR1, CDR2, and Light-Chain Diversity
It is to be understood that the libraries of HC CDR3 are constructed in the background of diversity in HC CDR1, HC CDR2, and light chains. The light-chain diversity may be encoded in the same DNA molecule as the HC diversity or the LC and HC diversities may be encoded in separate DNA molecules. In Table 22 the fusion of a signal sequence:: VH::CH1::His6::Myc::IIIstump. CDR1 comprises residues 31-35; there is diversity at residues 31, 33, and 35. In one embodiment, residues 31, 33, and 35 can be any amino-acid type except cysteine. CDR2 comprises residues 50 through 65. There is diversity at positions 50, 52, 52a, 56, and 58. In one embodiment, residues 50, and 52 can be any of the types Ser, Gly, Val, Trp, Arg, Tyr; residue 52a can be Pro or Ser and residues 56 and 58 can be any amino-acid type except Cys. The diversity of HC CDR3 is cloned into a diversity of HC CDR1 and 2 that is at least 1. E 4, 1. E 5, 1. E 6, 1.E 7, 5.E 7, or 1.E 8.
In one embodiment, residues 31, 33, 35, 50, 52, 56, and 58 can be any amino-acid type except Cys and residue 52a can be Gly, Ser, Pro, or Tyr. The diversity of HC CDR3 is cloned into a diversity of HC CDR1 and 2 that is at least 1. E 4, 1. E 5, 1. E 6, 1. E 7, 5. E 7, or 1. E 8.
In one embodiment, the diversity of the HC is cloned into a vector (phage or phagemid) that contains a diversity of light chains. This diversity is at least 25, 50, 100, 500, 1. E 3, 1. E 4, 1. E 5, 1. E 6, or 1. E7. The diversity of HC CDR3 is at least 221, 272, 500, 1000, 1. E 4, 1. E 5, 1.E 6, 1. E7, or 1. E 8.
In one embodiment, the diversity of the HC is cloned into a phage vector that displays the HC on a phage protein such as III, VIII, VII, VI, or IX or a fragment of one of these sufficient to cause display and light chains are combined with the HC by infecting a cell collection wherein each cell secrets a light chain. The diversity of the light chains in the cells is at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, or 100. The diversity of HC CDR3 is at least 221, 272, 500, 1000, 1. E 4, 1. E 5, 1. E 6, 1. E7, or 1. E 8.
Table 30 shows the sequence of the phage vector DY3FHC87 (SEQ ID NO:894) which carries a bla gene, a display cassette for heavy chains under control of a Plac promoter. DY3FHC87 contains all the genes of M13 as well. Infecting F+ E. coli cells that harbor a diversity of light chains in a vector such as pLCSK23 (Sequence in Table 40) (SEQ ID NO:896). The vector pLCSK23 carries a KanR gene. Under the control of Plac promoter, there is a gene beginning at base 2215 having a signal sequence (bases 2215-2277), a VL (in this sequence the VL encodes the sequence shown in (SEQ ID NO:897) from base 2278 to base 2598, Ckappa from base 2599 to 2922, a linker that allows an NotI site from 2923 to 2931, and a V5 tag (bases 2932-2973). There are an SfiI site at 2259-2271 and a KpnI site at 2602-2605 to allow easy replacement of Vkappas. (SEQ ID NO:897) is an example of the proteins that are secreted. It is to be understood that CKappa and the V5 tag are constant. All of the proteins shown in Table 19 (VK1O2gl-JK3, VK1O2var1, VK1O2var2, VK1O2var3, VK1O2var4, VK1O2var5, VK3L6gl-JK4, VK3L6var1, VK3L6var2, VK3L6var3, VK3L6var4, VK3L6var5, VK3L6var6, VK3L6var7, VK3L6var8, VK3A27gl-JK3, VK3A27var1, VK3A27var2, VK3A27var3, VK3A27var4, VK3A27var5, VK3A27var6, VK3A27var7, VK3L2gl-JK3, and VK1glL8-JK5) will have these sequences attached at the carboxy end.
Methods of Using the Libraries
Off-Rate Selection.
Since a slow dissociation rate can be predictive of high affinity, particularly with respect to interactions between polypeptides and their targets, the methods described herein can be used to isolate ligands with a desired kinetic dissociation rate (i.e., reduced) for a binding interaction to a target.
To select for slow dissociating antibodies from a display library, the library is contacted to an immobilized target. The immobilized target is then washed with a first solution that removes non-specifically or weakly bound antibodies. Then the bound antibodies are eluted with a second solution that includes a saturating amount of free target, i.e., replicates of the target that are not attached to the particle. The free target binds to antibodies that dissociate from the target. Rebinding of the eluted antibodies is effectively prevented by the saturating amount of free target relative to the much lower concentration of immobilized target.
The second solution can have solution conditions that are substantially physiological or that are stringent (e.g., low pH, high pH, or high salt). Typically, the solution conditions of the second solution are identical to the solution conditions of the first solution. Fractions of the second solution are collected in temporal order to distinguish early from late fractions. Later fractions include antibodies that dissociate at a slower rate from the target than biomolecules in the early fractions. Further, it is also possible to recover antibodies that remain bound to the target even after extended incubation. These can either be dissociated using chaotropic conditions or can be amplified while attached to the target. For example, phage bound to the target can be contacted to bacterial cells.
Selecting or Screening for Specificity.
The display library screening methods described herein can include a selection or screening process that discards antibodies that bind to a non-target molecule. Examples of non-target molecules include, e.g., a carbohydrate molecule that differs structurally from the target molecule, e.g., a carbohydrate molecule that has a different biological property from the target molecule. In the case of a sulfated carbohydrate, a non-target may be the same carbohydrate without the sulfate or with the sulfate in a different position. In the case of a phosphopeptide, the non-target may be the same peptide without the phosphate or a different phosphopeptide.
In one implementation, a so-called “negative selection” step is used to discriminate between the target and related non-target molecule and a related, but distinct non-target molecules. The display library or a pool thereof is contacted to the non-target molecule. Members that do not bind the non-target are collected and used in subsequent selections for binding to the target molecule or even for subsequent negative selections. The negative selection step can be prior to or after selecting library members that bind to the target molecule.
In another implementation, a screening step is used. After display library members are isolated for binding to the target molecule, each isolated library member is tested for its ability to bind to a non-target molecule (e.g., a non-target listed above). For example, a high-throughput ELISA screen can be used to obtain this data. The ELISA screen can also be used to obtain quantitative data for binding of each library member to the target. The non-target and target binding data are compared (e.g., using a computer and software) to identify library members that specifically bind to the target.
In certain embodiments, the antibodies comprising the CDR3s of the invention may be able to bind carbohydrates. Methods for evaluating antibodies for carbohydrate binding include ELISA, immunohistochemistry, immunoblotting, and fluorescence-activated cell sorting. These methods can be used to identify antibodies which have a KD of better than a threshold, e.g., better than 100 nM, 50 nM, 10 nM, 5 nM, 1 nM, 500 μM, 100 μM, or 10 μM.
ELISA.
Proteins encoded by a display library can also be screened for a binding property using an ELISA assay. For example, each protein is contacted to a microtitre plate whose bottom surface has been coated with the target, e.g., a limiting amount of the target. The plate is washed with buffer to remove non-specifically bound polypeptides. Then the amount of the protein bound to the plate is determined by probing the plate with an antibody that can recognize the polypeptide, e.g., a tag or constant portion of the polypeptide. The antibody is linked to an enzyme such as alkaline phosphatase, which produces a calorimetric product when appropriate substrates are provided. The protein can be purified from cells or assayed in a display library format, e.g., as a fusion to a filamentous bacteriophage coat. Alternatively, cells (e.g., live or fixed) that express the target molecule, e.g., a target that contains a carbohydrate moiety, can be plated in a microtitre plate and used to test the affinity of the peptides/antibodies present in the display library or obtained by selection from the display library.
In another version of the ELISA assay, each polypeptide of a diversity strand library is used to coat a different well of a microtitre plate. The ELISA then proceeds using a constant target molecule to query each well.
Cell Binding Assays.
Antibodies can be evaluated for their ability to interact with one or more cell types, e.g., a hematopoietic cell. Fluorescent activated cell sorting (FACS) is one exemplary method for testing an interaction between a protein and a cell. The antibody is labeled directly or indirectly with a fluorophore, before or after, binding to the cells, and then cells are counted in a FACS sorter.
Other cell types can be prepared for FACS by methods known in the art.
Homogeneous Binding Assays.
The binding interaction of candidate polypeptide with a target can be analyzed using a homogenous assay, i.e., after all components of the assay are added, additional fluid manipulations are not required. For example, fluorescence resonance energy transfer (FRET) can be used as a homogenous assay (see, for example, Lakowicz et al., U.S. Pat. No. 5,631,169; Stavrianopoulos, et al., U.S. Pat. No. 4,868,103). A fluorophore label on the first molecule (e.g., the molecule identified in the fraction) is selected such that its emitted fluorescent energy can be absorbed by a fluorescent label on a second molecule (e.g., the target) if the second molecule is in proximity to the first molecule. The fluorescent label on the second molecule fluoresces when it absorbs to the transferred energy. Since the efficiency of energy transfer between the labels is related to the distance separating the molecules, the spatial relationship between the molecules can be assessed. In a situation in which binding occurs between the molecules, the fluorescent emission of the ‘acceptor’ molecule label in the assay should be maximal. A binding event that is configured for monitoring by FRET can be conveniently measured through standard fluorometric detection means well known in the art (e.g., using a fluorimeter). By titrating the amount of the first or second binding molecule, a binding curve can be generated to estimate the equilibrium binding constant.
Another example of a homogenous assay is Alpha Screen (Packard Bioscience, Meriden Conn.). Alpha Screen uses two labeled beads. One bead generates singlet oxygen when excited by a laser. The other bead generates a light signal when singlet oxygen diffuses from the first bead and collides with it. The signal is only generated when the two beads are in proximity. One bead can be attached to the display library member, the other to the target. Signals are measured to determine the extent of binding.
The homogenous assays can be performed while the candidate polypeptide is attached to the display library vehicle, e.g., a bacteriophage.
Surface Plasmon Resonance (SPR).
The binding interaction of a molecule isolated from a display library and a target can be analyzed using SPR. SPR or Biomolecular Interaction Analysis (BIA) detects biospecific interactions in real time, without labeling any of the interactants. Changes in the mass at the binding surface (indicative of a binding event) of the BIA chip result in alterations of the refractive index of light near the surface (the optical phenomenon of surface plasmon resonance (SPR)). The changes in the refractivity generate a detectable signal, which are measured as an indication of real-time reactions between biological molecules. Methods for using SPR are described, for example, in U.S. Pat. No. 5,641,640; Raether (1988) Surface Plasmons Springer Verlag; Sjolander and Urbaniczky (1991) Anal. Chem. 63:2338-2345; Szabo et al. (1995) Curr. Opin. Struct. Biol. 5:699-705 and on-line resources provide by BIAcore International AB (Uppsala, Sweden).
Information from SPR can be used to provide an accurate and quantitative measure of the equilibrium dissociation constant (KD), and kinetic parameters, including kon and koff, for the binding of a biomolecule to a target. Such data can be used to compare different biomolecules. For example, proteins encoded by nucleic acid selected from a library of diversity strands can be compared to identify individuals that have high affinity for the target or that have a slow koff. This information can also be used to develop structure-activity relationships (SAR). For example, the kinetic and equilibrium binding parameters of matured versions of a parent protein can be compared to the parameters of the parent protein. Variant amino acids at given positions can be identified that correlate with particular binding parameters, e.g., high affinity and slow koff. This information can be combined with structural modeling (e.g., using homology modeling, energy minimization, or structure determination by crystallography or NMR). As a result, an understanding of the physical interaction between the protein and its target can be formulated and used to guide other design processes.
Protein Arrays.
Proteins identified from the display library can be immobilized on a solid support, for example, on a bead or an array. For a protein array, each of the polypeptides is immobilized at a unique address on a support. Typically, the address is a two-dimensional address. Methods of producing polypeptide arrays are described, e.g., in De Wildt et al. (2000) Nat. Biotechnol. 18:989-994; Lueking et al. (1999) Anal. Biochem. 270:103-111; Ge (2000) Nucleic Acids Res. 28, e3, I-V11; MacBeath and Schreiber (2000) Science 289:1760-1763; WO 01/40803 and WO 99/51773A1. Polypeptides for the array can be spotted at high speed, e.g., using commercially available robotic apparati, e.g., from Genetic MicroSystems or BioRobotics. The array substrate can be, for example, nitrocellulose, plastic, glass, e.g., surface-modified glass. The array can also include a porous matrix, e.g., acrylamide, agarose, or another polymer.
Kits
Also provided are kits for use in carrying out a method according to any aspect of the invention. The kits may include the necessary vectors. One such vector will typically have an origin of replication for single stranded bacteriophage and either contain the sbp member nucleic acid or have a restriction site for its insertion in the 5′ end region of the mature coding sequence of a phage capsid protein, and with a secretory leader coding sequence upstream of said site which directs a fusion of the capsid protein exogenous polypeptide to the periplasmic space.
Also provided are packages encoding the HC CDR3s as defined above and polypeptides comprising the HC CDR3s and fragments and derivatives thereof, obtainable by use of any of the above defined methods. The derivatives may comprise polypeptides fused to another molecule such as an enzyme or a Fc tail.
The kit may include a phage vector (e.g., DY3F87HC) which has a site for insertion of HC CDR3s for expression of the encoded polypeptide in free form. The kit may also include a plasmid vector for expression of soluble light chains, e.g., pLCSK23. The kit may also include a suitable cell line (e.g., TG1). The diversity of light chains encoded by pLCSK23 may be 10, 15, 20, 25, 30, or 50. The LCs in the diversity may be constructed or picked to have certain desirable properties, such as, being germline in the framework regions and having diversity in CDR3 and/or CDR1. The germlines may be of highly utilized ones, e.g., VK1_2-O2, VK3_1-A27, VK3_5-L6, VK3_3-L2 for kappa and VL2_2a2, VL1_1c, VL1_1g, VL3_3r for lambda.
For example, one could clone genes for
VK1O2gl-JK3, VK1O2var1, VK1O2var2, VK1O2var3, VK1O2var4, VK1O2var5, VK3L6gl-JK4, VK3L6var1, VK3L6var2, VK3L6var3, VK3L6var4, VK3L6var5, VK3L6var6, VK3L6var7, VK3L6var8, VK3A27gl-JK3, VK3A27var1, VK3A27var2, VK3A27var3, VK3A27var4, VK3A27var5, VK3A27var6, VK3A27var7, VK3L2gl-JK3, VK1glL8-JK5, and VK1GLO12-JK3 (amino-acid sequences shown in Table 19) into pLCSK23.







TABLE 19





26 VL to be used in pLCSK23.
















VK1O2gl-JK3 (SEQ ID NO: 4)



DIQMTQSPSS LSASVGDRVT ITCRASQSIS SYLNWYQQKP GKAPKLLIYA ASSLQSGVPS
60


RFSGSGSGTD FTLTISSLQP EDFATYYCQQ SYSTPFTFGP GTKVDIK
107


 


VK1O2var1 (SEQ ID NO: 5) S28D



DIQMTQSPSS LSASVGDRVT ITCRASQDIS SYLNWYQQKP GKAPKLLIYA ASSLQSGVPS
60


RFSGSGSGTD FTLTISSLQP EDFATYYCQQ SYSTPFTFGP GTKVDIK
107


 


VK1O2var2 (SEQ ID NO: 6) S91R



DIQMTQSPSS LSASVGDRVT ITCRASQSIS SYLNWYQQKP GKAPKLLIYA ASSLQSGVPS
60


RFSGSGSGTD FTLTISSLQP EDFATYYCQQ RYSTPFTFGP GTKVDIK
107


 


VK1O2var3 (SEQ ID NO: 7) S91E



DIQMTQSPSS LSASVGDRVT ITCRASQSIS SYLNWYQQKP GKAPKLLIYA ASSLQSGVPS
60


RFSGSGSGTD FTLTISSLQP EDFATYYCQQ EYSTPFTFGP GTKVDIK
107


 


VK1O2var4 (SEQ ID NO: 8) S31R



DIQMTQSPSS LSASVGDRVT ITCRASQSIS RYLNWYQQKP GKAPKLLIYA ASSLQSGVPS
60


RFSGSGSGTD FTLTISSLQP EDFATYYCQQ SYSTPFTFGP GTKVDIK
107


 


VK1O2var5 (SEQ ID NO: 9) S31E, S93R



DIQMTQSPSS LSASVGDRVT ITCRASQSIS EYLNWYQQKP GKAPKLLIYA ASSLQSGVPS
60


RFSGSGSGTD FTLTISSLQP EDFATYYCQQ SYRTPFTFGP GTKVDIK
107


 


VK3L6gl-JK4 (SEQ ID NO: 10)



EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ASNRATGIPA
60


RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RSNWPLTFGG GTKVEIK
107


 


VK3L6var1 (SEQ ID NO: 11) S31R



EIVLTQSPAT LSLSPGERAT LSCRASQSVS RYLAWYQQKP GQAPRLLIYD ASNRATGIPA
60


RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RSNWPLTFGG GTKVEIK
107


 


VK3L6var2 (SEQ ID NO: 12) S92R



EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ASNRATGIPA
60


RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RRNWPLTFGG GTKVEIK
107


 


VK3L6var3 (SEQ ID NO: 13) S92G



EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ASNRATGIPA
60


RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RGNWPLTFGG GTKVEIK
107


 


VK3L6var4 (SEQ ID NO: 14) S92Y



EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ASNRATGIPA
60


RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RYNWPLTFGG GTKVEIK
107


 


VK3L6var5 (SEQ ID NO: 15) S92E



EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ASNRATGIPA
60


RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RENWPLTFGG GTKVEIK
107


 


VK3L6var6 (SEQ ID NO: 16) Y32F



EIVLTQSPAT LSLSPGERAT LSCRASQSVS SFLAWYQQKP GQAPRLLIYD ASNRATGIPA
60


RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RSNWPLTFGG GTKVEIK
107


 


VK3L6var7 (SEQ ID NO: 17) Y32D



EIVLTQSPAT LSLSPGERAT LSCRASQSVS SDLAWYQQKP GQAPRLLIYD ASNRATGIPA
60


RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RSNWPLTFGG GTKVEIK
107


 


VK3L6var8 (SEQ ID NO: 18) N93G



EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ASNRATGIPA
60


RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RSGWPLTFGG GTKVEIK
107


 


VK3A27gl-JK3 (SEQ ID NO: 19)



EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP
60


DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYGSSPFTFG PGTKVDIK
108


 


VK3A27var1 (SEQ ID NO: 20) S31R



EIVLTQSPGT LSLSPGERAT LSCRASQSVS RSYLAWYQQK PGQAPRLLIY GASSRATGIP
60


DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYGSSPFTFG PGTKVDIK
108


 


VK3A27var2 (SEQ ID NO: 21) S32R



EIVLTQSPGT LSLSPGERAT LSCRASQSVS SRYLAWYQQK PGQAPRLLIY GASSRATGIP
60


DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYGSSPFTFG PGTKVDIK
108


 


VK3A27var3 (SEQ ID NO: 22) S32D



EIVLTQSPGT LSLSPGERAT LSCRASQSVS SDYLAWYQQK PGQAPRLLIY GASSRATGIP
60


DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYGSSPFTFG PGTKVDIK
108


 


VK3A27var4 (SEQ ID NO: 23) G93E



EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP
60


DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYESSPFTFG PGTKVDIK
108


 


VK3A27var5 (SEQ ID NO: 24) G93R



EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP
60


DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYRSSPFTFG PGTKVDIK
108


 


VK3A27var6 (SEQ ID NO: 25) S30D, G93E



EIVLTQSPGT LSLSPGERAT LSCRASQSVD SSYLAWYQQK PGQAPRLLIY GASSRATGIP
60


DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYESSPFTFG PGTKVDIK
108


 


VK3A27var7 (SEQ ID NO: 26) S94R



EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP
60


DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYGRSPFTFG PGTKVDIK
108


 


VK3L2gl-JK3 (SEQ ID NO: 27)



EIVMTQSPAT LSVSPGERAT LSCRASQSVS SNLAWYQQKP GQAPRLLIYG ASTRATGIPA
60


RFSGSGSGTE FTLTISSLQS EDFAVYYCQQ YNNWPFTFGP GTKVDIK
107


 


VK1glL8-JK5 (SEQ ID NO: 28)



DIQLTQSPSF LSASVGDRVT ITCRASQGIS SYLAWYQQKP GKAPKLLIYA ASTLQSGVPS
60


RFSGSGSGTE FTLTISSLQP EDFATYYCQQ LNSYPITFGQ GTRLEIK
107


 


VK1GLO12-JK3 (SEQ ID NO: 897)



DIQMTQSPSS LSASVGDRV TITCRASQSI SSYLNWYQQK PGKAPKLLIY AASSLQSGVP
60


SRFSGSGSGT DFTLTISSL QPEDFATYYC QQSYSTPFTF GPGTKVDIKR GTVAAPSVFI
120


FPPSDEQLKS GTASVVCLL NNFYPREAKV QWKVDNALQS GNSQESVTEQ DSKDSTYSLS
180


STLTLSKADY EKHKVYACE VTHQGLSSPV TKSFNRGECA AAGKPIPNPL LGLDST
236









The kits may include ancillary components required for carrying out the method, the nature of such components depending of course on the particular method employed. Useful ancillary components may comprise helper phage, PCR primers, buffers, and/or enzymes of various kinds. Buffers and enzymes are typically used to enable preparation of nucleotide sequences encoding Fv, scFv or Fab fragments derived from rearranged or unrearranged immunoglobulin genes according to the strategies described herein.
Methods of Introducing Diversity
There are many ways of generating DNA that is variable. One way is to use mixed-nucleotide synthesis (MNS). One version of MNS uses equimolar mixtures of nucleotides as shown in Table 5. For example, using NNK codons gives all twenty amino acids and one TAG stop codon. The distribution is 3(R/S/L): 2(A/G/V/T/P): 1(C/D/E/F/H/I/K/M/N/Q/W/Y) (e.g., 3 of each of Arg, Ser, and Leu, and so forth). An alternative, herein termed “wobbling”, uses mixed nucleotides but not in equimolar amounts. For example, if a parental codon were TTC (encoding Phe), we could use a mixture of (0.082 T, 0.06 C, 0.06 A, and 0.06 G) in place of T and a mixture of (0.082 C, 0.06 T, 0.06 A, and 0.06 G) in place of C. This would give TTC or TTT (encoding Phe) 59% of the time and Leu 13%, S/V/I/C/Y  ̃5%, and other amino-acid types less often.
Van den Brulle et al. (Biotechniques 45:340-3 (2008)) describe a method of synthesis of variable DNA in which type IIs restriction enzymes are used to transfer trinucleotides from an anchored hair-pin oligonucleotide (PHONs) to a so called “splinker”. By using mixtures of anchored PHONs and splinkers, one can build libraries in which desired amino-acid types are allowed in designer-determined ratios. Thus, one can direct that one amino-acid type is present, for example 82% of the time and 18 other amino-acid types (all non-parental amino-acid types except Cys) are present at 2% each. Herein, we will refer to such a synthesis as “dobbling” (digital wobbling). In some aspects, dobbling is preferred to wobbling, but wobbling provides useful embodiments, partly because the structure of the genetic code table causes wobbling to make mostly conservative substitutions. Dobbling does offer the possibility to exclude unwanted amino-acid types. In CDRs, unpaired cysteines are known, even in Abs approved as therapeutics, but in some embodiments, one would like to avoid them. In some embodiments, when diversifying a D region that contains a pair of cysteines, the cysteins are not allowed to vary because the disulfide-closed loop is an important structural element and because one does not want unpaired cysteines.
In addition, one can synthesize a DNA molecule that encodes a parental amino-acid sequence and subject that DNA to error-prone PCR using primers that cover the framework regions so that mutations in the framework regions are avoided.







TABLE 5





Standard codes for mixed nucleotides


















N is equimolar A, C, G, T




B is equimolar C, G, T
(not A)



D is equimolar A, G, T
(not C)



H is equimolar A, C, T
(not G)



V is equimolar A, C, G
(not T)



K is equimolar G, T
(Keto)



M is equimolar A, C
(aMino)



R is equimolar A, G
(puRine)



S is equimolar C, G
(Strong)



W is equimolar A, T
(weak)



Y is equimolar C, T
(pYrimidine)

















TABLE 6





Example of mixed nucleotides for wobbling

















e = 0.82 A + 0.06 C + 0.06 G + 0.06 T



q = 0.06 A + 0.82 C + 0.06 G + 0.06 T



j = 0.06 A + 0.06 C + 0.82 G + 0.06 T



z = 0.06 A + 0.06 C + 0.06 G + 0.82 T










EXEMPLIFICATION
The present invention is further illustrated by the following examples which should not be construed as limiting in any way. The contents of all references, pending patent applications and published patents, cited throughout this application are hereby expressly incorporated by reference.
Prophetic Example 1: Libraries With Very Short HC CDR3s
Very short HC CDR3s have been described in the art. Kadirvelraj et al. (2006) Proc. Natl. Acad. Sci. USA 103:8149-54 have described a four amino-acid HC CDR3 sequence in an antibody that binds Streptococcus Type B III Ag (GBS-Ag) but not to Streptococcus pneumoniae capsular Ag. GBS-Ag is sialylated at regular intervals. S. pneumoniae capsular Ag (SPC-Ag) is very similar but lacks the sialic acid groups. Such a short HC CDR3 creates a wide groove into which a carbohydrate could bind, and such Abs are very, very rare in existing antibody libraries. Thus, current libraries do not afford a large variety of potential binders to carbohydrates.
Ab 1B1 is the murine mAb that binds GBS-Ag; Ab 1QFU is the mAb having a known 3D structure and the closest sequence; and 1NSN is an antibody of known 3D structure having a HC CDR3 of length 4. Examination of a 3-23 HC structure gives a distance from Ca of R94 (which ends FR3) to the Ca of the W104 (which begins FR4) of  ̃10 Å. The CDR3 of 1B1 (NWDY (SEQ ID NO:29)) shows that the AAs need not have only small side groups or be mostly of glycine. Three amino acids (AAs) can bridge 10 Å, although PPP might not work. Indeed, we have obtained a few Fabs with CDR3s as short as 3 AAs, but they are very rare.
Although short and very short HC CDR3s have been described, no one hassuggested making an Ab library having many members (e.g., greater than about 50%, about 60%, about 70%, about 80%, about 90%, or about 95% of members) with short HC CDR3s (e.g., HC CDR3s of 3 to 5 amino acids). One approach to building an effective library is to first design amino-acid sequences that could arise from V-J or V-D-J coupling. For CDR3 length 3, 4, or 5, we start with the amino-acid sequences shown in Table 7. For example, Sequence V-3JH1 shows the C-terminal end of 3-23 FR3 (TAVYYCAK (SEQ ID NO:30)) followed by JH1 which has been trimmed from the N-terminal end until three amino-acids before the Trp-Gly that starts FR4. V-3JH2 shows the end of FR3 followed by the trimmed JH2. The sequence following V-3JH6 are constructed by joining FR4 to a trimer taken from a human D segment followed by the FR4 region of a human JH segment. 3D3-3.3.2 would be a trimer from segment D3-3, third reading frame starting at the second amino acid. 5D5-12.2.3 is a pentamer from D5-12 in reading frame 2 starting at amino acid 3. Some of the germ-line D segments contain stop codons, yet they appear in natural antibodies when the stop codons are edited away. Here we assume that the most likely change fro TAA and TAG codons is to Tyr (Y) and that TGA stops are most likely mutated to Trp (W). Table 20 shows the amino-acid sequences of the human D segments; the types of stop codons is indicated by the use of * for TAG, @ for TAA, and $ for TGA. In Table 11 are 266 distinct trimers that can be constructed from human D segments. The TAA and TAG stops have been changed to Tyr shown as “y” (i.e., lowercase). These could also be changed to Ser, Cys, Phe, Gln, Lys, or Glu by single base changes. TAG could be changed by single base changes to Trp as well as Tyr, Gln, Lys, Glu, Ser, and Leu. Table 12 shows the 266 distinct tetramers that can be obtained by trimming human D segments. Table 13 shows the 215 pentamers that can be obtained from trimming human D segments. Table 14 shows the 155 hexamers that can be obtained by trimming human D segments. The libraries to be built have substantial diversity in HC CDR1 and HC CDR2. The sequence diversity of HC CDR3 may be less important than having a short, but acceptable sequence. The diversity of JH segments or fragments (e.g., 3 or more amino acids) of D segments provides sequences that could be built by the human immune system and so are less likely to be immunogenic.
In one embodiment, the trimers, tetramers, and pentamers that contain a Cys are eliminated.
In one embodiment, the trimers, tetramers, and pentamers that contain a Cys or the came from a D fragment containing a stop are eliminated.
The short libraries constructed using the trimers of Table 11, tetramers of Table 12, pentamers of Table 13 have substantial diversity: 266, 266, and 215 respectively. This is to be compared to the number of peptides of these lengths: 8000, 160000, and 3200000 respectively.
V-3D1-1.1.1-JH1 contains the final portion of FR3 followed by three amino acids from D1-1 (RF1), viz. GTT (SEQ ID NO:257). V-3D1-1.2-JH1 uses amino acids 2-4 of D1-1 (RF1) as the parental CDR3. V-3D3-3.3.3-JH2 shows the end of FR3 followed by amino acids 3-5 of D3-3 (RF 3). The invention comprises any amino-acid sequence comprising FR3::(three, four, or five stop-free AAs of a human D segment)::FR4 from a human JH. Fragments of D regions containing unpaired Cys residues are less preferred than those that are free of unpaired Cys residues. In V-5JH3, there is a Tyr shown as ‘y’ because JH3 has only 4 codons before the codons for Trp-Gly that define the beginning of FR4. V-5JH4 has a Ser shown as ‘s’ for the same reason. If wobbling is used, the preferred level of purity is between 0.75 and 0.90. The invention comprises the sequences V-3JH1 through V-3JH6, V-4JH1 through V-4JH6, and V-5JH1 through V-5JH6, and libraries containing the same The invention also comprises the sequences in which the CDR region is replaced by a 3, 4, or 5 amino-acid segment from a human D region, and libraries containing the same. The invention further comprises DNA in which the parental sequence has been mutated in the CDR3 region, and libraries containing the same. A preferred embodiment is one in which the average number of base changes per CDR3 is one, two, or three. The methods of mutagenesis include error-prone PCR, wobbling, and dobbling.







TABLE 7







Amino-acid sequences of parental CDR3s











...FR3-----
CDR3-
FR4--------














Length 3






V-3JH1
TAVYYCAK
FQH
WGQGTLVTVSS
(SEQ ID NO: 31)


 


V-3JH2
TAVYYCAK
FDL
WGRGTLVTVSS
(SEQ ID NO: 32)


 


V-3JH3
TAVYYCAK
FDI
WGQGTMVTVSS
(SEQ ID NO: 33)


 


V-3JH4
TAVYYCAK
FDY
WGQGTLVTVSS
(SEQ ID NO: 34)


 


V-3JH5
TAVYYCAK
FDP
WGQGTLVTVSS
(SEQ ID NO: 35)


 


V-3JH6
TAVYYCAK
MDV
WGQGTTVTVSS
(SEQ ID NO: 36)


 


V-3D1-1.1.1-JH1
TAVYYCAK
GTT
WGQGTLVTVSS
(SEQ ID NO: 37)


 


V-3D1-1.1.2-JH1
TAVYYCAK
TTG
WGQGTLVTVSS
(SEQ ID NO: 38)


 


V-3D3-3.3.3-JH2
TAVYYCAK
IFG
WGRGTLVTVSS
(SEQ ID NO: 39)


 


Length 4






V-4JH1
TAVYYCAK
YFQH
WGQGTLVTVSS
(SEQ ID NO: 40)


 


V-4JH2
TAVYYCAK
YFDL
WGRGTLVTVSS
(SEQ ID NO: 41)


 


V-4JH3
TAVYYCAK
AFDI
WGQGTMVTVSS
(SEQ ID NO: 42)


 


V-4JH4
TAVYYCAK
YFDY
WGQGTLVTVSS
(SEQ ID NO: 43)


 


V-4JH5
TAVYYCAK
WFDP
WGQGTLVTVSS
(SEQ ID NO: 44)


 


V-4JH6
TAVYYCAK
GMDV
WGQGTTVTVSS
(SEQ ID NO: 45)


 


V-4D3-10.1a-JH2
TAVYYCAK
LLWF
WGRGTLVTVSS
(SEQ ID NO: 46)


 


Length 5






V-5JH1
TAVYYCAK
EYFQH
WGQGTLVTVSS
(SEQ ID NO: 47)


 


V-5JH2
TAVYYCAK
WYFDL
WGRGTLVTVSS
(SEQ ID NO: 48)


 


V-5JH3
TAVYYCAK
yAFDI
WGQGTMVTVSS
(SEQ ID NO: 49)


 


V-5JH4
TAVYYCAK
sYFDY
WGQGTLVTVSS
(SEQ ID NO: 50)


 


V-5JH5
TAVYYCAK
NWFDP
WGQGTLVTVSS
(SEQ ID NO: 51)


 


V-5JH6
TAVYYCAK
YGMDV
WGQGTTVTVSS
(SEQ ID NO: 52)


 


V-5D2-8.2a-JH2
TAVYYCAK
DIVLM
WGRGTLVTVSS
(SEQ ID NO: 53)
















TABLE 8





DNA encoding V-5D2-8.2a-JH2 for wobbling















!                                               CDR3.......


!   A  E  D  T  A  V  Y  Y  C  A  K  D  I  V  L  M


  |gct|gag|gaT|aCT|GCA|GtT|taT|taC|tgc|gct aag jez ezq jzz qzz ezj


!


!    W   G   Q   G   T   T   V   T   V   S   S (SEQ ID NO: 54)


    tgg ggc cag ggt act acG GTC ACC gtc tcc agt-3′ (SEQ ID NO: 55)


!                BstEII...









Alternatively, one could synthesize three fragments of DNA that correspond to the region from XbaI to BstEII and having residue 94 being K or R followed by 3, 4, or 5 NNK codons, followed by WG . . . of FR4. The allowed variation is 203+204+205=3,368,000. After amplification, these DNA molecules would be mixed in the ratio 1:10:100 (so that shorter sequences are relatively oversampled) and cloned into the phagemid encoding the kappa library with HC CDR1/2 diversity. A library of 1×109 would give significant diversity and will allow isolation of antibodies that bind to targets that have small to medium protrusions. For example, various carbohydrates, loops of proteins that are not well ordered (such as GPCRs) may benefit from a groove in the antibody created by having a very short HC CDR3. We can also build a lambda library. The ratio of AA sequences is 1:20:400, and it may be important to sample the shorter sequences more densely. Getting a big, wide gulley in the Ab may require exactly one 3 AA CDR3, but with a 4 AA CDR3, one probably has more leeway and with 5 AAs, even more leeway. In this Example, we use the JH6 version of FR4 from the WG motif onward.
We can select from our current kappa library a collection of, for example, 25 kappa light chains that are a) germline in the framework regions, b) show suitable diversity in CDRs, and c) are of types that produce well and pair well with 3-23. These LCs will be made in E. coli from a vector that carries KanR and no phage packaging signal. We would then build our HC library in a phage vector that has no LC. HC and LC will be crossed by infecting the LC producing cells with the HC phage. HC phage that are selected can be combined with the LC of the cell that produces ELISA phage or the HCs can be cloned into pMID21 that have the whole LC diversity. Alternatively, the selected HC can be moved into pHCSK85 and used with ROLIC to combine with all the LCs of our collection. Lambda LCs could also be used. Thus, a library of 1×109 HC in phage can be expanded into a Fab library of 1.2×1011 (1.×109×117). If we combined 1×107 CDR1-2s with 106 HC CDR3s, we could make a library of 5×107 in which each CDR3 is coupled with 50 CDR1-2s. A library of 5×107 HCs in phage could give results similar to an old-style library of 6×109.







TABLE 1





Designs of very short exemplary HC CDR3s















C3XXX


!  scab DNA   S  R  D  N  S  K  N  T  L  Y  L  Q  M  N  S


5′-ttc|act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|aac|agC-


!              XbaI...


!


!                                                      CDR3.......


!  L  R  A  E  D  T  A  V  Y  Y  C  A  K|R any any any  W  G


  |TTA|AGg|gct|gag|gaT|aCT|GCA|GtT|taT|taC|tgc|gct aRg nnk nnk nnk tgg ggc-


!


!   Q   G   T   T   V   T   V   S   S (SEQ ID NO: 56)


   cag ggt act acG GTC ACC gtc tcc agt-3′ (SEQ ID NO: 57)


!                BstEII...


!


(C3XXX)5′-T|GCA|GtT|taT|taC|tgc|gct aRg nnk nnk nnk tgg ggc cag ggt act ac-3′


(SEQ ID NO: 58)


(ON_5) 5′-AcTggAgAcggTgAccgTAgTAcccTggccccA-3′ ! 33 bases (SEQ ID NO: 58)


(ON_5 is reverse complement of 5′-tgg ggc cag ggt act acG GTC ACC gtc tcc


agt-3′ (SEQ ID NO: 59))


! Use ON-1 and ON-3 shown below


!-----------------------------------------------


!


C3X4


!  scab DNA   S  R  D  N  S  K  N  T  L  Y  L  Q  M  N  S


5′-ttc|act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|aac|agC-


!              XbaI...


!


!                                                      CDR3...........


!   L  R  A  E  D  T  A  V  Y  Y  C  A  K|R any any any any  W


  |TTA|AGg|gct|gag|gaT|aCT|GCA|GtT|taT|taC|tgc|gct aRg nnk nnk nnk nnk tgg-


!


!   G   Q   G   T   T   V   T   V   S   S (SEQ ID NO: 60)


   ggc cag ggt act acG GTC ACC gtc tcc agt-3′ (SEQ ID NO: 61)


!                    BstEII...


!


(C3X4)5′-GCA|GtT|taT|taC|tgc|gct aRg nnk nnk nnk nnk tgg-


           ggc cag ggt act ac-3′ (SEQ ID NO: 62)


! Use ON-1, ON-3, and ON-5


!----------------------------------------------------------


C3X5


!  scab DNA   S  R  D  N  S  K  N  T  L  Y  L  Q  M  N  S


5′-ttc|act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|aac|agC-


!              XbaI...


!


!                                                      CDR3...............


!   L  R  A  E  D  T  A  V  Y  Y  C  A  K|R any any any any any


  |TTA|AGg|gct|gag|gaT|aCT|GCA|GtT|taT|taC|tgc|gct aRg nnk nnk nnk nnk nnk-


!


!   W   G   Q   G   T   T   V   T   V   S   S (SEQ ID NO: 63)


   tgg ggc cag ggt act acG GTC ACC gtc tcc agt-3′ (SEQ ID NO: 64)


!                        BstEII...


(C3X5)5′-GCA|GtT|taT|taC|tgc|gct aRg nnk nnk nnk nnk nnk tgg-


           ggc cag ggt act ac-3′ (SEQ ID NO: 65)


!-------------------------------------------------





aRg encodes K or R






Alternatively, the current HC diversity can be cloned into DY3F87HC and the CDR3 diversity described above is cloned into that diversity as XbaI-BstEII fragments. A library of, for example, 25 LC are cloned into pLCSK23 and used to create a cell line in TG1 E. coli. These cells are infected with the DY3F87HC phage which harbor the novel HC CDR3 (and CDR1-2) diversity. The phage obtained from this infection are selected for binding to a desired target. After two to four rounds of selection, the selected HCs are transferred to pHCSK22 and used to create a cell line which can be used with ROLIC to combine the selected HC with all the LCs in the ROLIC LC library. In this way, a library of 1. E 9 can be give Abs that normally would require construction of a library of 1. E 16 (assuming a LC diversity of 1. E 7).
Prophetic Example 2: Libraries with Very Long HC CDR3s
Sidhu et al. (J Mol Biol. 2004 338:299-310. and US application 20050119455A1) report high-affinity Abs selected from a library in which only Y and S were allowed in the CDRs which were limited in length to 20 amino acids. It may be possible to generate high affinity Abs from a library that has HC CDR3s with one or more of the following forms of diversity: a) several (but not all) sites allowing Y or S, b) including 4-6 NNK codons, c) introducing D segments (with or without diversification in the D), and/or d) using error-prone PCR. We have already sampled the Ab space in which HC CDR3 is in the range  ̃8 to  ̃22 with a median length of 13. Thus, libraries in which HC CDR3 is either  ̃23 AAs or  ̃35 AAs are possible and may have advantages with certain types of targets. For example, GPCRs are integral membrane proteins with seven helical segments transversing the lipid bilayer of the call that are thought to have multiple states. An antibody having a very long HC CDR3 could form a protuberance that fits into the channel formed by the seven strands. Finding Abs that bind GPCRs has been difficult and intentionally building libraries in which all the members have very long HC CDR3s may ameliorate this problem. The lengths may be made somewhat variable, say 23, 24, or 25 in one library and 33, 34, or 35 in a second.
Below are a number of representative designs. The CDR3 have been broken up and diversity generated that lets the various parts have differing relationships depending on the value of X. A full-length JH1 has been used, and in some designs diversity allowed diversity in the CDR3 part of JH1. Other JHs could be used. In the designs, the D segments are either rich in Y or have an S-rich disulfide loop. The amino-acid sequences of human D segments are shown in Table 3. The places where the D region has either S or Y or allowed other combinations have in particular been varied. Table 4 shows the amino-acid sequences of human J regions.
Each of the libraries could be built in at least four ways: 1) DNA encoding a particular amino acid sequence is first synthesized and subjected to error-prone PCR, 2) the library can be synthesized by wobbling or with mixtures of nucleotides, 3) the library can be built using dobbling, and 4) routes (2) or (3) could be followed by error-prone PCR. As an example of route (1), in Design 12, DNA encoding SEQ ID NO:908 could be synthesized, as shown in SEQ ID NO:911. This DNA could be subjected to error-prone PCR using the primers shown in SEQ ID NO:909 and SEQ ID NO:910. Because these primers cover the framework regions, the errors will occur only in the CDR3.
A library of HCs with CDR3 with length 23 of, for example, 2×109 members and a second library with HC CDR3s of length  ̃35 also having 2×109 members could be built. Alternatively, the DNA could be mixed to build one library of 4×109.







TABLE 4





Human JH amino-acid sequences




















    H3





  ------





   CDR3





 --------





    100       110





      |         |




JH1
---AEYFQHWGQGTLVTVSS
(SEQ ID NO: 66)



JH2
---YWYFDLWGRGTLVTVSS
(SEQ ID NO: 67)



JH3
-----AFDIWGQGTMVTVSS
(SEQ ID NO: 2)



JH4
-----YFDYWGQGTLVTVSS
(SEQ ID NO: 1)



JH5
----NWFDPWGQGTLVTVSS
(SEQ ID NO: 68)



JH6
YYYYYGMDVWGQGTTVTVSS
(SEQ ID NO: 3)









In each of the following designs, the amino-acid sequence begins with YYCA(K/R) which is the end of FR3. FR4 starts with WG and is shown bold.
Design 1








XX::D2-2.2::XX::JH1










               1    1    2  2




  FR3 1   5    0    5    0  3FR4



YYCAK DYGYCSSTSCYTKLYSYAEYFQHWGQGTLVTVSS
(SEQ ID NO: 898)


YYCAK XXGYCSXXSCYTXXYSYAEYFQHWGQGTLVTVSS
(SEQ ID NO: 69)


    R   GYCSSTSCYT     AEYFQHWGQGTLVTVSS (JH1)



       (SEQ ID NO: 70)   (SEQ ID NO: 66)



           1  1              1     1



    9 9    0  0              0     1



    4 5    0  3abcdefghijklmn4     0



 


Amino-acid diversity    = 1.28 E 8



 


DNA diversity           = 2.15 E 9



 


Stop-free               = 83%



 


Gratuitous Cys-free     = 83%



 


Free of stop and Cys    = 68%







Design 1(C23D222) has 94 being R or K, then 2 Xs, D2-2 in second reading frame with two Xs in the loop, followed by two Xs, and JH1. D2-2 2nd reading frame has a disulfide-closed loop into which diversity at two points has been introduced. This CDR3 is 23 long. Using primers that include DNA up to . . . YYCA and from WGQG . . . , error-prone PCR on the CDR3 could be performed before amplifying out to XbaI and BstEII for cloning into the library of kappa LC and HC CDR1/2. Thus, the AAs that are shown as fixed will be allowed to vary some. The AAs that are part of the PCR overlap region will be reinforced by the final non-error prone PCR. Error-prone PCR is not a necessary part of the design.









C23D222JH1










!  scab DNA     S   R   D   N   S   K   N   T   L   Y   L   Q   M   N   S
(SEQ ID NO: 71)



5′-ttc|act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|aac|agC-
(SEQ ID NO: 72)


!              XbaI...



!



!   L   R   A   E   D   T   A   V   Y   Y   C   A  K|R



  |TTA|AGg|gct|gag|gaT|aCT|GCA|GtT|taT|taC|tgc|gct aRg-



!



! CDR3----------------------------------------------------------------



!  X   X  D2-2  RF2.............................   X   X              JH1..



!  any any  G   Y   C   S  any any  S   C   Y   T  any any  Y   S   Y   A



   nnk nnk ggt tat tgt tcc nnk nnk tct tgc tat act nnk nnk tat tcc tac gct-



!



!  CDR3---------------



!   E   Y   F   Q   H



   gaa tat ttc cag cac-



!



!   W   G   Q   G   T   L   V   T   V   S   S



   tgg ggc cag ggt act ctG GTC ACC gtc tcc agt-3′



!                        BstEII...



(ON_C23D222) 5′-GCA|GtT|taT|taC|tgc|gct aRg nnk nnk ggt tat tgt tcc nnk-
(SEQ ID NO: 73)


     nnk tct tgc tat act nnk nnk tat tcc tac gct gaa tat ttc cag cac-



     tgg ggc cag ggt act ct-3′ ! 107 bases



 


(ON_1) 5′-GCA|GtT|taT|taC|tgc|gct-3′
(SEQ ID NO: 74)


 


(ON_2) 5′-AgAgTAcccTggccccAgAcgTccATAccgTAATAgT-3′ ! 37 bases
(SEQ ID NO: 75)


(ON_2 is reverse complement of 5′-ac tat tac ggt atg gac gtc tgg
(SEQ ID NO: 76)


ggc cag ggt act ct-3′)



 


(ON_3) 5′-ttc|act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|-
(SEQ ID NO: 77)


          aac|agC|TTA|AGg|gct|gag|gaT|aCT|GCA|GtT|taT|taC|tgc|gct-3′



 


(ON_4) 5′-AcTggAgAcggTgAccAgAgTAcccTggccccA-3′ ! 33 bases
(SEQ ID NO: 78)


(5′-tgg ggc cag ggt act ctG GTC ACC gtc tcc agt-3′ [RC] 
(SEQ ID NO: 79))






Design 2










               1    1    2  2 




      1   5    0    5    0  3



YYCAK GSYYYGSGSYYNMDSYYAEYFQHWGQGTLVTVSS
(SEQ ID NO: 899)


YYCAK XXYYYGXGSXYNXXSYYAEYFQHWGQGTLVTVSS
(SEQ ID NO: 80)


    R   YYYGSGSYYN     AEYFQHWGQGTLVTVSS (JH1)



       (SEQ ID NO: 81) (SEQ ID NO: 66)



 


Amino-acid diversity   = 1.28 E 8



 


DNA diversity          = 2.15 E 9



 


Stop-free              = 83%



 


Gratuitous Cys-free    = 83%



 


Free of stop and Cys   = 68%







Design 2 (C23D310) has 94 as R or K, two Xs, D3-10 (RF2) with 5th and 8th residues changed to X, 2 Xs, SYY, and JH1. The CDR3 is 23 AA long and could be further diversified by use of error-prone PCR.









C23D310JH1










!  scab DNA     S   R   D   N   S   K   N   T   L   Y   L   Q   M   N   S
(SEQ ID NO: 82)



5′-ttc|act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|aac|agC-
(SEQ ID NO: 83)


!              XbaI...



!



!    L   R   A   E   D   T   A   V   Y   Y   C   A  K|R



   |TTA|AGg|gct|gag|gaT|aCT|GCA|GtT|taT|taC|tgc|gct aRg-



!



!  CDR3-------------------------------------------------------------------



!



!  any any  Y   Y   Y   G  any  G   S  any  Y   N  any any  S   Y   Y



   nnk nnk tac tac tat ggt nnk ggc tct nnk tac aat nnk nnk tct tat tac



!



!   A   E   Y   F   Q   H



   gct gag tac ttt caa cat



!



!   JH1......................................



!   W   G   Q   G   T   L   V   T   V   S   S



   tgg ggc cag ggt act ctG GTC ACC gtc tcc agt-3′



!                        BstEII...



 


(C23D310) 5′-GCA|GtT|taT|taC|tgc|gct aRg nnk nnk tac tac tat ggt nnk ggc-
(SEQ ID NO: 84)


 tct nnk tac aat nnk nnk tct tat tac gct gag tac ttt caa cat tgg ggc cag-



 ggt act ct-3′



 


ON_1, ON_2, ON_3, and ON_4 as above.







Design 3










               1    1    2  2




      1   5    0    5    0  3



YYCAK EYYYYGSGSYYNSTTTSAEYFQHWGQGTLVTVSS
(SEQ ID NO: 900)


YYCAK XZYZZGZGZXYNZXZYZAXZFQHWGQGTLVTVSS
(SEQ ID NO: 84)


    R   YYYGSGSYYN     AEYFQHWGQGTLVTVSS (JH1)



       (SEQ ID NO: 81) (SEQ ID NO: 66)



 


Amino-acid diversity   = 1.64 E 8



 


DNA diversity          = 1.07 E 9



 


Stop-free              = 88%



 


Gratuitous Cys-free    = 88%



 


Free of stop and Cys   = 77%







Design 3 (C23D310B) has 94 as R or K, XZ, D3-10 (RF2) with 2nd, 3rd, 5th, and 7th as Z(Y|S) and 8th residue changed to X, ZXZYZ (SEQ ID NO:936), and JH1 (with the E changed to X). Z is either Y or S. The CDR3 is 23 AA long and could be further diversified by use of error-prone PCR.










               A   V   Y   Y   C   A  R|K any Y|S  Y  Y|S Y|S  G  Y|S
(SEQ ID NO: 85)



(C23D310b) 5′-GCA|GtT|taT|taC|tgc|gct aRg nnk tmc tac tmc tmt ggt tmc ggc-
(SEQ ID NO: 86)


 


  Y|S any  Y   N  Y|S any Y|S  Y  Y|S  A  any Y|S  F   Q   H   W   G   Q



  tmt nnk tac aat tmt nnk tmc tat tmc gct nnk tmc ttt caa cat tgg ggc cag-



 


   G   T   L



  ggt act ct-3′



 


ON_1, ON_2, ON_3, and ON_4 as above.







Design 4










               1    1    2  2 2    3    3




      1   5    0    5    0  3 5    0    5



YYCAK YYSFSYYPYYYDSSGYYYAYYSDYSYSYYAEYFQHWGQGTLVTVSS
(SEQ ID NO: 901)


YYCAK YYSXSYYXYZYDSZGYZYXYYSXYZYZZZAZZFQHWGQGTLVTVSS
(SEQ ID NO: 87)


    R         YYYDSSGYYY           AEYFQHWGQGTLVTVSS (JH1)



              (SEQ ID NO: 88)         (SEQ ID NO: 66)



           1  1                          1     1



    9 9    0  0                          0     1



    4 5    0  3abcdefghijklmnopqrstuvwxya4     0



 


Amino-acid diversity       = 1.64 E 8



 


DNA diversity              = 1.07 E 9



 


Stop-free                  = 88%



 


Gratuitous Cys-free        = 88%



 


Free of stop and Cys       = 77%







Design 4 has CDR3 of length 35. Residue 94 can be K or R, then YYS::X::SYY::X::D3-22(2nd RF with one S as X and 3 Zs)::X::YYS::XYZ::YZZZ (SEQ ID NO:937)::JH1 with 2 Zs). Error-prone PCR could be used to add more diversity.









C35D322JH1










!  scab DNA     S   R   D   N   S   K   N   T   L   Y   L   Q   M   N   S
(SEQ ID NO: 89)



5′-ttc|act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|aac|agC-
(SEQ ID NO: 90)


!              XbaI...



!



!   L   R   A   E   D   T   A   V   Y   Y   C   A  K|R



  |TTA|AGg|gct|gag|gaT|aCT|GCA|GtT|taT|taC|tgc|gct aRg-



!



!  CDR3-------------------------------------------------------------------



!



!   Y   Y   S  any  S   Y   Y  any  Y  Y|S  Y   D   S  Y|S  G   Y  Y|S  Y



   tac tat tcc nnk tct tac tat nnk tat tmt tac gat agt tmt ggt tac tmc tat



!



   any  Y   Y   S  any  Y  Y|S  Y  Y|S Y|S Y|S  A  Y|S Y|S  F   Q   H



   nnk tac tat agc nnk tat tmc tac tmc tmt tmc gct tmt tmc ttc caa cac



!



!   W   G   Q   G   T   L   V   T   V   S   S



   tgg ggc cag ggt act ctG GTC ACC gtc tcc agt-3′



!                        BstEII...



 


(c35d322B) 5′-GCA|GtT|taT|taC|tgc|gct aRg tac tat tcc nnk tct tac tat nnk-
(SEQ ID NO: 91)


  tat tmt tac gat agt tmt ggt tac tmc tat nnk tac tat agc nnk tat tmc tac-



  tmc tmt tmc gct tmt tmc ttc caa cac tgg ggc cag ggt act ct-3′



 


ON_1, ON_2, ON_3, and ON_4 as above.







Design 5










               1    1    2  2




      1   5    0    5    0  3



YYCAK SSGYCSSTSCYTNPYYYAEYFQHWGQGTLVTVSS
(SEQ ID NO: 902)


YYCAK ZZGZCZZXZCZTXXYZYXZYFQHWGQGTLVTVSS
(SEQ ID NO: 92)


    R   GYCSSTSCYT     AEYFQHWGQGTLVTVSS (JH1)



       (SEQ ID NO: 70) (SEQ ID NO: 66)



 


Amino-acid diversity     = 1.64 E 8



 


DNA diversity            = 1.07 E 9



 


Stop-free                = 88%



 


Gratuitous Cys-free      = 88%



 


Free of stop and Cys     = 77%







Design 5(C23D222b) is like design 1 but uses many Z(Y or S) variable codons. This CDR3 is 23 long.









C23D222JH1b










!  scab DNA     S   R   D   N   S   K   N   T   L   Y   L   Q   M   N   S
(SEQ ID NO: 93)



5′-ttc|act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|aac|agC-
(SEQ ID NO: 94)


!              XbaI...



!



!   L   R   A   E   D   T   A   V   Y   Y   C   A  K|R



  |TTA|AGg|gct|gag|gaT|aCT|GCA|GtT|taT|taC|tgc|gct aRg-



!



!  CDR3-------------------------------------------------------------------



!  Y|S Y|S  G  Y|S  C  Y|S Y|S any Y|S  C  Y|S  T  any any  Y  Y|S  Y  any



   tmc tmt ggt tmt tgc tmc tmt nnk tmt tgt tmc acc nnk nnk tat tmt tac nnk



!



!  Y|S  Y   F   Q   H



   tmt tat ttc cag cac



!



!   W   G   Q   G   T   L   V   T   V   S   S



   tgg ggc cag ggt act ctG GTC ACC gtc tcc agt-3′



!                        BstEII...



 


(C23D222JH1b) 5′-GCA|GtT|taT|taC|tgc|gct aRg tmc tmt ggt tmt tgc tmc tmt-
(SEQ ID NO: 95)


 nnk tmt tgt tmc acc nnk nnk tat tmt tac nnk tmt tat ttc cag cac tgg ggc-



 cag ggt act ct-3′







Design 6










               1    1    2  2 2    3    3




      1   5    0    5    0  3 5    0    5



YYCAK SYQYYGYCSSTSCYTYYSYWSYSSYYSYYAEYFQHWGQGTLVTVSS
(SEQ ID NO: 903)


YYCAK ZYXZYGZCZZXSCZTYZSZXZYSZYZSZYAEZFQHWGQGTLVTVSS
(SEQ ID NO: 96)


    R      GYCSSTSCYT D2-2.2       AEYFQHWGQGTLVTVSS (JH1)



            (SEQ ID NO: 70)          (SEQ ID NO: 66)
 


 


Amino-acid diversity       = 2.00 E 8



 


DNA diversity              = 5.37 E 8



 


Stop-free                  = 91%



 


Gratuitous Cys-free        = 91%



 


Free of stop and Cys       = 83%



 


C35D222JH1



!



!  scab DNA     S   R   D   N   S   K   N   T   L   Y   L   Q   M   N   S
(SEQ ID NO: 97)


5′-ttc|act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|aac|agC-
(SEQ ID NO: 98)


!              XbaI...



!



!   L   R   A   E   D   T   A   V   Y   Y   C   A  K|R



  |TTA|AGg|gct|gag|gaT|aCT|GCA|GtT|taT|taC|tgc|gct aRg-



!



!  CDR3-------------------------------------------------------------------



!  Y|S  Y  any Y|S  Y   G  Y|S  C  Y|S Y|S any  S   C  Y|S  T   Y  Y|S  S



   tmt tac nnk tmc tac ggc tMt tgc tmt tmc nnk tCt tgt tmc acc tat tmt tcc



!



!  Y|S any Y|S  Y   S  any  Y  Y|S  S  Y|S  Y   A   E   Y   F   Q   H



   tmt nnk tmc tat tct nnk tac tmc agt tmt tat gct gag tat ttc cag cac



!



!   W   G   Q   G   T   L   V   T   V   S   S



   tgg ggc cag ggt act ctG GTC ACC gtc tcc agt-3′



!                        BstEII...



 


(C35D222JH1)5′-GCA|GtT|taT|taC|tgc|gct aRg tmt tac nnk tmc tac ggc tat-tgc tmt tmc
(SEQ ID NO: 99)


nnk tmt tgt tmc acc tat tmt tcc tmt nnk tmc tat tct nnk tac-



tmc agt tmt tat gct gag tat ttc cag cac tgg ggc cag ggt act ct-3′







Design 7










               1    1    2  2 2    3    3




      1   5    0    5    0  3 5    0    5



YYCAK YYSYYGYCSSTSCYTYSSSPSYSYYSSYYAEYFQHWGQGTLVTVSS
(SEQ ID NO: 904)


YYCAK ZYZZYGZCZZXZCZTYZSZXZYSZYZSZYAψZJQBWGQGTLVTVSS
(SEQ ID NO: 100)


    R      GYCSSTSCYT D2-2.2       AEYFQHWGQGTLVTVSS (JH1)



            (SEQ ID NO: 70)          (SEQ ID NO: 66)



 


(J = FSY, B = YHND, ψ = EKQ)



 


Amino-acid diversity       = 9.44 E 8



 


DNA diversity              = 2.42 E 9



 


Stop-free                  = 93%



 


Gratuitous Cys-free        = 93%



 


Free of stop and Cys       = 88%



 


C35D222JH1B



!



!  scab DNA     S   R   D   N   S   K   N   T   L   Y   L   Q   M   N   S
(SEQ ID NO: 101)


5′-ttc|act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|aac|agC-
(SEQ ID NO: 102)


!              XbaI...



!



!   L   R   A   E   D   T   A   V   Y   Y   C   A  K|R



  |TTA|AGg|gct|gag|gaT|aCT|GCA|GtT|taT|taC|tgc|gct aRg-



!



!   CDR3----------------------------------------------------------------



!   Y|S  Y  Y|S Y|S  Y   G  Y|S  C  Y|S Y|S any Y|S  C  Y|S  T   Y  Y|S  S



    tmt tac tmc tmc tac ggc tMt tgc tmt tmc nnk tmt tgt tmc acc tat tmt tcc



!



!                                                    Q       Y      N|D



!   Y|S any Y|S  Y   S  Y|S  Y  Y|S  S  Y|S  Y   A  E|K Y|S F|S  Q  H|Y



    tmt nnk tmc tat tct tmt tac tmc agt tmt tat gct Vag tmt tHc cag Nac



!



!    W   G   Q   G   T   L   V   T   V   S   S



    tgg ggc cag ggt act ctG GTC ACC gtc tcc agt-3′



!                         BstEII...







Design 8










               1    1    2  2 2    3    3




      1   5    0    5    0  3 5    0    5



YYCAK SPSYYDYVWGSYRYTSSYTYYSYSYSSYAEYFQHWGQGTLVTVSS
(SEQ ID NO: 905)


YYCAK ZXZYZBZVWGZZRZTZSZXZYZZZYZSZAψZFQHWGQGTLVTVSS
(SEQ ID NO: 103)


    R    YYDYVWGSYRYT D3-16.2     AEYFQHWGQGTLVTVSS (JH1)



            (SEQ ID NO: 104)          (SEQ ID NO: 66)



 


(J = FSY, B = YHND, ψ = EKQ)



 


Amino-acid diversity       = 9.44 E 8



 


DNA diversity              = 1.61 E 9



 


Stop-free                  = 93%



 


Gratuitous Cys-free        = 93%



 


Free of stop and Cys       = 88%



 


C34D316JH1A



!



!  scab DNA     S   R   D   N   S   K   N   T   L   Y   L   Q   M   N   S
(SEQ ID NO: 105)


5′-ttc|act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|aac|agC-
(SEQ ID NO: 106)


!              XbaI...



!



!   L   R   A   E   D   T   A   V   Y   Y   C   A  K|R



  |TTA|AGg|gct|gag|gaT|aCT|GCA|GtT|taT|taC|tgc|gct aRg-



!



!  CDR3----------------------------------------------------------------



!                      N|D



!  Y|S any Y|S  Y  Y|S Y|H Y|S  V   W   G  Y|S Y|S  R  Y|S  T  Y|S



   tmt nnk tmc tac tmt Nat tmt gtt tgg ggt tmt tmc cgt tmt act tmt



!



!   S  Y|S any Y|S  Y  Y|S Y|S Y|S  Y  Y|S  S  Y|S



   agt tmc nnk tmt tac tmc tmt tmc tat tmc agt tmt



!



!       Q



!   A  E|K Y|S  F   Q   H



   GCT vag tmc ttc cag cat



!



!   W   G   Q   G   T   L   V   T   V   S   S



   tgg ggc cag ggt act ctG GTC ACC gtc tcc agt-3′



!                        BstEII...



 


(C34D316JH1A) 5′-GCA|GtT|taT|taC|tgc|gct aRg tmt nnk tmc tac tmt Nat tmt-
(SEQ ID NO: 107)


 gtt tgg ggt tmt tmc cgt tmt act tmt agt tmc nnk tmt tac tmc tmt tmc tat-



 tmc agt tmt GCT vag tmc ttc cag cat tgg ggc cag ggt act ct-3′







Design 9

Design 9 is like 8 except the D segment is moved to the right









               1    1    2  2 2    3    3



       1  5    0    5    0  3 5    0    5









YYCAK YAYSSESYYSSYYDYVWGSYRYTYSSYYAEYFQHWGQGTLVTVSS
(SEQ ID NO: 906)



YYCAK ZXZZZXZYZZZYZBZVWGZZRZTYZSZYAψZFQHWGQGTLVTVSS
(SEQ ID NO: 108)


    R  D3-16.2   YYDYVWGSYRYT     AEYFQHWGQGTLVTVSS 
(JH1)








                (SEQ ID NO: 104)  (SEQ ID NO: 66)



 


(J = FSY, B = YHND, ψ = EKQ)


 









Amino-acid diversity =
1.31 E 8



 


DNA diversity =                          
5.37 E 8


 


Stop-free =
91%


 


Gratuitous Cys-free =
91%


 


Free of stop and Cys =
83%


 








C34D316JH1B



!


!  scab DNA     S   R   D   N   S   K   N   T   L   Y   L   Q   M   N   S


5′-ttc|act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|aac|agC-


!              XbaI . . .


!


!   L   R   A   E   D   T   A   V   Y   Y   C   A  K|R


  |TTA|AGg|gct|gag|gaT|aCT|GCA|GtT|taT|taC|tgc|gct aRg -


!


!  CDR3-------------------------------------------------------------------


!  Y|S any Y|S Y|S Y|S any Y|S  Y  Y|S Y|S Y|S


   tmt nnk tmc tmt tmc nnk tmt tac tmc tmt tmc


!


!          N|D


!   Y  Y|S Y|H Y|S  V   W   G  Y|S Y|S  R  Y|S  T


   tac tmt Nat tmt gtt tgg ggt tmt tmc cgt tmt act


!


!   Y  Y|S  S  Y|S  Y


   tat tmc agt tmt tac


!


!       Q


!   A  E|K Y|S  F   Q   H


   GCT vag tmc ttc cag cat


!









!   W   G   Q   G   T   L   V   T   V   S   S
(SEQ ID NO: 109)



   tgg ggc cag ggt act ctG GTC ACC gtc tcc agt-3′
(SEQ ID NO: 110)








!                        BstEII . . .



 


(C35D316JH1B)


!


(SEQ ID NO: 111)



5′-GCA|GtT|taT|taC|tgc|gct aRg tmt nnk tmc tmt tmc nnk tmt tac tmc tmt tmc



 


tac tmt Nat tmt gtt tgg ggt tmt tmc cgt tmt act tat tmc agt tmt tac GCT vag


 


tmc ttc cag cat tgg ggc cag ggt act ct-3′ 






Design 10









               1    1    2   2



      1   5    0    5    0   4









YYCAK GSSYYYGSGSYYNSEYYSAEYFQHWGQGTLVTVSS
(SEQ ID NO: 907)



YYCAK XZZYZZGZGZXYNZXZYZAXZFQHWGQGTLVTVSS
(SEQ ID NO: 112)


    R    YYYGSGSYYN     AEYFQHWGQGTLVTVSS 
(JH1)








        (SEQ ID NO: 81)   (SEQ ID NO: 66)







Design 10 (C24D310B) is like Design 3, but the CDR3 is of length 24. Design 10 has 94 as R or K, XZZ, D3-10 (RF2) with 2nd, 3rd, 5th, and 7th as Z(Y|S) and 8th residue changed to X, ZXZYZ (SEQ ID NO:938), and JH1 (with the E changed to X). Z is either Y or S. The CDR3 is 24 AA long and could be further diversified by use of error-prone PCR.









(SEQ ID NO: 113)



(C24D310b) 5′-GCA|GtT|taT|taC|tgc|gct aRg nnk tmc tmc tac tmc tmt ggt tmc-



ggc tmt nnk tac aat tmt nnk tmc tat tmc gct nnk tmc ttt caa cat tgg ggc-


cag ggt act ct-3′ 


ON_1, ON_2, ON_3, and ON_4 as above.






Design 11









               1    1    2   2



      1   5    0    5    0   5









YYCAR SSRSGYCTNGVCYTSKSYWYFDLWGRGTLVTVSS
(SEQ ID NO: 907)



YYCAR ZZXZGZC32GVCZ3ZXZZ4Z12LWGRGTLVTVSS
(SEQ ID NO: 114)


    K     GYCTNGVCYT   YWYFDLWGRGTLVTVSS 
D2-8.2 JH2








         (SEQ ID NO: 115)   (SEQ ID NO: 67)



(1 = FYS(THT), 2 = YHND(NAT), 3 = ITKR(ANA), 4 = LSW(TBG))


 


(SEQ ID NO: 116)



(C24D282) 5′-GCA|GtT|taT|taC|tgc|gct aRg tmc tmt nnk tmt ggt tmc tgt ana-



nat ggt gtc tgc tmt ana tmc nnk tmt tmt tbg tmt tht nat ctg tgg ggc-


cag ggt act ct-3′ 


 


(SEQ ID NO: 117)



(C24D282.1) 5′-GCA|GtT|taT|taC|tgc|gct aRg tmc tmt nnk tmc ggt tmc tgc ana-



nat ggc gtc tgc tmt ana tmc nnk tmt tmt tbg tmt tht nat ctg tgg ggc-


cag ggt act ct-3′ 


 


(SEQ ID NO: 118)



(C24D282.1) 5′-GCA|GtT|taT|taC|tgc|gct aRg tmc tmt nnk tmc ggt tmc tgc ana-



nat ggc gtc tgc t-3′  


(needs R, M, N, K)


(SEQ ID NO: 119)



(C24D282.2) 5′-Ag AgT Acc cTg gcc ccA cAg ATN ADA AKA cVA AKA AKA MNN gKA TNT AKA gcA



gAc gcc ATN TNT gcA gKA Acc g-3′  


! 75 bases


(SEQ ID NO: 120)



(5′-c ggt tmc tgc ana-



nat ggc gtc tgc tmt ana tmc nnk tmt tmt tbg tmt tht nat ctg tgg ggc-


cag ggt act ct-3′ [RC]  


(needs N, M, K, B, H))






Design 12









               1    1    2    2    3    3



      1   5    0    5    0    5    0    5









YYCAR SSYYSYGYCTNGVCYTYSYSYYSYSYSYWYFDLWGRGTLVTVSS
(SEQ ID NO: 908)



YYCAR ZZZZZZGZC32GVCZ3ZZZZYZZYZYZZ4Z12LWGRGTLVTVSS
(SEQ ID NO: 121)


    K       GYCTNGVCYT           YWYFDLWGRGTLVTVSS 
D2-8.2 JH2








           (SEQ ID NO: 115)      (SEQ ID NO: 67)



(1 = FYS, 2 = YHND, 3 = ITKR, 4 = LSW, Z = YS)


 









(C33D282TP) 5′-GCA|GtT|taT|taC|tgc|gct-3′
(SEQ ID NO: 909)



(C33D282BP) 5′-ag agt acc ctg gcc cca-3′
(SEQ ID NO: 910)


 








(SEQ ID NO: 122)



(C33D282) 5′-GCA|GtT|taT|taC|tgc|gct aRg tmt tmc tmc tmt tmc tmc ggt-



tmt tgt ana nat ggc gtg tgc tmt ana tmc tmc tmc tmt tat tmt tmc tat tmt-


tac tmt tmc tbg tmc tht nat ctg tgg ggc cag ggt act ct-3′


 


(SEQ ID NO: 911)



(C33D282F) 5′-GCA|GtT|taT|taC|tgc|gct agg tct tcc tac tat tcc tac ggt-



tat tgt aca aat ggc gtg tgc tat aca tac tcc tac tct tat tat tcc tat tct-


tac tct tac tgg tac ttt gat ctg tgg ggc cag ggt act ct-3′






Design 13

Design 13 places a germ-line D segment in the middle of a sea of Zs so that one can make two pieces of DNA that overlap throughout the constant region. HC CDR3 is 34 long and diversity is 223 ̃8×106.









               1    1    2    2    3    3



      1   5    0    5    0    5    0    5









YYCAR SSSYYSYYSSGYCTNGVCYTYSSYYSSYYWYFDLWGRGTLVTVSS
(SEQ ID NO: 912)



YYCAR ZZZZZZZZZZGYCTNGVCYTZZZZZZZZZWZF2LWGRGTLVTVSS
(SEQ ID NO: 123)


    K           GYCTNGVCYT        YWYFDLWGRGTLVTVSS 
D2-8.2 JH2








                 (SEQ ID NO: 115)      (SEQ ID NO: 67)



(2 = YHND)


(SEQ ID NO: 124)



(C34D282.2A) 5′-GCA|GtI|taT|taC|tgc|gct aRg tmt tmc tmc tmt tmt tmc tmc tmt-



tmc tmc ggt tat tgt act aac ggc gtt tgc tat act-3′


 


(SEQ ID NO: 125)



(C34D282.2B) 5′-Ag AgT Acc cTg gcc ccA cAg gTN gAA AKA ccA AKA AKA AKA gKA-



gKA gKA gKA AKA AKA AgT ATA gcA AAc gcc gTT AgT AcA ATA-3′ 


! 86 bases


 


(SEQ ID NO: 126)



(5′- tat tgt act aac ggc gtt tgc tat act tmt tmt tmc tmc tmc tmc-



tmt tmt tmt tgg tmt ttc Nac ctg tgg ggc cag ggt act ct-3′


[RC])






Design 14

Design 14 is like 9 except the D segment is mostly germline.









               1    1    2  2 2    3    3



      1   5    0    5    0  3 5    0    5









YYCAK YSYYSSSYYYSDYVWGSYRYTSYYSYYYAEYFQHWGQGTLVTVSS
(SEQ ID NO: 913)



YYCAK ZZZZZZZZZZZDYVWGSYRZTZZZZZZZAEZFQHWGQGTLVTVSS
(SEQ ID NO: 127)


    R  D3-16.2 YYDYVWGSYRYT       AEYFQHWGQGTLVTVSS 
(JH1)








              (SEQ ID NO: 104)    (SEQ ID NO: 66)



 


(SEQ ID NO: 128)



(C34D316.2A) 5′-GCA|GtT|taT|taC|tgc|gct aRg tmt tmc tmc tmt tmt tmc tmc tmt-



tmc tmc tmc gat tat gtc tgg ggt act tat cgt-3′ 


 


(SEQ ID NO: 129)



(C34D316.2B) 5′-Ag AgT Acc cTg gcc ccA ATg cTg gAA AKA cTc Agc gKA gKA gKA-



gKA gKA gKA AKA AgT gKA Acg ATA AgT Acc ccA gAc ATA ATC-3′ 


! 86 bases


 


(SEQ ID NO: 130)



(5′-gat tat gtc tgg ggt act tat cgt tmc act tmt tmc tmc tmc tmc-



tmc tmc gct gag tmt ttc cag cat tgg ggc cag ggt act ct-3′


[RC]






Design 15

Design 15 allows some diversity in the overlap, 5 two-way flip-flops. There are only 32 overlap sequences and even if there are mismatches, they will not change the allowed diversity.









               1    1    2  2 2    3    3



      1   5    0    5    0  3 5    0    5









YYCAK SYYYSSYSYYYDYVWGSYRYTSYSSSSYYAEYFQHWGQGTLVTVSS
(SEQ ID NO: 914)



YYCAK ZZZZZZZZZZZDZVWGZZRZTZZZZZZZZAEZFQHWGQGTLVTVSS
(SEQ ID NO: 131)








               YYDYVWGSYRYT        AEYFQHWGQGTLVTVSS



                 (SEQ ID NO: 104)       (SEQ ID NO: 66)


 


(SEQ ID NO: 132)



(C35D316.2A) 5′-GCA|GtT|taT|taC|tgc|gct aRg tmt tmc tmc tmt tmt tmc tmc tmt-



tmc tmc tmc gac tmt gtc tgg ggt tmc tmc cgt tmc acc t-3′ 


 


(SEQ ID NO: 133)



(C35D316.2B) 5′-Ag AgT Acc cTg gcc ccA ATg cTg gAA AKA cTc Agc gKA gKA-



gKA gKA gKA gKA gKA AKA ggT gKA Acg gKA gKA Acc ccA gAc AKA gTc gKA g-3′


 


(SEQ ID NO: 134)



(5′-c tmc gac tmt gtc tgg ggt tmc tmc cgt tmc acc tmt tmc tmc-



tmc tmc tmc tmc tmc gct gag tmt ttc cag cat tgg ggc cag ggt act ct-3′


[RC])






Design 16

Design 16 provides a CDR3 of 35. There are 4 two-way flip-flops in the overlap, thus 16 sequences.









               1    1    2  2 2    3    3



      1   5    0    5    0  3 5    0    5









YYCAK SSSYYSYSYSGYCSGGSCYSSYYYSSYYSAEYFQGWGQGTLVTVSS
(SEQ ID NO: 915)



YYCAK ZZZZZZZZZZGZCZGGZCZSZZZZZZZZZAEZFQHWGQGTLVTVSS
(SEQ ID NO: 135)


    R           GYCSGGSCYS  2-25.2 AEYFQHWGQGTLVTVSS
JH1








                (SEQ ID NO: 136)   (SEQ ID NO: 66)



 


(SEQ ID NO: 137)



(C35D225.2A) 5′-GCA|GtT|taT|taC|tgc|gct aRg tmt tmt tmt tmt tmt tmt tmt tmt-



tmc tmc ggc tmc tgt tmc ggt ggc tmc tgc tmc tcc t-3′


 


(SEQ ID NO: 138)



(C35D225.2B) 5′-Ag AgT Acc cTg gcc ccA ATg TTg gAA AKA TTc Agc gKA gKA-



gKA gKA gKA gKA gKA gKA gKA gKA ggA gcA gKA gcc Acc gKA AcA gKA gcc gKA g-3′


! 96 bases






If we add C34D225.2A and C34D225.2B to the mixture, then we get CDR3s of lengths 33, 34, and 35.









(SEQ ID NO: 139)



(C34D225.2A) 5′-GCA|GtT|taT|taC|tgc|gct aRg tmt tmt tmt tmt tmt tmt tmt-



tmc tmc ggc tmc tgt tmc ggt ggc tmc tgc tmc tcc t-3′


 


(SEQ ID NO: 140)



(C34D225.2B) 5′-Ag AgT Acc cTg gcc ccA ATg TTg gAA AKA TTc Agc gKA gKA-



gKA gKA gKA gKA gKA gKA gKA ggA gcA gKA gcc Acc gKA AcA gKA gcc gKA g-3′


! 93 bases






Design 17









               1    1    2  2 2    3    3



      1   5    0    5    0  3 5    0    5









YYCAK YSSYSYYDYVWGSYRYTSSSYSYYSYYYAEYFQGWGQGTLVTVSS
(SEQ ID NO: 916)



YYCAK ZZZZZZZDZVWGZZRZTZZZZZZZZZZZAEZFQHWGQGTLVTVSS
(SEQ ID NO: 141)


    R      YYDYVWGSYRYT D3-16.2   AEYFQHWGQGTLVTVSS 
(JH1)








          (SEQ ID NO: 104)        (SEQ ID NO: 66)



 


(SEQ ID NO: 142)



(C35D3162A) 5′- GCA|GtT|taT|taC|tgc|gct aRg tmt tmt tmt tmt tmt tmt tmc gac-



tmc gtc tgg ggt tmt tmc cgt tmt acc t-3′ 


 


(SEQ ID NO: 143)



(C35D3162B)5′-Ag AgT Acc cTg gcc ccA gTg cTg gAA gKA cTc Agc gKA gKA gKA-



gKA gKA gKA gKA gKA gKA gKA gKA gKA gKA ggT AKA Acg gKA AKA Acc ccA gAc-


gKA gTc g-3′ 






Design 18









               1    1    2  2 2    3    3



      1   5    0    5    0  3 5    0    5









YYCAK SSYYYSSSYYDYVWGSYRYTSSYYSYSYAEYFQGWGQGTLVTVSS
(SEQ ID NO: 917)



YYCAK ZZZZZZZZZZDZVWGZZRZTZZZZZZZZAEZFQHWGQGTLVTVSS
(SEQ ID NO: 144)


    R         YYDYVWGSYRYT D3-16.2AEYFQHWGQGTLVTVSS 
(JH1)








              (SEQ ID NO: 104)    (SEQ ID NO: 66)



 


(SEQ ID NO: 145)



(C35D3162C) 5′- GCA|GtT|taT|taC|tgc|gct aRg tmt tmt tmt tmt tmt tmt tmc-



tmc tmc tmc gac tmc gtc tgg ggt tmc tmc cgt tmc acc t-3′ 


82 bases


(SEQ ID NO: 146)



(C35D3162B) 5′-Ag AgT Acc cTg gcc ccA gTg cTg gAA gKA cTc Agc gKA gKA-



gKA gKA gKA gKA gKAgKA gKA gKA ggT gKA Acg gKA gKA Acc ccA gAc gKA-


gTc g-3′ 






Design 19









               1    1    2  2 2    3    3



      1   5    0    5    0  3 5    0    5









YYCAK YSSSSYSYYYYDSSGYYYSYYSSSYYSYYAEYFQGWGQGTLVTVSS
(SEQ ID NO: 918)



YYCAK ZZZZZZZZZZZDSSGZZZZZZZZZZZZZZAEZFQHWGQGTLVTVSS
(SEQ ID NO: 147)


    R         YYYDSSGYYY           AEYFQHWGQGTLVTVSS 
(JH1)








                 (SEQ ID NO: 88)        (SEQ ID NO: 66)



          1   1                          1     1


    9 9   0   0                          0     1


    4 5   0   3abcdefghijklmnopqrstuvwxya4     0


                                        ′


 









Amino-acid diversity =
6.7 E 7



 


DNA diversity =
6.7 E 7


 


Stop-free =
100


 


Gratuitous Cys-free =
100


 


Free of stop and Cys =
100%






Design 19 has CDR3 of length 35. Residue 94 can be K or R, The ZZZZZZZZZ::D3-22(2nd RF with six Ys as Z)::ZZZZZZZZZZZ (SEQ ID NO:939)::JH1(with 1 Z). Error-prone PCR could be used to add more diversity.









C35D322AJH1



!  scab DNA     S   R   D   N   S   K   N   T   L   Y   L   Q   M   N   S


5′-ttc|act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|aac|agC-


!              XbaI . . .


!


!   L   R   A   E   D   T   A   V   Y   Y   C   A  K|R


  |TTA|AGg|gct|gag|gaT|aCT|GCA|GtT|taT|taC|tgc|gct aRg -


!


!  CDR3-------------------------------------------------------------------


!


!  Y|S Y|S Y|S Y|S Y|S Y|S Y|S Y|S Y|S Y|S Y|S  D   S   S   G  Y|S Y|S Y|S


   tmc tmt tmc tmc tmt tmc tmt tmc tmc tmc tmc gac agc tcc ggc tmc tmc tmt


!


   Y|S Y|S Y|S Y|S Y|S Y|S Y|S Y|S Y|S Y|S Y|S  A   E  Y|S  F   Q   H


   tmc tmt tmc tmc tmt tmc tmt tmc tmc tmc tmc gct gaa tmc ttc caa cac


!









!   W   G   Q   G   T   L   V   T   V   S   S
(SEQ ID NO: 148)



   tgg ggc cag ggt act ctG GTC ACC gtc tcc agt-3′
(SEQ ID NO: 149)








!                        BstEII . . .



 


(SEQ ID NO: 150)



(C35D322AJH1_T)5′-GCA|GtI|taT|taC|tgc|gct aRg tmctmt tmc tmc tmt-



tmc tmt tmc tmc tmc tmc gac agc tcc ggc tmc tmc t-3′


 


(SEQ ID NO: 151)



(C35D322AJH1_B) 5′-cAg AgT Acc cTg gcc ccA gTg TTggAA gKA TTc Agc gKA-



gKA gKA gKA AKA gKA AKA gKA gKA AKA gKA AKA gKA gKA gcc ggA gcT gTc-


gKA gKA g-3′


 


ON_1, ON_2, ON_3, and ON_4 as above.






Design 20









                 1    1    2  2 2      3    3



      1   5      0    5    0  3 5      0    5









YYCAK YSSYSS   YYYYDSSGYYYSSYSSYS   YYYAEYFQGWGQGTLVTVSS
(SEQ ID NO: 919)



YYCAK ZZZZZZ(Z)ZZZZDSSGZZZZZZZZZZ(Z)ZZZAEZFQHWGQGTLVTVSS
(SEQ ID NO: 152)


    R           YYYDSSGYYY             AEYFQHWGQGTLVTVSS
(JH1)








              (SEQ ID NO: 88)     (SEQ ID NO: 66)



           1    1                            1     1


    9 9    0    0                            0     1


    4 5    0    3abcdefghijklmnop q rstuvwxya4     0


                                            ′


 









Amino-acid diversity =
6.7 E 7



 


DNA diversity =
6.7 E 7


 


Stop-free =
100


 


Gratuitous Cys-free =
100


 


Free of stop and Cys =
100%






Design 20 has CDR3s of length 33, 34, or 35. Residue 94 can be K or R, The ZZZZZZ(Z)ZZ::D3-22 22(2nd RF with six Ys as Z)::ZZZZZZZ(Z)ZZZ (SEQ ID NO:940)::JH1 (with 1 Z). PCR combining (C35D322AJH1_T), (C34D322AJH1_T), (C35D322AJH1_B), and (C34D322AJH1_B) allows length as well as sequence diversity.









(C35D322AJH1_T) 5′-GCA|GtT|taT|taC|tgc|gct aRg tmc tmt tmc tmc-



 tmt tmc tmt tmc tmc tmc tmc gac agc tcc ggc tmc tmc t-3′ (SEQ ID NO: 153)


(C34D322AJH1_T) 5′-GCA|GtT|taT|taC|tgc|gct aRg tmc tmc tmc tmt-


 tmc tmt tmc tmc tmc tmc gac agc tcc ggc tmc tmc t-3′ (SEQ ID NO: 154)


(C35D322AJH1_B) 5′-cAg AgT Acc cTg gcc ccA gTg TTg gAA gKA TTc Agc gKA-


   gKA gKA gKA AKA gKA AKA gKA gKA AKA gKA AKA gKA gKA gcc ggA gcT gTc-


   gKA gKA g-3′ (SEQ ID NO: 920)


(C34D322AJH1_B) 5′-cAg AgT Acc cTg gcc ccA gTg TTg gAA gKA TTc Agc gKA-


   gKA gKA gKA AKA gKA AKA gKA gKA AKA AKA gKA gKA gcc ggA gcT gTc-


   gKA gKA g-3′ (SEQ ID NO: 155)






Selection Against Stop Codons:

Because some of these libraries have NNK codons, they will have some TAG stop codons. We could remove the clones with TAG by cloning the amplified DNA into an XbaI-BstEII site between the signal sequence for a bla gene and the actual bla protein and express in Sup0 cells. BlaR colonies do not contain TAG stops. Alternatively, we could clone the XbaI-BstEII fragments ahead of a kanamycin-resistance gene and select for KanR. We would then move the XbaI-BstEII cassette into the phage library.







TABLE 20







Human D regions


!* for TAG; @ for TAA; $ for TGA


D - Amino acid sequence alignment (RF: reading frame)












RF 1
RF 2
RF 3
Used in designs















D1
1-1
(SEQ ID NO: 156)
(SEQ ID NO: 157)
(SEQ ID NO: 158)





GTTGT
VQLER
YNWND




1-7
(SEQ ID NO: 159)
(SEQ ID NO: 160)
(SEQ ID NO: 161)





GITGT
V*LEL
YNWNY




1-20
(SEQ ID NO: 159)
(SEQ ID NO: 162)
(SEQ ID NO: 163)





GITGT
V*LER
YNWND




1-26
(SEQ ID NO: 164)
(SEQ ID NO: 165)
(SEQ ID NO: 166)





GIVGAT
V*WELL
YSGSYY



 


D2
2-2
(SEQ ID NO: 167)
(SEQ ID NO: 70)
(SEQ ID NO: 168)





RIL**YQLLY
GYCSSTSCYT
DIVVVPAAI
1, 5, 6, 7,



2-8
(SEQ ID NO: 169)
(SEQ ID NO: 115)
(SEQ ID NO: 170)





RILY@WCMLY
GYCTNGVCYT
DIVLMVYAI
20, 21, 22,



2-15
(SEQ ID NO: 171)
(SEQ ID NO: 136)
(SEQ ID NO: 172)





RIL*WW*LLL
GYCSGGSCYS
DIVVVVAAT
25,



2-21
(SEQ ID NO: 173)
(SEQ ID NO: 174)
(SEQ ID NO: 175)





SILWW$LLF
AYCGGDCYS
HIVVVTAI



 


D3
3-3
(SEQ ID NO: 176)
(SEQ ID NO: 177)
(SEQ ID NO: 178)





VLRFLEWLLY
YYDFWSGYYT
ITIFGVVII




3-9
(SEQ ID NO: 179)
(SEQ ID NO: 180)
(SEQ ID NO: 181)





VLRYFDWLL@
YYDILTGYYN
ITIF*LVII




3-10
(SEQ ID NO: 182)
(SEQ ID NO: 81)
(SEQ ID NO: 183)





VLLWFGELL@
YYYGSGSYYN
ITMVRGVII




3-16
(SEQ ID NO: 184)
(SEQ ID NO: 104)
(SEQ ID NO: 185)





VL$LRLGELSLY
YYDYVWGSYRYT
IMITFGGVIVI
8, 9, 14, 15, 17, 18



3-22
(SEQ ID NO: 186)
(SEQ ID NO: 187)
(SEQ ID NO: 188)





VLL***WLLL
YYYDSSGYYY
ITMIVVVIT
4, 19, 20


 


D4
4-4
(SEQ ID NO: 189)
(SEQ ID NO: 88)
(SEQ ID NO: 190)





$LQ@L
DYSNY
TTVT




4-11
(SEQ ID NO: 191)
(SEQ ID NO: 192)
(SEQ ID NO: 193)





$LQ@L
DYSNY
TTVT




4-17
(SEQ ID NO: 194)
(SEQ ID NO: 195)
(SEQ ID NO: 196)





$LR@L
DYGDY
TTVT




4-23
(SEQ ID NO: 197)
(SEQ ID NO: 198)
(SEQ ID NO: 199)





$LRW@L
DYGGNS
TTVVT



 


D5
5-5
(SEQ ID NO: 200)
(SEQ ID NO: 201)
(SEQ ID NO: 202)





VDTAMV
WIQLWL
GYSYGY




5-12
(SEQ ID NO: 203)
(SEQ ID NO: 204)
(SEQ ID NO: 205)





VDIVATI
WI*WLRL
GYSGYDY




5-18
(SEQ ID NO: 206)
(SEQ ID NO: 207)
(SEQ ID NO: 208)





VDTAMV
WIQLWL
GYSYGY




5-24
(SEQ ID NO: 209)
(SEQ ID NO: 210)
(SEQ ID NO: 211)





VEMATI
*RWLQL
RDGYNY



 


D6
6-6
(SEQ ID NO: 212)
(SEQ ID NO: 213)
(SEQ ID NO: 214)





EYSSSS
SIAAR
V*QLV




6-13
(SEQ ID NO: 215)
(SEQ ID NO: 216)
(SEQ ID NO: 217)





GYSSSWY
GIAAAG
V*QQLV




6-19
(SEQ ID NO: 218)
(SEQ ID NO: 219)
(SEQ ID NO: 220)





GYSSGWY
GIAVAG
V*QWLV



 


D7
7-27
(SEQ ID NO: 221)
(SEQ ID NO: 222)
(SEQ ID NO: 223)





LTG
@LG
NWG
















TABLE 3





Human JH segments


JH - Amino acid sequence alignment

















    H3



  ------



   CDR3



 --------



    100       110



      |  FR4--------    Used in examples









JH1
---AEYFQHWGQGTLVTVSS 1-8,
(SEQ ID NO: 66)


JH2
---YWYFDLWGRGTLVTVSS
(SEQ ID NO: 67)


JH3
-----AFDIWGQGTMVTVSS
(SEQ ID NO: 2)


JH4
-----YFDYWGQGTLVTVSS
(SEQ ID NO: 1)


JH5
----NWFDPWGQGTLVTVSS
(SEQ ID NO: 68)


JH6
YYYYYGMDVWGQGTTVTVSS
(SEQ ID NO: 3)



   123456
















TABLE 10





DNA encoding V-5D2-8.2a-JH2 for wobbling















!                                               CDR3.......


!   A  E  D  T  A  V  Y  Y  C  A  K  D  I  V  L  M


  |gct|gag|gaT|aCT|GCA|GtT|taT|taC|tgc|gct aag jez ezq jzz qzz ezj


!


!    W   G   Q   G   T   T   V   T   V   S   S (SEQ ID NO: 224)


    tgg ggc cag ggt act acG GTC ACC gtc tcc agt-3′ (SEQ ID NO: 225)


!                BstEII...
















TABLE 11





Trimers that can be extracted


from human D segments


In Tables 11-14, the use of a lower case letter in


an amino acid sequence indicates that a stop


codon was changed to the residue listed as the


lower case letter. For example, in the amino acid


sequence “yLE”, a Tyr residue


was introduced in place of a stop codon.




















GTT
D1-1.1.1
1



 



VQL
D1-1.2.1
2



 



YNW
D1-1.3.1
3



 



TTG
D1-1.1.2
4



 



QLE
D1-1.2.2
5



 



NWN
D1-1.3.2
6



 



TGT
D1-1.1.3
7



 



LER
D1-1.2.3
8



 



WND
D1-1.3.3
9



 



GIT
D1-7.1.1
10



 



VyL
D1-7.2.1
11
*


 



ITG
D1-7.1.2
12



 



yLE
D1-7.2.2
13
*


 



LEL
D1-7.2.3
14



 



WNY
D1-7.3.3
15



 



GIV
D1-26.1.1
16



 



VyW
D1-26.2.1
17
*


 



YSG
D1-26.3.1
18



 



IVG
D1-26.1.2
19



 



yWE
D1-26.2.2
20
*


 



SGS
D1-26.3.2
21



 



VGA
D1-26.1.3
22



 



WEL
D1-26.2.3
23



 



GSY
D1-26.3.3
24



 



GAT
D1-26.1.4
25



 



ELL
D1-26.2.4
26



 



SYY
D1-26.3.4
27



 



RIL
D2-2.1.1
28



 



GYC
D2-2.2.1
29
#


 



DIV
D2-2.3.1
30



 



ILy
D2-2.1.2
31
*


 



YCS
D2-2.2.2
32
#


 



IVV
D2-2.3.2
33



 



Lyy
D2-2.1.3
34
*


 



CSS
D2-2.2.3
35
#


 



VVV
D2-2.3.3
36



 



yyY
D2-2.1.4
37
*


 



SST
D2-2.2.4
38



 



VVP
D2-2.3.4
39



 



yYQ
D2-2.1.5
40
*


 



STS
D2-2.2.5
41



 



VPA
D2-2.3.5
42



 



YQL
D2-2.1.6
43



 



TSC
D2-2.2.6
44
#


 



PAA
D2-2.3.6
45



 



QLL
D2-2.1.7
46



 



SCY
D2-2.2.7
47
#


 



AAI
D2-2.3.7
48



 



LLY
D2-2.1.8
49



 



CYT
D2-2.2.8
50
#


 



ILY
D2-8.1.2
51



 



YCT
D2-8.2.2
52
#


 



IVL
D2-8.3.2
53



 



LYy
D2-8.1.3
54
*


 



CTN
D2-8.2.3
55
#


 



VLM
D2-8.3.3
56



 



YyW
D2-8.1.4
57
*


 



TNG
D2-8.2.4
58



 



LMV
D2-8.3.4
59



 



yWC
D2-8.1.5
60
*#


 



NGV
D2-8.2.5
61



 



MVY
D2-8.3.5
62



 



WCM
D2-8.1.6
63
#


 



GVC
D2-8.2.6
64
#


 



VYA
D2-8.3.6
65



 



CML
D2-8.1.7
66
#


 



VCY
D2-8.2.7
67
#


 



YAI
D2-8.3.7
68



 



MLY
D2-8.1.8
69



 



LyW
D2-15.1.3
70
*


 



CSG
D2-15.2.3
71
#


 



yWW
D2-15.1.4
72
*


 



SGG
D2-15.2.4
73



 



WWy
D2-15.1.5
74
*


 



GGS
D2-15.2.5
75



 



VVA
D2-15.3.5
76



 



WyL
D2-15.1.6
77
*


 



GSC
D2-15.2.6
78
#


 



VAA
D2-15.3.6
79



 



yLL
D2-15.1.7
80
*


 



AAT
D2-15.3.7
81



 



LLL
D2-15.1.8
82



 



CYS
D2-15.2.8
83
#


 



SIL
D2-21.1.1
84



 



AYC
D2-21.2.1
85
#


 



HIV
D2-21.3.1
86



 



ILW
D2-21.1.2
87



 



YCG
D2-21.2.2
88
#


 



LWW
D2-21.1.3
89



 



CGG
D2-21.2.3
90
#


 



WWw
D2-21.1.4
91
*


 



GGD
D2-21.2.4
92



 



VVT
D2-21.3.4
93



 



WwL
D2-21.1.5
94
*


 



GDC
D2-21.2.5
95
#


 



VTA
D2-21.3.5
96



 



wLL
D2-21.1.6
97
*


 



DCY
D2-21.2.6
98
#


 



TAI
D2-21.3.6
99



 



LLF
D2-21.1.7
100



 



VLR
D3-3.1.1
101



 



YYD
D3-3.2.1
102



 



ITI
D3-3.3.1
103



 



LRF
D3-3.1.2
104



 



YDF
D3-3.2.2
105



 



TIF
D3-3.3.2
106



 



RFL
D3-3.1.3
107



 



DFW
D3-3.2.3
108



 



IFG
D3-3.3.3
109



 



FLE
D3-3.1.4
110



 



FWS
D3-3.2.4
111



 



FGV
D3-3.3.4
112



 



LEW
D3-3.1.5
113



 



WSG
D3-3.2.5
114



 



GVV
D3-3.3.5
115



 



EWL
D3-3.1.6
116



 



SGY
D3-3.2.6
117



 



VVI
D3-3.3.6
118



 



WLL
D3-3.1.7
119



 



GYY
D3-3.2.7
120



 



VII
D3-3.3.7
121



 



YYT
D3-3.2.8
122



 



LRY
D3-9.1.2
123



 



YDI
D3-9.2.2
124



 



RYF
D3-9.1.3
125



 



DIL
D3-9.2.3
126



 



IFy
D3-9.3.3
127
*


 



YFD
D3-9.1.4
128



 



ILT
D3-9.2.4
129



 



FyL
D3-9.3.4
130
*


 



FDW
D3-9.1.5
131



 



LTG
D3-9.2.5
132



 



yLV
D3-9.3.5
133
*


 



DWL
D3-9.1.6
134



 



TGY
D3-9.2.6
135



 



LVI
D3-9.3.6
136



 



LLy
D3-9.1.8
137
*


 



YYN
D3-9.2.8
138



 



VLL
D3-10.1.1
139



 



YYY
D3-10.2.1
140



 



ITM
D3-10.3.1
141



 



LLW
D3-10.1.2
142



 



YYG
D3-10.2.2
143



 



TMV
D3-10.3.2
144



 



LWF
D3-10.1.3
145



 



YGS
D3-10.2.3
146



 



MVR
D3-10.3.3
147



 



WFG
D3-10.1.4
148



 



GSG
D3-10.2.4
149



 



VRG
D3-10.3.4
150



 



FGE
D3-10.1.5
151



 



RGV
D3-10.3.5
152



 



GEL
D3-10.1.6
153



 



GVI
D3-10.3.6
154



 



VLw
D3-16.1.1
155
*


 



IMI
D3-16.3.1
156



 



LwL
D3-16.1.2
157
*


 



YDY
D3-16.2.2
158



 



MIT
D3-16.3.2
159



 



wLR
D3-16.1.3
160
*


 



DYV
D3-16.2.3
161



 



ITF
D3-16.3.3
162



 



LRL
D3-16.1.4
163



 



YVW
D3-16.2.4
164



 



TFG
D3-16.3.4
165



 



RLG
D3-16.1.5
166



 



VWG
D3-16.2.5
167



 



FGG
D3-16.3.5
168



 



LGE
D3-16.1.6
169



 



WGS
D3-16.2.6
170



 



GGV
D3-16.3.6
171



 



ELS
D3-16.1.8
172



 



SYR
D3-16.2.8
173



 



VIV
D3-16.3.8
174



 



LSL
D3-16.1.9
175



 



YRY
D3-16.2.9
176



 



IVI
D3-16.3.9
177



 



SLY
D3-16.1.10
178



 



RYT
D3-16.2.10
179



 



LLw
D3-22.1.2
180
*


 



TMI
D3-22.3.2
181



 



Lwy
D3-22.1.3
182
*


 



YDS
D3-22.2.3
183



 



MIV
D3-22.3.3
184



 



wyy
D3-22.1.4
185
*


 



DSS
D3-22.2.4
186



 



yyW
D3-22.1.5
187
*


 



SSG
D3-22.2.5
188



 



yWL
D3-22.1.6
189
*


 



VIT
D3-22.3.7
190



 



wLQ
D4-4.1.1
191
*


 



DYS
D4-4.2.1
192



 



TTV
D4-4.3.1
193



 



LQy
D4-4.1.2
194
*


 



YSN
D4-4.2.2
195



 



TVT
D4-4.3.2
196



 



QyL
D4-4.1.3
197
*


 



SNY
D4-4.2.3
198



 



DYG
D4-17.2.1
199



 



LRw
D4-17.1.2
200
*


 



YGD
D4-17.2.2
201



 



RwL
D4-17.1.3
202
*


 



GDY
D4-17.2.3
203



 



LRW
D4-23.1.2
204



 



YGG
D4-23.2.2
205



 



TVV
D4-23.3.2
206



 



RWy
D4-23.1.3
207
*


 



GGN
D4-23.2.3
208



 



GNS
D4-23.2.4
209



 



VDT
D5-5.1.1
210



 



WIQ
D5-5.2.1
211



 



GYS
D5-5.3.1
212



 



DTA
D5-5.1.2
213



 



IQL
D5-5.2.2
214



 



YSY
D5-5.3.2
215



 



TAM
D5-5.1.3
216



 



QLW
D5-5.2.3
217



 



SYG
D5-5.3.3
218



 



AMV
D5-5.1.4
219



 



LWL
D5-5.2.4
220



 



YGY
D5-5.3.4
221



 



VDI
D5-12.1.1
222



 



WIy
D5-12.2.1
223
*


 



IyW
D5-12.2.2
224
*


 



IVA
D5-12.1.3
225



 



VAT
D5-12.1.4
226



 



WLR
D5-12.2.4
227



 



GYD
D5-12.3.4
228



 



ATI
D5-12.1.5
229



 



VEM
D5-24.1.1
230



 



yRW
D5-24.2.1
231
*


 



RDG
D5-24.3.1
232



 



EMA
D5-24.1.2
233



 



RWL
D5-24.2.2
234



 



DGY
D5-24.3.2
235



 



MAT
D5-24.1.3
236



 



WLQ
D5-24.2.3
237



 



GYN
D5-24.3.3
238



 



LQL
D5-24.2.4
239



 



YNY
D5-24.3.4
240



 



EYS
D6-6.1.1
241



 



SIA
D6-6.2.1
242



 



VyQ
D6-6.3.1
243
*


 



YSS
D6-6.1.2
244



 



IAA
D6-6.2.2
245



 



yQL
D6-6.3.2
246
*


 



SSS
D6-6.1.3
247



 



AAR
D6-6.2.3
248



 



QLV
D6-6.3.3
249



 



GIA
D6-13.2.1
250



 



yQQ
D6-13.3.2
251
*


 



AAA
D6-13.2.3
252



 



QQL
D6-13.3.3
253



 



SSW
D6-13.1.4
254



 



AAG
D6-13.2.4
255



 



SWY
D6-13.1.5
256



 



IAV
D6-19.2.2
257



 



yQW
D6-19.3.2
258
*


 



AVA
D6-19.2.3
259



 



QWL
D6-19.3.3
260



 



SGW
D6-19.1.4
261



 



VAG
D6-19.2.4
262



 



WLV
D6-19.3.4
263



 



GWY
D6-19.1.5
264



 



yLG
D7-27.2.1
265
*


 



NWG
D7-27.3.1
266
















TABLE 12





Distinct tetramers that can be extracted


from human D segments




















GTTG
D1-1.1.1
(SEQ ID NO: 257)
1


 



VQLE
D1-1.2.1
(SEQ ID NO: 258)
2


 



YNWN
D1-1.3.1
(SEQ ID NO: 259)
3


 



TTGT
D1-1.1.2
(SEQ ID NO: 263)
4


 



QLER
D1-1.2.2
(SEQ ID NO: 264)
5


 



NWND
D1-1.3.2
(SEQ ID NO: 265)
6


 



GITG
D1-7.1.1
(SEQ ID NO: 266)
7


 



VyLE
D1-7.2.1
(SEQ ID NO: 267)
8


 



ITGT
D1-7.1.2
(SEQ ID NO: 271)
9


 



yLEL
D1-7.2.2
(SEQ ID NO: 272)
10


 



NWNY
D1-7.3.2
(SEQ ID NO: 273)
11


 



yLER
D1-20.2.2
(SEQ ID NO: 275)
12


 



GIVG
D1-26.1.1
(SEQ ID NO: 276)
13


 



VyWE
D1-26.2.1
(SEQ ID NO: 277)
14


 



YSGS
D1-26.3.1
(SEQ ID NO: 278)
15


 



IVGA
D1-26.1.2
(SEQ ID NO: 285)
16


 



yWEL
D1-26.2.2
(SEQ ID NO: 286)
17


 



SGSY
D1-26.3.2
(SEQ ID NO: 287)
18


 



VGAT
D1-26.1.3
(SEQ ID NO: 291)
19


 



WELL
D1-26.2.3
(SEQ ID NO: 292)
20


 



GSYY
D1-26.3.3
(SEQ ID NO: 293)
21


 



RILy
D2-2.1.1
(SEQ ID NO: 294)
22


 



GYCS
D2-2.2.1
(SEQ ID NO: 295)
23


 



DIVV
D2-2.3.1
(SEQ ID NO: 296)
24


 



ILyy
D2-2.1.2
(SEQ ID NO: 303)
25


 



YCSS
D2-2.2.2
(SEQ ID NO: 304)
26


 



IVVV
D2-2.3.2
(SEQ ID NO: 305)
27


 



LyyY
D2-2.1.3
(SEQ ID NO: 312)
28


 



CSST
D2-2.2.3
(SEQ ID NO: 313)
29


 



VVVP
D2-2.3.3
(SEQ ID NO: 314)
30


 



yyYQ
D2-2.1.4
(SEQ ID NO: 321)
31


 



SSTS
D2-2.2.4
(SEQ ID NO: 322)
32


 



VVPA
D2-2.3.4
(SEQ ID NO: 323)
33


 



yYQL
D2-2.1.5
(SEQ ID NO: 330)
34


 



STSC
D2-2.2.5
(SEQ ID NO: 331)
35


 



VPAA
D2-2.3.5
(SEQ ID NO: 332)
36


 



YQLL
D2-2.1.6
(SEQ ID NO: 338)
37


 



TSCY
D2-2.2.6
(SEQ ID NO: 339)
38


 



PAAI
D2-2.3.6
(SEQ ID NO: 340)
39


 



QLLY
D2-2.1.7
(SEQ ID NO: 343)
40


 



SCYT
D2-2.2.7
(SEQ ID NO: 344)
41


 



RILY
D2-8.1.1
(SEQ ID NO: 345)
42


 



GYCT
D2-8.2.1
(SEQ ID NO: 346)
43


 



DIVL
D2-8.3.1
(SEQ ID NO: 347)
44


 



ILYy
D2-8.1.2
(SEQ ID NO: 354)
45


 



YCTN
D2-8.2.2
(SEQ ID NO: 355)
46


 



IVLM
D2-8.3.2
(SEQ ID NO: 356)
47


 



LYyW
D2-8.1.3
(SEQ ID NO: 363)
48


 



CTNG
D2-8.2.3
(SEQ ID NO: 364)
49


 



VLMV
D2-8.3.3
(SEQ ID NO: 365)
50


 



YyWC
D2-8.1.4
(SEQ ID NO: 372)
51


 



TNGV
D2-8.2.4
(SEQ ID NO: 373)
52


 



LMVY
D2-8.3.4
(SEQ ID NO: 374)
53


 



yWCM
D2-8.1.5
(SEQ ID NO: 381)
54


 



NGVC
D2-8.2.5
(SEQ ID NO: 382)
55


 



MVYA
D2-8.3.5
(SEQ ID NO: 383)
56


 



WCML
D2-8.1.6
(SEQ ID NO: 389)
57


 



GVCY
D2-8.2.6
(SEQ ID NO: 390)
58


 



VYAI
D2-8.3.6
(SEQ ID NO: 391)
59


 



CMLY
D2-8.1.7
(SEQ ID NO: 394)
60


 



VCYT
D2-8.2.7
(SEQ ID NO: 395)
61


 



ILyW
D2-15.1.2
(SEQ ID NO: 401)
62


 



YCSG
D2-15.2.2
(SEQ ID NO: 402)
63


 



LyWW
D2-15.1.3
(SEQ ID NO: 409)
64


 



CSGG
D2-15.2.3
(SEQ ID NO: 410)
65


 



VVVV
D2-15.3.3
(SEQ ID NO: 411)
66


 



yWWy
D2-15.1.4
(SEQ ID NO: 418)
67


 



SGGS
D2-15.2.4
(SEQ ID NO: 419)
68


 



VVVA
D2-15.3.4
(SEQ ID NO: 420)
69


 



WWyL
D2-15.1.5
(SEQ ID NO: 427)
70


 



GGSC
D2-15.2.5
(SEQ ID NO: 428)
71


 



VVAA
D2-15.3.5
(SEQ ID NO: 429)
72


 



WyLL
D2-15.1.6
(SEQ ID NO: 435)
73


 



GSCY
D2-15.2.6
(SEQ ID NO: 436)
74


 



VAAT
D2-15.3.6
(SEQ ID NO: 437)
75


 



yLLL
D2-15.1.7
(SEQ ID NO: 440)
76


 



SCYS
D2-15.2.7
(SEQ ID NO: 441)
77


 



SILW
D2-21.1.1
(SEQ ID NO: 442)
78


 



AYCG
D2-21.2.1
(SEQ ID NO: 443)
79


 



HIVV
D2-21.3.1
(SEQ ID NO: 444)
80


 



ILWW
D2-21.1.2
(SEQ ID NO: 451)
81


 



YCGG
D2-21.2.2
(SEQ ID NO: 452)
82


 



LWWw
D2-21.1.3
(SEQ ID NO: 459)
83


 



CGGD
D2-21.2.3
(SEQ ID NO: 460)
84


 



VVVT
D2-21.3.3
(SEQ ID NO: 461)
85


 



WWwL
D2-21.1.4
(SEQ ID NO: 468)
86


 



GGDC
D2-21.2.4
(SEQ ID NO: 469)
87


 



VVTA
D2-21.3.4
(SEQ ID NO: 470)
88


 



WwLL
D2-21.1.5
(SEQ ID NO: 476)
89


 



GDCY
D2-21.2.5
(SEQ ID NO: 477)
90


 



VTAI
D2-21.3.5
(SEQ ID NO: 478)
91


 



wLLF
D2-21.1.6
(SEQ ID NO: 481)
92


 



DCYS
D2-21.2.6
(SEQ ID NO: 482)
93


 



VLRF
D3-3.1.1
(SEQ ID NO: 483)
94


 



YYDF
D3-3.2.1
(SEQ ID NO: 484)
95


 



ITIF
D3-3.3.1
(SEQ ID NO: 485)
96


 



LRFL
D3-3.1.2
(SEQ ID NO: 492)
97


 



YDFW
D3-3.2.2
(SEQ ID NO: 493)
98


 



TIFG
D3-3.3.2
(SEQ ID NO: 494)
99


 



RFLE
D3-3.1.3
(SEQ ID NO: 501)
100


 



DFWS
D3-3.2.3
(SEQ ID NO: 502)
101


 



IFGV
D3-3.3.3
(SEQ ID NO: 503)
102


 



FLEW
D3-3.1.4
(SEQ ID NO: 510)
103


 



FWSG
D3-3.2.4
(SEQ ID NO: 511)
104


 



FGVV
D3-3.3.4
(SEQ ID NO: 512)
105


 



LEWL
D3-3.1.5
(SEQ ID NO: 519)
106


 



WSGY
D3-3.2.5
(SEQ ID NO: 520)
107


 



GVVI
D3-3.3.5
(SEQ ID NO: 521)
108


 



EWLL
D3-3.1.6
(SEQ ID NO: 527)
109


 



SGYY
D3-3.2.6
(SEQ ID NO: 528)
110


 



VVII
D3-3.3.6
(SEQ ID NO: 529)
111


 



WLLY
D3-3.1.7
(SEQ ID NO: 532)
112


 



GYYT
D3-3.2.7
(SEQ ID NO: 533)
113


 



VLRY
D3-9.1.1
(SEQ ID NO: 534)
114


 



YYDI
D3-9.2.1
(SEQ ID NO: 535)
115


 



LRYF
D3-9.1.2
(SEQ ID NO: 542)
116


 



YDIL
D3-9.2.2
(SEQ ID NO: 543)
117


 



TIFy
D3-9.3.2
(SEQ ID NO: 544)
118


 



RYFD
D3-9.1.3
(SEQ ID NO: 551)
119


 



DILT
D3-9.2.3
(SEQ ID NO: 552)
120


 



IFyL
D3-9.3.3
(SEQ ID NO: 553)
121


 



YFDW
D3-9.1.4
(SEQ ID NO: 560)
122


 



ILTG
D3-9.2.4
(SEQ ID NO: 561)
123


 



FyLV
D3-9.3.4
(SEQ ID NO: 562)
124


 



FDWL
D3-9.1.5
(SEQ ID NO: 569)
125


 



LTGY
D3-9.2.5
(SEQ ID NO: 570)
126


 



yLVI
D3-9.3.5
(SEQ ID NO: 571)
127


 



DWLL
D3-9.1.6
(SEQ ID NO: 577)
128


 



TGYY
D3-9.2.6
(SEQ ID NO: 578)
129


 



LVII
D3-9.3.6
(SEQ ID NO: 579)
130


 



WLLy
D3-9.1.7
(SEQ ID NO: 582)
131


 



GYYN
D3-9.2.7
(SEQ ID NO: 583)
132


 



VLLW
D3-10.1.1
(SEQ ID NO: 584)
133


 



YYYG
D3-10.2.1
(SEQ ID NO: 585)
134


 



ITMV
D3-10.3.1
(SEQ ID NO: 586)
135


 



LLWF
D3-10.1.2
(SEQ ID NO: 593)
136


 



YYGS
D3-10.2.2
(SEQ ID NO: 594)
137


 



TMVR
D3-10.3.2
(SEQ ID NO: 595)
138


 



LWFG
D3-10.1.3
(SEQ ID NO: 602)
139


 



YGSG
D3-10.2.3
(SEQ ID NO: 603)
140


 



MVRG
D3-10.3.3
(SEQ ID NO: 604)
141


 



WFGE
D3-10.1.4
(SEQ ID NO: 611)
142


 



GSGS
D3-10.2.4
(SEQ ID NO: 612)
143


 



VRGV
D3-10.3.4
(SEQ ID NO: 613)
144


 



FGEL
D3-10.1.5
(SEQ ID NO: 620)
145


 



RGVI
D3-10.3.5
(SEQ ID NO: 621)
146


 



GELL
D3-10.1.6
(SEQ ID NO: 626)
147


 



GVII
D3-10.3.6
(SEQ ID NO: 627)
148


 



ELLy
D3-10.1.7
(SEQ ID NO: 630)
149


 



SYYN
D3-10.2.7
(SEQ ID NO: 631)
150


 



VLwL
D3-16.1.1
(SEQ ID NO: 632)
151


 



YYDY
D3-16.2.1
(SEQ ID NO: 633)
152


 



IMIT
D3-16.3.1
(SEQ ID NO: 634)
153


 



LwLR
D3-16.1.2
(SEQ ID NO: 641)
154


 



YDYV
D3-16.2.2
(SEQ ID NO: 642)
155


 



MITF
D3-16.3.2
(SEQ ID NO: 643)
156


 



wLRL
D3-16.1.3
(SEQ ID NO: 650)
157


 



DYVW
D3-16.2.3
(SEQ ID NO: 651)
158


 



ITFG
D3-16.3.3
(SEQ ID NO: 652)
159


 



LRLG
D3-16.1.4
(SEQ ID NO: 659)
160


 



YVWG
D3-16.2.4
(SEQ ID NO: 660)
161


 



TFGG
D3-16.3.4
(SEQ ID NO: 661)
162


 



RLGE
D3-16.1.5
(SEQ ID NO: 668)
163


 



VWGS
D3-16.2.5
(SEQ ID NO: 669)
164


 



FGGV
D3-16.3.5
(SEQ ID NO: 670)
165


 



LGEL
D3-16.1.6
(SEQ ID NO: 677)
166


 



WGSY
D3-16.2.6
(SEQ ID NO: 678)
167


 



GGVI
D3-16.3.6
(SEQ ID NO: 679)
168


 



GELS
D3-16.1.7
(SEQ ID NO: 686)
169


 



GSYR
D3-16.2.7
(SEQ ID NO: 687)
170


 



GVIV
D3-16.3.7
(SEQ ID NO: 688)
171


 



ELSL
D3-16.1.8
(SEQ ID NO: 694)
172


 



SYRY
D3-16.2.8
(SEQ ID NO: 695)
173


 



VIVI
D3-16.3.8
(SEQ ID NO: 696)
174


 



LSLY
D3-16.1.9
(SEQ ID NO: 699)
175


 



YRYT
D3-16.2.9
(SEQ ID NO: 700)
176


 



VLLw
D3-22.1.1
(SEQ ID NO: 701)
177


 



YYYD
D3-22.2.1
(SEQ ID NO: 702)
178


 



ITMI
D3-22.3.1
(SEQ ID NO: 703)
179


 



LLwy
D3-22.1.2
(SEQ ID NO: 710)
180


 



YYDS
D3-22.2.2
(SEQ ID NO: 711)
181


 



TMIV
D3-22.3.2
(SEQ ID NO: 712)
182


 



Lwyy
D3-22.1.3
(SEQ ID NO: 719)
183


 



YDSS
D3-22.2.3
(SEQ ID NO: 720)
184


 



MIVV
D3-22.3.3
(SEQ ID NO: 721)
185


 



wyyW
D3-22.1.4
(SEQ ID NO: 728)
186


 



DSSG
D3-22.2.4
(SEQ ID NO: 729)
187


 



yyWL
D3-22.1.5
(SEQ ID NO: 736)
188


 



SSGY
D3-22.2.5
(SEQ ID NO: 737)
189


 



VVVI
D3-22.3.5
(SEQ ID NO: 738)
190


 



yWLL
D3-22.1.6
(SEQ ID NO: 744)
191


 



VVIT
D3-22.3.6
(SEQ ID NO: 745)
192


 



WLLL
D3-22.1.7
(SEQ ID NO: 748)
193


 



GYYY
D3-22.2.7
(SEQ ID NO: 749)
194


 



wLQy
D4-4.1.1
(SEQ ID NO: 750)
195


 



DYSN
D4-4.2.1
(SEQ ID NO: 751)
196


 



TTVT
D4-4.3.1
(SEQ ID NO: 752)
197


 



LQyL
D4-4.1.2
(SEQ ID NO: 755)
198


 



YSNY
D4-4.2.2
(SEQ ID NO: 756)
199


 



wLRw
D4-17.1.1
(SEQ ID NO: 757)
200


 



DYGD
D4-17.2.1
(SEQ ID NO: 758)
201


 



LRwL
D4-17.1.2
(SEQ ID NO: 761)
202


 



YGDY
D4-17.2.2
(SEQ ID NO: 762)
203


 



wLRW
D4-23.1.1
(SEQ ID NO: 763)
204


 



DYGG
D4-23.2.1
(SEQ ID NO: 764)
205


 



TTVV
D4-23.3.1
(SEQ ID NO: 765)
206


 



LRWy
D4-23.1.2
(SEQ ID NO: 771)
207


 



YGGN
D4-23.2.2
(SEQ ID NO: 772)
208


 



TVVT
D4-23.3.2
(SEQ ID NO: 773)
209


 



RWyL
D4-23.1.3
(SEQ ID NO: 776)
210


 



GGNS
D4-23.2.3
(SEQ ID NO: 777)
211


 



VDTA
D5-5.1.1
(SEQ ID NO: 778)
212


 



WIQL
D5-5.2.1
(SEQ ID NO: 779)
213


 



GYSY
D5-5.3.1
(SEQ ID NO: 780)
214


 



DTAM
D5-5.1.2
(SEQ ID NO: 787)
215


 



IQLW
D5-5.2.2
(SEQ ID NO: 788)
216


 



YSYG
D5-5.3.2
(SEQ ID NO: 789)
217


 



TAMV
D5-5.1.3
(SEQ ID NO: 793)
218


 



QLWL
D5-5.2.3
(SEQ ID NO: 794)
219


 



SYGY
D5-5.3.3
(SEQ ID NO: 795)
220


 



VDIV
D5-12.1.1
(SEQ ID NO: 796)
221


 



WIyW
D5-12.2.1
(SEQ ID NO: 797)
222


 



GYSG
D5-12.3.1
(SEQ ID NO: 798)
223


 



DIVA
D5-12.1.2
(SEQ ID NO: 805)
224


 



IyWL
D5-12.2.2
(SEQ ID NO: 806)
225


 



YSGY
D5-12.3.2
(SEQ ID NO: 807)
226


 



IVAT
D5-12.1.3
(SEQ ID NO: 814)
227


 



yWLR
D5-12.2.3
(SEQ ID NO: 815)
228


 



SGYD
D5-12.3.3
(SEQ ID NO: 816)
229


 



VATI
D5-12.1.4
(SEQ ID NO: 820)
230


 



WLRL
D5-12.2.4
(SEQ ID NO: 821)
231


 



GYDY
D5-12.3.4
(SEQ ID NO: 822)
232


 



VEMA
D5-24.1.1
(SEQ ID NO: 823)
233


 



yRWL
D5-24.2.1
(SEQ ID NO: 824)
234


 



RDGY
D5-24.3.1
(SEQ ID NO: 825)
235


 



EMAT
D5-24.1.2
(SEQ ID NO: 832)
236


 



RWLQ
D5-24.2.2
(SEQ ID NO: 833)
237


 



DGYN
D5-24.3.2
(SEQ ID NO: 834)
238


 



MATI
D5-24.1.3
(SEQ ID NO: 838)
239


 



WLQL
D5-24.2.3
(SEQ ID NO: 839)
240


 



GYNY
D5-24.3.3
(SEQ ID NO: 840)
241


 



EYSS
D6-6.1.1
(SEQ ID NO: 841)
242


 



SIAA
D6-6.2.1
(SEQ ID NO: 842)
243


 



VyQL
D6-6.3.1
(SEQ ID NO: 843)
244


 



YSSS
D6-6.1.2
(SEQ ID NO: 848)
245


 



IAAR
D6-6.2.2
(SEQ ID NO: 849)
246


 



yQLV
D6-6.3.2
(SEQ ID NO: 850)
247


 



SSSS
D6-6.1.3
(SEQ ID NO: 852)
248


 



GYSS
D6-13.1.1
(SEQ ID NO: 853)
249


 



GIAA
D6-13.2.1
(SEQ ID NO: 854)
250


 



VyQQ
D6-13.3.1
(SEQ ID NO: 855)
251


 



IAAA
D6-13.2.2
(SEQ ID NO: 862)
252


 



yQQL
D6-13.3.2
(SEQ ID NO: 863)
253


 



SSSW
D6-13.1.3
(SEQ ID NO: 868)
254


 



AAAG
D6-13.2.3
(SEQ ID NO: 869)
255


 



QQLV
D6-13.3.3
(SEQ ID NO: 870)
256


 



SSWY
D6-13.1.4
(SEQ ID NO: 872)
257


 



GIAV
D6-19.2.1
(SEQ ID NO: 873)
258


 



VyQW
D6-19.3.1
(SEQ ID NO: 874)
259


 



YSSG
D6-19.1.2
(SEQ ID NO: 881)
260


 



IAVA
D6-19.2.2
(SEQ ID NO: 882)
261


 



yQWL
D6-19.3.2
(SEQ ID NO: 883)
262


 



SSGW
D6-19.1.3
(SEQ ID NO: 888)
263


 



AVAG
D6-19.2.3
(SEQ ID NO: 889)
264


 



QWLV
D6-19.3.3
(SEQ ID NO: 890)
265


 



SGWY
D6-19.1.4
(SEQ ID NO: 892)
266
















TABLE 13





Pentamers that can be extracted


from human D segments




















GTTGT
D1-1.1.1
(SEQ ID NO: 260)
1



 



VQLER
D1-1.2.1
(SEQ ID NO: 261)
2



 



YNWND
D1-1.3.1
(SEQ ID NO: 262)
3



 



GITGT
D1-7.1.1
(SEQ ID NO: 268)
4



 



VyLEL
D1-7.2.1
(SEQ ID NO: 269)
5



 



YNWNY
D1-7.3.1
(SEQ ID NO: 270)
6



 



VyLER
D1-20.2.1
(SEQ ID NO: 274)
7



 



GIVGA
D1-26.1.1
(SEQ ID NO: 279)
8



 



VyWEL
D1-26.2.1
(SEQ ID NO: 280)
9



 



YSGSY
D1-26.3.1
(SEQ ID NO: 281)
10



 



IVGAT
D1-26.1.2
(SEQ ID NO: 288)
11



 



yWELL
D1-26.2.2
(SEQ ID NO: 289)
12



 



SGSYY
D1-26.3.2
(SEQ ID NO: 290)
13



 



RILyy
D2-2.1.1
(SEQ ID NO: 297)
14



 



GYCSS
D2-2.2.1
(SEQ ID NO: 298)
15



 



DIVVV
D2-2.3.1
(SEQ ID NO: 299)
16



 



ILyyY
D2-2.1.2
(SEQ ID NO: 306)
17



 



YCSST
D2-2.2.2
(SEQ ID NO: 307)
18



 



IVVVP
D2-2.3.2
(SEQ ID NO: 308)
19



 



LyyYQ
D2-2.1.3
(SEQ ID NO: 315)
20



 



CSSTS
D2-2.2.3
(SEQ ID NO: 316)
21



 



VVVPA
D2-2.3.3
(SEQ ID NO: 317)
22



 



yyYQL
D2-2.1.4
(SEQ ID NO: 324)
23



 



SSTSC
D2-2.2.4
(SEQ ID NO: 325)
24



 



VVPAA
D2-2.3.4
(SEQ ID NO: 326)
25



 



yYQLL
D2-2.1.5
(SEQ ID NO: 333)
26



 



STSCY
D2-2.2.5
(SEQ ID NO: 334)
27



 



VPAAI
D2-2.3.5
(SEQ ID NO: 335)
28



 



YQLLY
D2-2.1.6
(SEQ ID NO: 341)
29



 



TSCYT
D2-2.2.6
(SEQ ID NO: 342)
30



 



RILYy
D2-8.1.1
(SEQ ID NO: 348)
31



 



GYCTN
D2-8.2.1
(SEQ ID NO: 349)
32



 



DIVLM
D2-8.3.1
(SEQ ID NO: 350)
33



 



ILYyW
D2-8.1.2
(SEQ ID NO: 357)
34



 



YCTNG
D2-8.2.2
(SEQ ID NO: 358)
35



 



IVLMV
D2-8.3.2
(SEQ ID NO: 359)
36



 



LYyWC
D2-8.1.3
(SEQ ID NO: 366)
37



 



CTNGV
D2-8.2.3
(SEQ ID NO: 367)
38



 



VLMVY
D2-8.3.3
(SEQ ID NO: 368)
39



 



YyWCM
D2-8.1.4
(SEQ ID NO: 375)
40



 



TNGVC
D2-8.2.4
(SEQ ID NO: 376)
41



 



LMVYA
D2-8.3.4
(SEQ ID NO: 377)
42



 



yWCML
D2-8.1.5
(SEQ ID NO: 384)
43



 



NGVCY
D2-8.2.5
(SEQ ID NO: 385)
44



 



MVYAI
D2-8.3.5
(SEQ ID NO: 386)
45



 



WCMLY
D2-8.1.6
(SEQ ID NO: 392)
46



 



GVCYT
D2-8.2.6
(SEQ ID NO: 393)
47



 



RILyW
D2-15.1.1
(SEQ ID NO: 396)
48



 



GYCSG
D2-15.2.1
(SEQ ID NO: 397)
49



 



ILyWW
D2-15.1.2
(SEQ ID NO: 403)
50



 



YCSGG
D2-15.2.2
(SEQ ID NO: 404)
51



 



IVVVV
D2-15.3.2
(SEQ ID NO: 405)
52



 



LyWWy
D2-15.1.3
(SEQ ID NO: 412)
53



 



CSGGS
D2-15.2.3
(SEQ ID NO: 413)
54



 



VVVVA
D2-15.3.3
(SEQ ID NO: 414)
55



 



yWWyL
D2-15.1.4
(SEQ ID NO: 421)
56



 



SGGSC
D2-15.2.4
(SEQ ID NO: 422)
57



 



VVVAA
D2-15.3.4
(SEQ ID NO: 423)
58



 



WWyLL
D2-15.1.5
(SEQ ID NO: 430)
59



 



GGSCY
D2-15.2.5
(SEQ ID NO: 431)
60



 



VVAAT
D2-15.3.5
(SEQ ID NO: 432)
61



 



WyLLL
D2-15.1.6
(SEQ ID NO: 438)
62



 



GSCYS
D2-15.2.6
(SEQ ID NO: 439)
63



 



SILWW
D2-21.1.1
(SEQ ID NO: 445)
64



 



AYCGG
D2-21.2.1
(SEQ ID NO: 446)
65



 



HIVVV
D2-21.3.1
(SEQ ID NO: 447)
66



 



ILWWw
D2-21.1.2
(SEQ ID NO: 453)
67



 



YCGGD
D2-21.2.2
(SEQ ID NO: 454)
68



 



IVVVT
D2-21.3.2
(SEQ ID NO: 455)
69



 



LWWwL
D2-21.1.3
(SEQ ID NO: 462)
70



 



CGGDC
D2-21.2.3
(SEQ ID NO: 463)
71



 



VVVTA
D2-21.3.3
(SEQ ID NO: 464)
72



 



WWwLL
D2-21.1.4
(SEQ ID NO: 471)
73



 



GGDCY
D2-21.2.4
(SEQ ID NO: 472)
74



 



VVTAI
D2-21.3.4
(SEQ ID NO: 473)
75



 



WwLLF
D2-21.1.5
(SEQ ID NO: 479)
76



 



GDCYS
D2-21.2.5
(SEQ ID NO: 480)
77



 



VLRFL
D3-3.1.1
(SEQ ID NO: 486)
78



 



YYDFW
D3-3.2.1
(SEQ ID NO: 487)
79



 



ITIFG
D3-3.3.1
(SEQ ID NO: 488)
80



 



LRFLE
D3-3.1.2
(SEQ ID NO: 495)
81



 



YDFWS
D3-3.2.2
(SEQ ID NO: 496)
82



 



TIFGV
D3-3.3.2
(SEQ ID NO: 497)
83



 



RFLEW
D3-3.1.3
(SEQ ID NO: 504)
84



 



DFWSG
D3-3.2.3
(SEQ ID NO: 505)
85



 



IFGVV
D3-3.3.3
(SEQ ID NO: 506)
86



 



FLEWL
D3-3.1.4
(SEQ ID NO: 513)
87



 



FWSGY
D3-3.2.4
(SEQ ID NO: 514)
88



 



FGVVI
D3-3.3.4
(SEQ ID NO: 515)
89



 



LEWLL
D3-3.1.5
(SEQ ID NO: 522)
90



 



WSGYY
D3-3.2.5
(SEQ ID NO: 523)
91



 



GVVII
D3-3.3.5
(SEQ ID NO: 524)
92



 



EWLLY
D3-3.1.6
(SEQ ID NO: 530)
93



 



SGYYT
D3-3.2.6
(SEQ ID NO: 531)
94



 



VLRYF
D3-9.1.1
(SEQ ID NO: 536)
95



 



YYDIL
D3-9.2.1
(SEQ ID NO: 537)
96



 



ITIFy
D3-9.3.1
(SEQ ID NO: 538)
97



 



LRYFD
D3-9.1.2
(SEQ ID NO: 545)
98



 



YDILT
D3-9.2.2
(SEQ ID NO: 546)
99



 



TIFyL
D3-9.3.2
(SEQ ID NO: 547)
100



 



RYFDW
D3-9.1.3
(SEQ ID NO: 554)
101



 



DILTG
D3-9.2.3
(SEQ ID NO: 555)
102



 



IFyLV
D3-9.3.3
(SEQ ID NO: 556)
103



 



YFDWL
D3-9.1.4
(SEQ ID NO: 563)
104



 



ILTGY
D3-9.2.4
(SEQ ID NO: 564)
105



 



FyLVI
D3-9.3.4
(SEQ ID NO: 565)
106



 



FDWLL
D3-9.1.5
(SEQ ID NO: 572)
107



 



LTGYY
D3-9.2.5
(SEQ ID NO: 573)
108



 



yLVII
D3-9.3.5
(SEQ ID NO: 574)
109



 



DWLLy
D3-9.1.6
(SEQ ID NO: 580)
110



 



TGYYN
D3-9.2.6
(SEQ ID NO: 581)
111



 



VLLWF
D3-10.1.1
(SEQ ID NO: 587)
112



 



YYYGS
D3-10.2.1
(SEQ ID NO: 588)
113



 



ITMVR
D3-10.3.1
(SEQ ID NO: 589)
114



 



LLWFG
D3-10.1.2
(SEQ ID NO: 596)
115



 



YYGSG
D3-10.2.2
(SEQ ID NO: 597)
116



 



TMVRG
D3-10.3.2
(SEQ ID NO: 598)
117



 



LWFGE
D3-10.1.3
(SEQ ID NO: 605)
118



 



YGSGS
D3-10.2.3
(SEQ ID NO: 606)
119



 



MVRGV
D3-10.3.3
(SEQ ID NO: 607)
120



 



WFGEL
D3-10.1.4
(SEQ ID NO: 614)
121



 



GSGSY
D3-10.2.4
(SEQ ID NO: 615)
122



 



VRGVI
D3-10.3.4
(SEQ ID NO: 616)
123



 



FGELL
D3-10.1.5
(SEQ ID NO: 622)
124



 



RGVII
D3-10.3.5
(SEQ ID NO: 623)
125



 



GELLy
D3-10.1.6
(SEQ ID NO: 628)
126



 



GSYYN
D3-10.2.6
(SEQ ID NO: 629)
127



 



VLwLR
D3-16.1.1
(SEQ ID NO: 635)
128



 



YYDYV
D3-16.2.1
(SEQ ID NO: 636)
129



 



IMITF
D3-16.3.1
(SEQ ID NO: 637)
130



 



LwLRL
D3-16.1.2
(SEQ ID NO: 644)
131



 



YDYVW
D3-16.2.2
(SEQ ID NO: 645)
132



 



MITFG
D3-16.3.2
(SEQ ID NO: 646)
133



 



wLRLG
D3-16.1.3
(SEQ ID NO: 653)
134



 



DYVWG
D3-16.2.3
(SEQ ID NO: 654)
135



 



ITFGG
D3-16.3.3
(SEQ ID NO: 655)
136



 



LRLGE
D3-16.1.4
(SEQ ID NO: 662)
137



 



YVWGS
D3-16.2.4
(SEQ ID NO: 663)
138



 



TFGGV
D3-16.3.4
(SEQ ID NO: 664)
139



 



RLGEL
D3-16.1.5
(SEQ ID NO: 671)
140



 



VWGSY
D3-16.2.5
(SEQ ID NO: 672)
141



 



FGGVI
D3-16.3.5
(SEQ ID NO: 673)
142



 



LGELS
D3-16.1.6
(SEQ ID NO: 680)
143



 



WGSYR
D3-16.2.6
(SEQ ID NO: 681)
144



 



GGVIV
D3-16.3.6
(SEQ ID NO: 682)
145



 



GELSL
D3-16.1.7
(SEQ ID NO: 689)
146



 



GSYRY
D3-16.2.7
(SEQ ID NO: 690)
147



 



GVIVI
D3-16.3.7
(SEQ ID NO: 691)
148



 



ELSLY
D3-16.1.8
(SEQ ID NO: 697)
149



 



SYRYT
D3-16.2.8
(SEQ ID NO: 698)
150



 



VLLwy
D3-22.1.1
(SEQ ID NO: 704)
151



 



YYYDS
D3-22.2.1
(SEQ ID NO: 705)
152



 



ITMIV
D3-22.3.1
(SEQ ID NO: 706)
153



 



LLwyy
D3-22.1.2
(SEQ ID NO: 713)
154



 



YYDSS
D3-22.2.2
(SEQ ID NO: 714)
155



 



TMIVV
D3-22.3.2
(SEQ ID NO: 715)
156



 



LwyyW
D3-22.1.3
(SEQ ID NO: 722)
157



 



YDSSG
D3-22.2.3
(SEQ ID NO: 723)
158



 



MIVVV
D3-22.3.3
(SEQ ID NO: 724)
159



 



wyyWL
D3-22.1.4
(SEQ ID NO: 730)
160



 



DSSGY
D3-22.2.4
(SEQ ID NO: 731)
161



 



IVVVI
D3-22.3.4
(SEQ ID NO: 732)
162



 



yyWLL
D3-22.1.5
(SEQ ID NO: 739)
163



 



SSGYY
D3-22.2.5
(SEQ ID NO: 740)
164



 



VVVIT
D3-22.3.5
(SEQ ID NO: 741)
165



 



yWLLL
D3-22.1.6
(SEQ ID NO: 746)
166



 



SGYYY
D3-22.2.6
(SEQ ID NO: 747)
167



 



wLQyL
D4-4.1.1
(SEQ ID NO: 753)
168



 



DYSNY
D4-4.2.1
(SEQ ID NO: 754)
169



 



wLRwL
D4-17.1.1
(SEQ ID NO: 759)
170



 



DYGDY
D4-17.2.1
(SEQ ID NO: 760)
171



 



wLRWy
D4-23.1.1
(SEQ ID NO: 766)
172



 



DYGGN
D4-23.2.1
(SEQ ID NO: 767)
173



 



TTVVT
D4-23.3.1
(SEQ ID NO: 768)
174



 



LRWyL
D4-23.1.2
(SEQ ID NO: 774)
175



 



YGGNS
D4-23.2.2
(SEQ ID NO: 775)
176



 



VDTAM
D5-5.1.1
(SEQ ID NO: 781)
177



 



WIQLW
D5-5.2.1
(SEQ ID NO: 782)
178



 



GYSYG
D5-5.3.1
(SEQ ID NO: 783)
179



 



DTAMV
D5-5.1.2
(SEQ ID NO: 790)
180



 



IQLWL
D5-5.2.2
(SEQ ID NO: 791)
181



 



YSYGY
D5-5.3.2
(SEQ ID NO: 792)
182



 



VDIVA
D5-12.1.1
(SEQ ID NO: 799)
183



 



WIyWL
D5-12.2.1
(SEQ ID NO: 800)
184



 



GYSGY
D5-12.3.1
(SEQ ID NO: 801)
185



 



DIVAT
D5-12.1.2
(SEQ ID NO: 808)
186



 



IyWLR
D5-12.2.2
(SEQ ID NO: 809)
187



 



YSGYD
D5-12.3.2
(SEQ ID NO: 810)
188



 



IVATI
D5-12.1.3
(SEQ ID NO: 817)
189



 



yWLRL
D5-12.2.3
(SEQ ID NO: 818)
190



 



SGYDY
D5-12.3.3
(SEQ ID NO: 819)
191



 



VEMAT
D5-24.1.1
(SEQ ID NO: 826)
192



 



yRWLQ
D5-24.2.1
(SEQ ID NO: 827)
193



 



RDGYN
D5-24.3.1
(SEQ ID NO: 828)
194



 



EMATI
D5-24.1.2
(SEQ ID NO: 835)
195



 



RWLQL
D5-24.2.2
(SEQ ID NO: 836)
196



 



DGYNY
D5-24.3.2
(SEQ ID NO: 837)
197



 



EYSSS
D6-6.1.1
(SEQ ID NO: 844)
198



 



SIAAR
D6-6.2.1
(SEQ ID NO: 845)
199



 



VyQLV
D6-6.3.1
(SEQ ID NO: 846)
200



 



YSSSS
D6-6.1.2
(SEQ ID NO: 851)
201



 



GYSSS
D6-13.1.1
(SEQ ID NO: 856)
202



 



GIAAA
D6-13.2.1
(SEQ ID NO: 857)
203



 



VyQQL
D6-13.3.1
(SEQ ID NO: 858)
204



 



YSSSW
D6-13.1.2
(SEQ ID NO: 864)
205



 



IAAAG
D6-13.2.2
(SEQ ID NO: 865)
206



 



yQQLV
D6-13.3.2
(SEQ ID NO: 866)
207



 



SSSWY
D6-13.1.3
(SEQ ID NO: 871)
208



 



GYSSG
D6-19.1.1
(SEQ ID NO: 875)
209



 



GIAVA
D6-19.2.1
(SEQ ID NO: 876)
210



 



VyQWL
D6-19.3.1
(SEQ ID NO: 877)
211



 



YSSGW
D6-19.1.2
(SEQ ID NO: 884)
212



 



IAVAG
D6-19.2.2
(SEQ ID NO: 885)
213



 



yQWLV
D6-19.3.2
(SEQ ID NO: 886)
214



 



SSGWY
D6-19.1.3
(SEQ ID NO: 891)
215

















TABLE 14





All hexamers that can be extracted


from human D segments




















GIVGAT
D1-26.1.1
(SEQ ID NO: 282)
1



 



VyWELL
D1-26.2.1
(SEQ ID NO: 283)
2



 



YSGSYY
D1-26.3.1
(SEQ ID NO: 284)
3



 



RILyyY
D2-2.1.1
(SEQ ID NO: 300)
4



 



GYCSST
D2-2.2.1
(SEQ ID NO: 301)
5



 



DIVVVP
D2-2.3.1
(SEQ ID NO: 302)
6



 



ILyyYQ
D2-2.1.2
(SEQ ID NO: 309)
7



 



YCSSTS
D2-2.2.2
(SEQ ID NO: 310)
8



 



IVVVPA
D2-2.3.2
(SEQ ID NO: 311)
9



 



LyyYQL
D2-2.1.3
(SEQ ID NO: 318)
10



 



CSSTSC
D2-2.2.3
(SEQ ID NO: 319)
11



 



VVVPAA
D2-2.3.3
(SEQ ID NO: 320)
12



 



yyYQLL
D2-2.1.4
(SEQ ID NO: 327)
13



 



SSTSCY
D2-2.2.4
(SEQ ID NO: 328)
14



 



VVPAAI
D2-2.3.4
(SEQ ID NO: 329)
15



 



yYQLLY
D2-2.1.5
(SEQ ID NO: 336)
16



 



STSCYT
D2-2.2.5
(SEQ ID NO: 337)
17



 



RILYyW
D2-8.1.1
(SEQ ID NO: 351)
18



 



GYCTNG
D2-8.2.1
(SEQ ID NO: 352)
19



 



DIVLMV
D2-8.3.1
(SEQ ID NO: 353)
20



 



ILYyWC
D2-8.1.2
(SEQ ID NO: 360)
21



 



YCTNGV
D2-8.2.2
(SEQ ID NO: 361)
22



 



IVLMVY
D2-8.3.2
(SEQ ID NO: 362)
23



 



LYyWCM
D2-8.1.3
(SEQ ID NO: 369)
24



 



CTNGVC
D2-8.2.3
(SEQ ID NO: 370)
25



 



VLMVYA
D2-8.3.3
(SEQ ID NO: 371)
26



 



YyWCML
D2-8.1.4
(SEQ ID NO: 378)
27



 



TNGVCY
D2-8.2.4
(SEQ ID NO: 379)
28



 



LMVYAI
D2-8.3.4
(SEQ ID NO: 380)
29



 



yWCMLY
D2-8.1.5
(SEQ ID NO: 387)
30



 



NGVCYT
D2-8.2.5
(SEQ ID NO: 388)
31



 



RILyWW
D2-15.1.1
(SEQ ID NO: 398)
32



 



GYCSGG
D2-15.2.1
(SEQ ID NO: 399)
33



 



DIVVVV
D2-15.3.1
(SEQ ID NO: 400)
34



 



ILyWWy
D2-15.1.2
(SEQ ID NO: 406)
35



 



YCSGGS
D2-15.2.2
(SEQ ID NO: 407)
36



 



IVVVVA
D2-15.3.2
(SEQ ID NO: 408)
37



 



LyWWyL
D2-15.1.3
(SEQ ID NO: 415)
38



 



CSGGSC
D2-15.2.3
(SEQ ID NO: 416)
39



 



VVVVAA
D2-15.3.3
(SEQ ID NO: 417)
40



 



yWWyLL
D2-15.1.4
(SEQ ID NO: 424)
41



 



SGGSCY
D2-15.2.4
(SEQ ID NO: 425)
42



 



VVVAAT
D2-15.3.4
(SEQ ID NO: 426)
43



 



WWyLLL
D2-15.1.5
(SEQ ID NO: 433)
44



 



GGSCYS
D2-15.2.5
(SEQ ID NO: 434)
45



 



SILWWw
D2-21.1.1
(SEQ ID NO: 448)
46



 



AYCGGD
D2-21.2.1
(SEQ ID NO: 449)
47



 



HIVVVT
D2-21.3.1
(SEQ ID NO: 450)
48



 



ILWWwL
D2-21.1.2
(SEQ ID NO: 456)
49



 



YCGGDC
D2-21.2.2
(SEQ ID NO: 457)
50



 



IVVVTA
D2-21.3.2
(SEQ ID NO: 458)
51



 



LWWwLL
D2-21.1.3
(SEQ ID NO: 465)
52



 



CGGDCY
D2-21.2.3
(SEQ ID NO: 466)
53



 



VVVTAI
D2-21.3.3
(SEQ ID NO: 467)
54



 



WWwLLF
D2-21.1.4
(SEQ ID NO: 474)
55



 



GGDCYS
D2-21.2.4
(SEQ ID NO: 475)
56



 



VLRFLE
D3-3.1.1
(SEQ ID NO: 489)
57



 



YYDFWS
D3-3.2.1
(SEQ ID NO: 490)
58



 



ITIFGV
D3-3.3.1
(SEQ ID NO: 491)
59



 



LRFLEW
D3-3.1.2
(SEQ ID NO: 498)
60



 



YDFWSG
D3-3.2.2
(SEQ ID NO: 499)
61



 



TIFGVV
D3-3.3.2
(SEQ ID NO: 500)
62



 



RFLEWL
D3-3.1.3
(SEQ ID NO: 507)
63



 



DFWSGY
D3-3.2.3
(SEQ ID NO: 508)
64



 



IFGVVI
D3-3.3.3
(SEQ ID NO: 509)
65



 



FLEWLL
D3-3.1.4
(SEQ ID NO: 516)
66



 



FWSGYY
D3-3.2.4
(SEQ ID NO: 517)
67



 



FGVVII
D3-3.3.4
(SEQ ID NO: 518)
68



 



LEWLLY
D3-3.1.5
(SEQ ID NO: 525)
69



 



WSGYYT
D3-3.2.5
(SEQ ID NO: 526)
70



 



VLRYFD
D3-9.1.1
(SEQ ID NO: 539)
71



 



YYDILT
D3-9.2.1
(SEQ ID NO: 540)
72



 



ITIFyL
D3-9.3.1
(SEQ ID NO: 541)
73



 



LRYFDW
D3-9.1.2
(SEQ ID NO: 548)
74



 



YDILTG
D3-9.2.2
(SEQ ID NO: 549)
75



 



TIFyLV
D3-9.3.2
(SEQ ID NO: 550)
76



 



RYFDWL
D3-9.1.3
(SEQ ID NO: 557)
77



 



DILTGY
D3-9.2.3
(SEQ ID NO: 558)
78



 



IFyLVI
D3-9.3.3
(SEQ ID NO: 559)
79



 



YFDWLL
D3-9.1.4
(SEQ ID NO: 566)
80



 



ILTGYY
D3-9.2.4
(SEQ ID NO: 567)
81



 



FyLVII
D3-9.3.4
(SEQ ID NO: 568)
82



 



FDWLLy
D3-9.1.5
(SEQ ID NO: 575)
83



 



LTGYYN
D3-9.2.5
(SEQ ID NO: 576)
84



 



VLLWFG
D3-10.1.1
(SEQ ID NO: 590)
85



 



YYYGSG
D3-10.2.1
(SEQ ID NO: 591)
86



 



ITMVRG
D3-10.3.1
(SEQ ID NO: 592)
87



 



LLWFGE
D3-10.1.2
(SEQ ID NO: 599)
88



 



YYGSGS
D3-10.2.2
(SEQ ID NO: 600)
89



 



TMVRGV
D3-10.3.2
(SEQ ID NO: 601)
90



 



LWFGEL
D3-10.1.3
(SEQ ID NO: 608)
91



 



YGSGSY
D3-10.2.3
(SEQ ID NO: 609)
92



 



MVRGVI
D3-10.3.3
(SEQ ID NO: 610)
93



 



WFGELL
D3-10.1.4
(SEQ ID NO: 617)
94



 



GSGSYY
D3-10.2.4
(SEQ ID NO: 618)
95



 



VRGVII
D3-10.3.4
(SEQ ID NO: 619)
96



 



FGELLy
D3-10.1.5
(SEQ ID NO: 624)
97



 



SGSYYN
D3-10.2.5
(SEQ ID NO: 625)
98



 



VLwLRL
D3-16.1.1
(SEQ ID NO: 638)
99



 



YYDYVW
D3-16.2.1
(SEQ ID NO: 639)
100



 



IMITFG
D3-16.3.1
(SEQ ID NO: 640)
101



 



LwLRLG
D3-16.1.2
(SEQ ID NO: 647)
102



 



YDYVWG
D3-16.2.2
(SEQ ID NO: 648)
103



 



MITFGG
D3-16.3.2
(SEQ ID NO: 649)
104



 



wLRLGE
D3-16.1.3
(SEQ ID NO: 656)
105



 



DYVWGS
D3-16.2.3
(SEQ ID NO: 657)
106



 



ITFGGV
D3-16.3.3
(SEQ ID NO: 658)
107



 



LRLGEL
D3-16.1.4
(SEQ ID NO: 665)
108



 



YVWGSY
D3-16.2.4
(SEQ ID NO: 666)
109



 



TFGGVI
D3-16.3.4
(SEQ ID NO: 667)
110



 



RLGELS
D3-16.1.5
(SEQ ID NO: 674)
111



 



VWGSYR
D3-16.2.5
(SEQ ID NO: 675)
112



 



FGGVIV
D3-16.3.5
(SEQ ID NO: 676)
113



 



LGELSL
D3-16.1.6
(SEQ ID NO: 683)
114



 



WGSYRY
D3-16.2.6
(SEQ ID NO: 684)
115



 



GGVIVI
D3-16.3.6
(SEQ ID NO: 685)
116



 



GELSLY
D3-16.1.7
(SEQ ID NO: 692)
117



 



GSYRYT
D3-16.2.7
(SEQ ID NO: 693)
118



 



VLLwyy
D3-22.1.1
(SEQ ID NO: 707)
119



 



YYYDSS
D3-22.2.1
(SEQ ID NO: 708)
120



 



ITMIVV
D3-22.3.1
(SEQ ID NO: 709)
121



 



LLwyyW
D3-22.1.2
(SEQ ID NO: 716)
122



 



YYDSSG
D3-22.2.2
(SEQ ID NO: 717)
123



 



TMIVVV
D3-22.3.2
(SEQ ID NO: 718)
124



 



LwyyWL
D3-22.1.3
(SEQ ID NO: 725)
125



 



YDSSGY
D3-22.2.3
(SEQ ID NO: 726)
126



 



MIVVVI
D3-22.3.3
(SEQ ID NO: 727)
127



 



wyyWLL
D3-22.1.4
(SEQ ID NO: 733)
128



 



DSSGYY
D3-22.2.4
(SEQ ID NO: 734)
129



 



IVVVIT
D3-22.3.4
(SEQ ID NO: 735)
130



 



yyWLLL
D3-22.1.5
(SEQ ID NO: 742)
131



 



SSGYYY
D3-22.2.5
(SEQ ID NO: 743)
132



 



wLRWyL
D4-23.1.1
(SEQ ID NO: 769)
133



 



DYGGNS
D4-23.2.1
(SEQ ID NO: 770)
134



 



VDTAMV
D5-5.1.1
(SEQ ID NO: 784)
135



 



WIQLWL
D5-5.2.1
(SEQ ID NO: 785)
136



 



GYSYGY
D5-5.3.1
(SEQ ID NO: 786)
137



 



VDIVAT
D5-12.1.1
(SEQ ID NO: 802)
138



 



WIyWLR
D5-12.2.1
(SEQ ID NO: 803)
139



 



GYSGYD
D5-12.3.1
(SEQ ID NO: 804)
140



 



DIVATI
D5-12.1.2
(SEQ ID NO: 811)
141



 



IyWLRL
D5-12.2.2
(SEQ ID NO: 812)
142



 



YSGYDY
D5-12.3.2
(SEQ ID NO: 813)
143



 



VEMATI
D5-24.1.1
(SEQ ID NO: 829)
144



 



yRWLQL
D5-24.2.1
(SEQ ID NO: 830)
145



 



RDGYNY
D5-24.3.1
(SEQ ID NO: 831)
146



 



EYSSSS
D6-6.1.1
(SEQ ID NO: 847)
147



 



GYSSSW
D6-13.1.1
(SEQ ID NO: 859)
148



 



GIAAAG
D6-13.2.1
(SEQ ID NO: 860)
149



 



VyQQLV
D6-13.3.1
(SEQ ID NO: 861)
150



 



YSSSWY
D6-13.1.2
(SEQ ID NO: 867)
151



 



GYSSGW
D6-19.1.1
(SEQ ID NO: 878)
152



 



GIAVAG
D6-19.2.1
(SEQ ID NO: 879)
153



 



VyQWLV
D6-19.3.1
(SEQ ID NO: 880)
154



 



YSSGWY
D6-19.1.2
(SEQ ID NO: 887)
155










Example 3: CDR3 of Length 6-20
Insertion of D segments into synthetic HC CDR3s can lead to greater stability and lower immunogenicity. Libraries are designed at the amino-acid level by joining a VH to an optional filler of some length which is joined to a D segment an optional second filler and a JH. For libraries of length six or eight, a full-length JH may follow VH and a short filler. Where D segments are used, the D segments D2-2(RF 2), D2-8(RF 2), D2-15(RF 2), D2-21(RF 2), D3-16(RF 2), D3-22 (RF 2), D3-3 (RF-2), D3-9 (RF 2), D3-10 (RF 2), D1-26 (RF 3), D4-11 (RF 2), D4-4 (RF 2), D5-5 (RF 3), D5-12 (RF 3), D5-18 (RF 3), D6-6 (RF1), D6-13 (RF 1), and D6-19 (RF 1) are preferred.
Once the parental amino-acid sequence has been designed, it can be diversified in several ways: error-prone PCR, wobbling, and dobbling. Table 14 shows a number of hexamers that can be derived from human D regions. In one embodiment, the hexamers that contain cysteine residues are excused. In one embodiment, the fragments of D regions that contain stops are excluded. In one embodiment, any TAG codon found in the D region is replaced by a codon picked from the set comprising TCG, TTG, TGG, CAG, AAG, TAT, and GAG. In one embodiment, any TAA codon found in the D region is replaced by a codon picked form the set comprising TCA, TTA, CAA, AAA, TAT, and GAA. In one embodiment, any TGA of the D region is replaced by a codon picked from the set comprising TGG, TCA, TTA, AGA, and GGA.
Table 21 shows exemplary parental amino-acid sequences for CDR3s from 6 to 20 amino acids. These parental sequences can be combined with diversity in HC CDR1 and CDR2 to form a library. The utility is likely to improve if the CDR3 regions are diversified by, for example, wobbling, dobbling, or error-prone PCR of the CDR3s. In Table 21, sequence 6a comprises the end of VH from 3-23 fused to whole JH1. Sequence 6b contains the end of 3-23 joined to a Y joined to D4-17 (RF 2) joined to the FR4 region of JH1. Sequence 6c contains the end of 3-23 followed by D5-5 (RF 3) followed by the FR4 part of JH1. Sequence 6d contains the end of 3-23 joined to SY joined to the whole JH4. Table 21 shows the level of doping that would be appropriate for the wobbling of the CDR3; other levels could be used as well. Other D regions or fragments of D regions could be used. Other JH sequences could be used.







TABLE 21







Parental amino-acid sequences for HC CDR3s of 6-20 AAs.














level of





Length
Parental sequence
doping
Comment
SEQ ID NO:





 6a
              yycakAEYFQHwgqgtlvtvss
70:10:10:10
JH1(whole)
226



 


 6b
              yycakYDYGDYwgqgtlvtvss
70:10:10:10
Y::D4-17(2)::FR4 of JH1
227


 


 6c
              yycakGYSYGYwgqgtlvtvss
70:10:10:10
D5-5(3)::FR4 of JH1
228


 


 6d
              yycakSYYFDYwgqgtlvtvss
70:10:10:10
SY::JH4(whole)
229


 


 8a
            yycakYYAEYFQHwgqgtlvtvss
73:9:9:9
YY:JH1(whole)
230


 


 8b
            yycakYGYSSSWYwgqgtlvtvss
73:9:9:9
Y::D6-13(1)::FR4 of JH1
231


 


 8c
            yycakYGDYYFDYwgqgtlvtvss
73:9:9:9
D4-17(2)[2-5]::JH4(whole)
232


 


10a
          yycakYYYDSSGYYYwgqgtlvtvss
73:9:9:9
D3-22(2)::Fr4 of JH1
233


 


10b
          yycakGYcSSTScYTwgqgtlvtvss
73:9:9:9
D2-2(2)::Fr4 of JH1
234


 


10c
          yycakYYSSAEYFQHwgqgtlvtvss
73:9:9:9
YYSS::JH1(whole)
235


 


10d
          yycakGYSYGYYFDYwgqgtlvtvss
73:9:9:9
D5-5(3)::JH4(whole)
236


 


12a
        yycakYYYDSSGYYYQHwgqgtlvtvss
85:5:5:5
D3-22(2)::QH::Fr4 of JH1
237


 


12b
        yycakGYcSSTScYTQHwgqgtlvtvss
85:5:5:5
D2-2(2)::QH::Fr4 of JH1
238


 


12c
        yycakYYSSYSAEYFQHwgqgtlvtvss
85:5:5:5
YYSSYS::JH1(whole)
239


 


12d
        yycakYYDYVWGSYRYTwgqgtlvtvss
85:5:5:5
D3-16(2)::Fr of JH1
240


 


12e
        yycakGYSYGYYWYFDLwgrgtlvtvss
85:5:5:5
D5-5(3)::JH2(whole)
241


 


14a
      yycakYYYDSSGYYYYFQHwgqgtlvtvss
73:9:9:9
D3-22(2)::YFQH::Fr of JH1
242


 


14b
      yycakGYcSSTScYTYFQHwgqgtlvtvss
73:9:9:9
D2-2(2)::YFQH::Fr of JH1
243


 


14c
      yycakSYGYcSSTScYTQHwgqgtlvtvss
73:9:9:9
SY::D2-2(2)::QH::Fr of JH1
244


 


14d
      yycakSYYYSSYSAEYFQHwgqgtlvtvss
73:9:9:9
SYYYSSYS::JH1(whole)
245


 


14e
      yycakAYcGGDcYSNWFDPwgqgtlvtvss
73:9:9:9
D2-21(2)::JH5(whole)
246


 


16a
    yycakYYYDSSGYYYAEYFQHwgqgtlvtvss
73:9:9:9
D3-22(2)::JH1(whole)
247


 


16b
    yycakGYcSSTScYTAEYFQHwgqgtlvtvss
73:9:9:9
D2-2(2)::JH1(whole)
248


 


16c
    yycakSYYSYSSYYSAEYFQHwgqgtlvtvss
73:9:9:9
SYYSYSSYYS::JH1(whole)
249


 


16d
    yycakSYSYGYcSSTScYTQHwgqgtlvtvss
73:9:9:9
SYSY::D2-2(2)::QH::Fr JH1
250


 


20a
yycakYSSYYYYDSSGYYYAEYFQHwgqgtlvtvss
73:9:9:9
YSSY::D3-22(2)::JH1(whole)
251


 


20b
yycakSYYSGYcSSTScYTAEYFQHwgqgtlvtvss
73:9:9:9
SYYS::D2-2(2)::JH1(whole)
252


 


20c
yycakSGYcSSTScYTYYSAEYFQHwgqgtlvtvss
73:9:9:9
S::D2-2(2)::YYS::JH1(whole)
253


 


20d
yycakYYYYDYVWGSYRYTSNWFDPwgqgtlvtvss
73:9:9:9
Y::D3-16(2)::S::JH5(whole)
254


 


20e
yycakYYYYDYVWGSYRYTSSYFDYwgqgtlvtvss
73:9:9:9
Y::D3-16(2)::SS::JH4(whole)
255
















TABLE 22





HC display cassette


















!

 Signal for VH-CH1-IIIstump



!

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


!

 M   K   Y   L   L   P   T   A   A   A   G   L   L   L   L



 946
atg aaa tac cta ttg cct acg gca gcc gct gga ttg tta tta ctc


!


!

 16  17  18  19  20  21  22


!

 A   A   Q   P   A   M   A



 991
gcG GCC cag ccG GCC atg gcc


!

  SfiI.............


!

          NgoMI...(1/2)


!

                 NcoI....


!


!
VH


!

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


!

                             1   2   3   4   5   6   7   8


!

                             E   V   Q   L   L   E   S   G



1012
                             gaa|gtt|CAA|TTG|tta|gag|tct|ggt|


!

                                    | MfeI  |


!


!

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


!

  9  10  11  12  13  14  15  16  17  18  19  20  21  22  23


!

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



1036
|ggc|ggt|ctt|gtt|cag|cct|ggt|ggt|tct|tta|cgt|ctt|tct|tgc|gct|


!


!

----FR1-------------------->|...CDR1............|---FR2------


!

 24  25  26  27  28  29  30  31  32  33  34  35  36  37  38


!

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



1081
|gct|TCC|GGA|ttc|act|ttc|tct|tCG|TAC|Gct|atg|tct|tgg|gtt|cgC|


!

    | BspEI |                 | BsiWI|                     |BstXI.


!


!

 -------FR2-------------------------------->|...CDR2.........


!

 39  40  41  42  43  44  45  46  47  48  49  50  51  52  52a


!

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



1126
|CAa|gct|ccT|GGt|aaa|ggt|ttg|gag|tgg|gtt|tct|gct|atc|tct|ggt|


!

...BstXI|


!


!

.....CDR2............................................|---FR3---


!

  53  54  55  56  57  58  59  60  61  62  63  64  65  66  67


!

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



1171
 |tct|ggt|ggc|agt|act|tac|tat|gct|gac|tcc|gtt|aaa|ggt|cgc|ttc|


!


!


!

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


!

 68  69  70  71  72  73  74  75  76  77  78  79  80  81  82


!

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



1216
|act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|


!

        | XbaI  |


!


!

---FR3----------------------------------------------------->|


!

82a 82b 82c  83  84  85  86  87  88  89  90  91  92  93  94


!

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



1261
|aac|agC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|tgc|gct|aaa|


!

       |AflII |               | PstI |(2/2)


!


!

.......CDR3.................|----FR4-------------------------


!

 95  96  97  98 98a 98b 98c  99  100 101 102 103 104 105 106


!

  D   Y   E   G   T   G   Y   A   F   D   I   W   G   Q   G



1306
|gac|tat|gaa|ggt|act|ggt|tat|gct|ttc|gaC|ATA|TGg|ggt|caa|ggt|


!

                                       | NdeI |


!


!

--------------FR4---------->|


!

 107 108 109 110 111 112 113


!

  T   M   V   T   V   S   S



1351
|act|atG|GTC|ACC|gtc|tct|agt


!

       | BstEII |  c tcg ag = XhoI.


!


!
CH1


!

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



1372
gcc tcc acc aag ggc cca tcg gtc ttc ccG CTA GCa ccc tcc tcc


!

                                      NheI....


!


!

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


!

 K   S   T   S   G   G   T   A   A   L   G   C   L   V   K



1417
aag agc acc tct ggg ggc aca gcg gcc ctg ggc tgc ctg gtc aag


!


!

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


!

 D   Y   F   P   E   P   V   T   V   S   W   N   S   G   A



1462
gac tac ttc ccc gaa ccg gtg acg gtg tcg tgg aac tca ggc gcc


!


!

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


!

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



1507
ctg acc agc ggc gtc cac acc ttc ccg gct gtc cta cag tcc tca


!


!

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


!

 G   L   Y   S   L   S   S   V   V   T   V   P   S   S   S



1552
gga ctc tac tcc ctc agc agc gta gtg acc gtg ccc tCC Agc agc


!

                                                 BstXI........


!


!

211 212 213 214 215 216 217 218 219 220 221 222 223 224 225


!

 L   G   T   Q   T   Y   I   C   N   V   N   H   K   P   S



1597
tTG Ggc acc cag acc tac atc tgc aac gtg aat cac aag ccc agc


!

BstXI........


!


!

226 227 228 229 230 231 232 233 234 235 236 237 238


!

 N   T   K   V   D   K   K   V   E   P   K   S   C



1642
aac acc aag gtg gac aaG AAA GTT GAG CCC AAA TCT TGT


!


!

139 140 141 His tag..............   cMyc tag......................


!

 A   A   A   H   H   H   H   H   H   G   A   A   E   Q   K   L   I



1681
GCG GCC GCa cat cat cat cac cat cac ggg gcc gca gaa caa aaa ctc atc


!

NotI......


!

 EagI....


!


!

  ..................................


!

 S   E   E   D   L   N   G   A   A   E   A   S   S   A   S   N   A   S



1732
tca gaa gag gat ctg aat ggg GCC gca gaG GCt agt tct gct agt aAC GCG Tct


!

                            BglI..........(3/4)              MluI....


!









!
Domain 3 (IIIstump)-----------------------------------------------------











!

 S   G   D   F   D   Y   E   K   M   A   N   A   N   K   G   A




1786
tcc ggt gat ttt gat tat gaa aag atg gca aac gct aat aag ggg gct


!


!

 M   T   E   N   A   D   E   N   A   L   Q   S   D   A   K   G



1834
atg acc gaa aat gcc gat gaa aac gcg cta cag tct gac gct aaa ggc


!


!

 K   L   D   S   V   A   T   D   Y   G   A   A   I   D   G   F



1882
aaa ctt gat tct gtc gct act gat tac ggt gct gct atc gat ggt ttc


!


!

 I   G   D   V   S   G   L   A   N   G   N   G   A   T   G   D



1930
att ggt gac gtt tcc ggc ctt gct aat ggt aat ggt gct act ggt gat


!


!

 F   A   G   S   N   S   Q   M   A   Q   V   G   D   G   D   N



1978
ttt gct ggc tct aat tcc caa atg gct caa gtc ggt gac ggt gat aat


!


!

 S   P   L   M   N   N   F   R   Q   Y   L   P   S   L   P   Q



2026
tca cct tta atg aat aat ttc cgt caa tat tta cct tcc ctc cct caa


!


!

 S   V   E   C   R   P   F   V   F   G   A   G   K   P   Y   E



2074
tcg gtt gaa tgt cgc cct ttt gtc ttt ggc gct ggt aaa cca tat gaa


!


!

 F   S   I   D   C   D   K   I   N   L   F   R



2122
ttt tct att gat tgt gac aaa ata aac tta ttc cgt


!

                                            End Domain 3


!


!

 G   V   F   A   F   L   L   Y   V   A   T   F   M   Y   V   F140



2158
ggt gtc ttt gcg ttt ctt tta tat gtt gcc acc ttt atg tat gta ttt


!

start transmembrane segment


!


!

 S   T   F   A   N   I   L



2206
tct acg ttt gct aac ata ctg


!


!

  R   N   K   E   S (SEQ ID NO: 892)



2227
cgt aat aag gag tct TAA tga aAC GCG Tga tga GAATTC (SEQ ID NO: 893)


!

Intracellular anchor.         MluI....       EcoRI.

















TABLE 25





The DNA sequence of DY3F85LC containing a sample germline



O12 kappa light chain. The antibody sequences shown are of the


form of actual antibody, but have not been identified as binding to


a particular antigen.


On each line, everything after an exclamation point (!) is commentary.


The DNA of DY3F85LC is SEQ ID NO: 27
















!----------------------------------------------------------------------------










1
AATGCTACTA CTATTAGTAG AATTGATGCC ACCTTTTCAG CTCGCGCCCC AAATGAAAAT



 


61
ATAGCTAAAC AGGTTATTGA CCATTTGCGA AATGTATCTA ATGGTCAAAC TAAATCTACT


 


121
CGTTCGCAGA ATTGGGAATC AACTGTTATA TGGAATGAAA CTTCCAGACA CCGTACTTTA


 


181
GTTGCATATT TAAAACATGT TGAGCTACAG CATTATATTC AGCAATTAAG CTCTAAGCCA


 


241
TCCGCAAAAA TGACCTCTTA TCAAAAGGAG CAATTAAAGG TACTCTCTAA TCCTGACCTG


 


301
TTGGAGTTTG CTTCCGGTCT GGTTCGCTTT GAAGCTCGAA TTAAAACGCG ATATTTGAAG


 


361
TCTTTCGGGC TTCCTCTTAA TCTTTTTGAT GCAATCCGCT TTGCTTCTGA CTATAATAGT


 


421
CAGGGTAAAG ACCTGATTTT TGATTTATGG TCATTCTCGT TTTCTGAACT GTTTAAAGCA


 


481
TTTGAGGGGG ATTCAATGAA TATTTATGAC GATTCCGCAG TATTGGACGC TATCCAGTCT


 


541
AAACATTTTA CTATTACCCC CTCTGGCAAA ACTTCTTTTG CAAAAGCCTC TCGCTATTTT


 


601
GGTTTTTATC GTCGTCTGGT AAACGAGGGT TATGATAGTG TTGCTCTTAC TATGCCTCGT


 


661
AATTCCTTTT GGCGTTATGT ATCTGCATTA GTTGAATGTG GTATTCCTAA ATCTCAACTG


 


721
ATGAATCTTT CTACCTGTAA TAATGTTGTT CCGTTAGTTC GTTTTATTAA CGTAGATTTT


 


781
TCTTCCCAAC GTCCTGACTG GTATAATGAG CCAGTTCTTA AAATCGCATA AGGTAATTCA


 


841
CAATGATTAA AGTTGAAATT AAACCATCTC AAGCCCAATT TACTACTCGT TCTGGTGTTT


 


901
CTCGTCAGGG CAAGCCTTAT TCACTGAATG AGCAGCTTTG TTACGTTGAT TTGGGTAATG


 


961
AATATCCGGT TCTTGTCAAG ATTACTCTTG ATGAAGGTCA GCCAGCCTAT GCGCCTGGTC


 


1021
TGTACACCGT TCATCTGTCC TCTTTCAAAG TTGGTCAGTT CGGTTCCCTT ATGATTGACC


 


1081
GTCTGCGCCT CGTTCCGGCT AAGTAACATG GAGCAGGTCG CGGATTTCGA CACAATTTAT


 


1141
CAGGCGATGA TACAAATCTC CGTTGTACTT TGTTTCGCGC TTGGTATAAT CGCTGGGGGT


 


1201
CAAAGATGAG TGTTTTAGTG TATTCTTTTG CCTCTTTCGT TTTAGGTTGG TGCCTTCGTA


 


1261
GTGGCATTAC GTATTTTACC CGTTTAATGG AAACTTCCTC ATGAAAAAGT CTTTAGTCCT


 


1321
CAAAGCCTCT GTAGCCGTTG CTACCCTCGT TCCGATGCTG TCTTTCGCTG CTGAGGGTGA


 


1381
CGATCCCGCA AAAGCGGCCT TTAACTCCCT GCAAGCCTCA GCGACCGAAT ATATCGGTTA


 


1441
TGCGTGGGCG ATGGTTGTTG TCATTGTCGG CGCAACTATC GGTATCAAGC TGTTTAAGAA


 


1501
ATTCACCTCG AAAGCAAGCT GATAAACCGA TACAATTAAA GGCTCCTTTT GGAGCCTTTT


 


1561
TTTTGGAGAT TTTCAACGTG AAAAAATTAT TATTCGCAAT TCCTTTAGTT GTTCCTTTCT


 


1621
ATTCTCACTC CGCTGAAACT GTTGAAAGTT GTTTAGCAAA ATCCCATACA GAAAATTCAT


 


1681
TTACTAACGT CTGGAAAGAC GACAAAACTT TAGATCGTTA CGCTAACTAT GAGGGCTGTC


 


1741
TGTGGAATGC TACAGGCGTT GTAGTTTGTA CTGGTGACGA AACTCAGTGT TACGGTACAT


 


1801
GGGTTCCTAT TGGGCTTGCT ATCCCTGAAA ATGAGGGTGG TGGCTCTGAG GGTGGCGGTT


 


1861
CTGAGGGTGG CGGTTCTGAG GGTGGCGGTA CTAAACCTCC TGAGTACGGT GATACACCTA


 


1921
TTCCGGGCTA TACTTATATC AACCCTCTCG ACGGCACTTA TCCGCCTGGT ACTGAGCAAA


 


1981
ACCCCGCTAA TCCTAATCCT TCTCTTGAGG AGTCTCAGCC TCTTAATACT TTCATGTTTC


 


2041
AGAATAATAG GTTCCGAAAT AGGCAGGGGG CATTAACTGT TTATACGGGC ACTGTTACTC


 


2101
AAGGCACTGA CCCCGTTAAA ACTTATTACC AGTACACTCC TGTATCATCA AAAGCCATGT


 


2161
ATGACGCTTA CTGGAACGGT AAATTCAGAG ACTGCGCTTT CCATTCTGGC TTTAATGAGG


 


2221
ATTTATTTGT TTGTGAATAT CAAGGCCAAT CGTCTGACCT GCCTCAACCT CCTGTCAATG


 


2281
CTGGCGGCGG CTCTGGTGGT GGTTCTGGTG GCGGCTCTGA GGGTGGTGGC TCTGAGGGTG


 


2341
GCGGTTCTGA GGGTGGCGGC TCTGAGGGAG GCGGTTCCGG TGGTGGCTCT GGTTCCGGTG


 


2401
ATTTTGATTA TGAAAAGATG GCAAACGCTA ATAAGGGGGC TATGACCGAA AATGCCGATG


 


2461
AAAACGCGCT ACAGTCTGAC GCTAAAGGCA AACTTGATTC TGTCGCTACT GATTACGGTG


 


2521
CTGCTATCGA TGGTTTCATT GGTGACGTTT CCGGCCTTGC TAATGGTAAT GGTGCTACTG


 


2581
GTGATTTTGC TGGCTCTAAT TCCCAAATGG CTCAAGTCGG TGACGGTGAT AATTCACCTT


 


2641
TAATGAATAA TTTCCGTCAA TATTTACCTT CCCTCCCTCA ATCGGTTGAA TGTCGCCCTT


 


2701
TTGTCTTTGG CGCTGGTAAA CCATATGAAT TTTCTATTGA TTGTGACAAA ATAAACTTAT


 


2761
TCCGTGGTGT CTTTGCGTTT CTTTTATATG TTGCCACCTT TATGTATGTA TTTTCTACGT


 


2821
TTGCTAACAT ACTGCGTAAT AAGGAGTCTT AATCATGCCA GTTCTTTTGG GTATTCCGTT


 


2881
ATTATTGCGT TTCCTCGGTT TCCTTCTGGT AACTTTGTTC GGCTATCTGC TTACTTTTCT


 


2941
TAAAAAGGGC TTCGGTAAGA TAGCTATTGC TATTTCATTG TTTCTTGCTC TTATTATTGG


 


3001
GCTTAACTCA ATTCTTGTGG GTTATCTCTC TGATATTAGC GCTCAATTAC CCTCTGACTT


 


3061
TGTTCAGGGT GTTCAGTTAA TTCTCCCGTC TAATGCGCTT CCCTGTTTTT ATGTTATTCT


 


3121
CTCTGTAAAG GCTGCTATTT TCATTTTTGA CGTTAAACAA AAAATCGTTT CTTATTTGGA


 


3181
TTGGGATAAA TAATATGGCT GTTTATTTTG TAACTGGCAA ATTAGGCTCT GGAAAGACGC


 


3241
TCGTTAGCGT TGGTAAGATT CAGGATAAAA TTGTAGCTGG GTGCAAAATA GCAACTAATC


 


3301
TTGATTTAAG GCTTCAAAAC CTCCCGCAAG TCGGGAGGTT CGCTAAAACG CCTCGCGTTC


 


3361
TTAGAATACC GGATAAGCCT TCTATATCTG ATTTGCTTGC TATTGGGCGC GGTAATGATT


 


3421
CCTACGATGA AAATAAAAAC GGCTTGCTTG TTCTCGATGA GTGCGGTACT TGGTTTAATA


 


3481
CCCGTTCTTG GAATGATAAG GAAAGACAGC CGATTATTGA TTGGTTTCTA CATGCTCGTA


 


3541
AATTAGGATG GGATATTATT TTTCTTGTTC AGGACTTATC TATTGTTGAT AAACAGGCGC


 


3601
GTTCTGCATT AGCTGAACAT GTTGTTTATT GTCGTCGTCT GGACAGAATT ACTTTACCTT


 


3661
TTGTCGGTAC TTTATATTCT CTTATTACTG GCTCGAAAAT GCCTCTGCCT AAATTACATG


 


3721
TTGGCGTTGT TAAATATGGC GATTCTCAAT TAAGCCCTAC TGTTGAGCGT TGGCTTTATA


 


3781
CTGGTAAGAA TTTGTATAAC GCATATGATA CTAAACAGGC TTTTTCTAGT AATTATGATT


 


3841
CCGGTGTTTA TTCTTATTTA ACGCCTTATT TATCACACGG TCGGTATTTC AAACCATTAA


 


3901
ATTTAGGTCA GAAGATGAAA TTAACTAAAA TATATTTGAA AAAGTTTTCT CGCGTTCTTT


 


3961
GTCTTGCGAT TGGATTTGCA TCAGCATTTA CATATAGTTA TATAACCCAA CCTAAGCCGG


 


4021
AGGTTAAAAA GGTAGTCTCT CAGACCTATG ATTTTGATAA ATTCACTATT GACTCTTCTC


 


4081
AGCGTCTTAA TCTAAGCTAT CGCTATGTTT TCAAGGATTC TAAGGGAAAA TTAATTAATA


 


4141
GCGACGATTT ACAGAAGCAA GGTTATTCAC TCACATATAT TGATTTATGT ACTGTTTCCA


 


4201
TTAAAAAAGG TAATTCAAAT GAAATTGTTA AATGTAATTA ATTTTGTTTT CTTGATGTTT


 


4261
GTTTCATCAT CTTCTTTTGC TCAGGTAATT GAAATGAATA ATTCGCCTCT GCGCGATTTT


 


4321
GTAACTTGGT ATTCAAAGCA ATCAGGCGAA TCCGTTATTG TTTCTCCCGA TGTAAAAGGT


 


4381
ACTGTTACTG TATATTCATC TGACGTTAAA CCTGAAAATC TACGCAATTT CTTTATTTCT


 


4441
GTTTTACGTG CAAATAATTT TGATATGGTA GGTTCTAACC CTTCCATAAT TCAGAAGTAT


 


4501
AATCCAAACA ATCAGGATTA TATTGATGAA TTGCCATCAT CTGATAATCA GGAATATGAT


 


4561
GATAATTCCG CTCCTTCTGG TGGTTTCTTT GTTCCGCAAA ATGATAATGT TACTCAAACT


 


4621
TTTAAAATTA ATAACGTTCG GGCAAAGGAT TTAATACGAG TTGTCGAATT GTTTGTAAAG


 


4681
TCTAATACTT CTAAATCCTC AAATGTATTA TCTATTGACG GCTCTAATCT ATTAGTTGTT


 


4741
AGTGCTCCTA AAGATATTTT AGATAACCTT CCTCAATTCC TTTCAACTGT TGATTTGCCA


 


4801
ACTGACCAGA TATTGATTGA GGGTTTGATA TTTGAGGTTC AGCAAGGTGA TGCTTTAGAT


 


4861
TTTTCATTTG CTGCTGGCTC TCAGCGTGGC ACTGTTGCAG GCGGTGTTAA TACTGACCGC


 


4921
CTCACCTCTG TTTTATCTTC TGCTGGTGGT TCGTTCGGTA TTTTTAATGG CGATGTTTTA


 


4981
GGGCTATCAG TTCGCGCATT AAAGACTAAT AGCCATTCAA AAATATTGTC TGTGCCACGT


 


5041
ATTCTTACGC TTTCAGGTCA GAAGGGTTCT ATCTCTGTTG GCCAGAATGT CCCTTTTATT


 


5101
ACTGGTCGTG TGACTGGTGA ATCTGCCAAT GTAAATAATC CATTTCAGAC GATTGAGCGT


 


5161
CAAAATGTAG GTATTTCCAT GAGCGTTTTT CCTGTTGCAA TGGCTGGCGG TAATATTGTT


 


5221
CTGGATATTA CCAGCAAGGC CGATAGTTTG AGTTCTTCTA CTCAGGCAAG TGATGTTATT


 


5281
ACTAATCAAA GAAGTATTGC TACAACGGTT AATTTGCGTG ATGGACAGAC TCTTTTACTC


 


5341
GGTGGCCTCA CTGATTATAA AAACACTTCT CAGGATTCTG GCGTACCGTT CCTGTCTAAA


 


5401
ATCCCTTTAA TCGGCCTCCT GTTTAGCTCC CGCTCTGATT CTAACGAGGA AAGCACGTTA


 


5461
TACGTGCTCG TCAAAGCAAC CATAGTACGC GCCCTGTAGC GGCGCATTAA GCGCGGCGGG


 


5521
TGTGGTGGTT ACGCGCAGCG TGACCGCTAC ACTTGCCAGC GCCCTAGCGC CCGCTCCTTT


 


5581
CGCTTTCTTC CCTTCCTTTC TCGCCACGTT CGCCGGCTTT CCCCGTCAAG CTCTAAATCG


 


5641
GGGGCTCCCT TTAGGGTTCC GATTTAGTGC TTTACGGCAC CTCGACCCCA AAAAACTTGA


 


5701
TTTGGGTGAT GGTTCACGTA GTGGGCCATC GCCCTGATAG ACGGTTTTTC GCCCTTTGAC


 


5761
GTTGGAGTCC ACGTTCTTTA ATAGTGGACT CTTGTTCCAA ACTGGAACAA CACTCAACCC


 


5821
TATCTCGGGC TATTCTTTTG ATTTATAAGG GATTTTGCCG ATTTCGGAAC CACCATCAAA


 


5881
CAGGATTTTC GCCTGCTGGG GCAAACCAGC GTGGACCGCT TGCTGCAACT CTCTCAGGGC


 


5941
CAGGCGGTGA AGGGCAATCA GCTGTTGCCC GTCTCACTGG TGAAAAGAAA AACCACCCTG


 


6001
GATCCAAGCT TGCAGGTGGC ACTTTTCGGG GAAATGTGCG CGGAACCCCT ATTTGTTTAT


 


6061
TTTTCTAAAT ACATTCAAAT ATGTATCCGC TCATGAGACA ATAACCCTGA TAAATGCTTC


 


6121
AATAATATTG AAAAAGGAAG AGTATGAGTA TTCAACATTT CCGTGTCGCC CTTATTCCCT


 


6181
TTTTTGCGGC ATTTTGCCTT CCTGTTTTTG CTCACCCAGA AACGCTGGTG AAAGTAAAAG


 


6241
ATGCTGAAGA TCAGTTGGGC GCACTAGTGG GTTACATCGA ACTGGATCTC AACAGCGGTA


 


6301
AGATCCTTGA GAGTTTTCGC CCCGAAGAAC GTTTTCCAAT GATGAGCACT TTTAAAGTTC


 


6361
TGCTATGTGG CGCGGTATTA TCCCGTATTG ACGCCGGGCA AGAGCAACTC GGTCGCCGCA


 


6421
TACACTATTC TCAGAATGAC TTGGTTGAGT ACTCACCAGT CACAGAAAAG CATCTTACGG


 


6481
ATGGCATGAC AGTAAGAGAA TTATGCAGTG CTGCCATAAC CATGAGTGAT AACACTGCGG


 


6541
CCAACTTACT TCTGACAACG ATCGGAGGAC CGAAGGAGCT AACCGCTTTT TTGCACAACA


 


6601
TGGGGGATCA TGTAACTCGC CTTGATCGTT GGGAACCGGA GCTGAATGAA GCCATACCAA


 


6661
ACGACGAGCG TGACACCACG ATGCCTGTAG CAATGGCAAC AACGTTGCGC AAACTATTAA


 


6721
CTGGCGAACT ACTTACTCTA GCTTCCCGGC AACAATTAAT AGACTGGATG GAGGCGGATA


 


6781
AAGTTGCAGG ACCACTTCTG CGCTCGGCCC TTCCGGCTGG CTGGTTTATT GCTGATAAAT


 


6841
CTGGAGCCGG TGAGCGTGGG TCTCGCGGTA TCATTGCAGC ACTGGGGCCA GATGGTAAGC


 


6901
CCTCCCGTAT CGTAGTTATC TACACGACGG GGAGTCAGGC AACTATGGAT GAACGAAATA


 


6961
GACAGATCGC TGAGATAGGT GCCTCACTGA TTAAGCATTG GTAACTGTCA GACCAAGTTT


 


7021
ACTCATATAT ACTTTAGATT GATTTAAAAC TTCATTTTTA ATTTAAAAGG ATCTAGGTGA


 


7081
AGATCCTTTT TGATAATCTC ATGACCAAAA TCCCTTAACG TGAGTTTTCG TTCCACTGTA


 


7141
CGTAAGACCC CCAAGCTTGT CGACTGAATG GCGAATGGCG CTTTGCCTGG TTTCCGGCAC


 


7201
CAGAAGCGGT GCCGGAAAGC TGGCTGGAGT GCGATCTTCC TGACGCTCGA GCGCAACGCA


 


!
                                                 XhoI...


 


7261
ATTAATGTGA GTTAGCTCAC TCATTAGGCA CCCCAGGCTT TACACTTTAT GCTTCCGGCT


 


7321
CGTATGTTGT GTGGAATTGT GAGCGGATAA CAATTTCACA CAGGAAACAG CTATGACCAT


 


7381
GATTACGCCA AGCTTTGGAG CCTTTTTTTT GGAGATTTTC AAC
















TABLE 30





DNA sequence of DY3FHC87 (SEQ ID NO: 894)

















1
aatgctacta ctattagtag aattgatgcc accttttcag ctcgcgcccc aaatgaaaat



 


61
atagctaaac aggttattga ccatttgcga aatgtatcta atggtcaaac taaatctact


 


121
cgttcgcaga attgggaatc aactgttata tggaatgaaa cttccagaca ccgtacttta


 


181
gttgcatatt taaaacatgt tgagctacag cattatattc agcaattaag ctctaagcca


 


241
tccgcaaaaa tgacctctta tcaaaaggag caattaaagg tactctctaa tcctgacctg


 


301
ttggagtttg cttccggtct ggttcgcttt gaagctcgaa ttaaaacgcg atatttgaag


 


361
tctttcgggc ttcctcttaa tctttttgat gcaatccgct ttgcttctga ctataatagt


 


421
cagggtaaag acctgatttt tgatttatgg tcattctcgt tttctgaact gtttaaagca


 


481
tttgaggggg attcaatgaa tatttatgac gattccgcag tattggacgc tatccagtct


 


541
aaacatttta ctattacccc ctctggcaaa acttcttttg caaaagcctc tcgctatttt


 


601
ggtttttatc gtcgtctggt aaacgagggt tatgatagtg ttgctcttac tatgcctcgt


 


661
aattcctttt ggcgttatgt atctgcatta gttgaatgtg gtattcctaa atctcaactg


 


721
atgaatcttt ctacctgtaa taatgttgtt ccgttagttc gttttattaa cgtagatttt


 


781
tcttcccaac gtcctgactg gtataatgag ccagttctta aaatcgcata aggtaattca


 


841
caatgattaa agttgaaatt aaaccatctc aagcccaatt tactactcgt tctggtgttt


 


901
ctcgtcaggg caagccttat tcactgaatg agcagctttg ttacgttgat ttgggtaatg


 


961
aatatccggt tcttgtcaag attactcttg atgaaggtca gccagcctat gcgcctggtc


 


1021
tgtacaccgt tcatctgtcc tctttcaaag ttggtcagtt cggttccctt atgattgacc


 


1081
gtctgcgcct cgttccggct aagtaacatg gagcaggtcg cggatttcga cacaatttat


 


1141
caggcgatga tacaaatctc cgttgtactt tgtttcgcgc ttggtataat cgctgggggt


 


1201
caaagatgag tgttttagtg tattcttttg cctctttcgt tttaggttgg tgccttcgta


 


1261
gtggcattac gtattttacc cgtttaatgg aaacttcctc atgaaaaagt ctttagtcct


 


1321
caaagcctct gtagccgttg ctaccctcgt tccgatgctg tctttcgctg ctgagggtga


 


1381
cgatcccgca aaagcggcct ttaactccct gcaagcctca gcgaccgaat atatcggtta


 


1441
tgcgtgggcg atggttgttg tcattgtcgg cgcaactatc ggtatcaagc tgtttaagaa


 


1501
attcacctcg aaagcaagct gataaaccga tacaattaaa ggctcctttt ggagcctttt


 


1561
tttttggaga ttttcaacgt gaaaaaatta ttattcgcaa ttcctttagt tgttcctttc


 


1621
tattctcact ccgctgaaac tgttgaaagt tgtttagcaa aatcccatac agaaaattca


 


1681
tttactaacg tctggaaaga cgacaaaact ttagatcgtt acgctaacta tgagggctgt


 


1741
ctgtggaatg ctacaggcgt tgtagtttgt actggtgacg aaactcagtg ttacggtaca


 


1801
tgggttccta ttgggcttgc tatccctgaa aatgagggtg gtggctctga gggtggcggt


 


1861
tctgagggtg gcggttctga gggtggcggt actaaacctc ctgagtacgg tgatacacct


 


1921
attccgggct atacttatat caaccctctc gacggcactt atccgcctgg tactgagcaa


 


1981
aaccccgcta atcctaatcc ttctcttgag gagtctcagc ctcttaatac tttcatgttt


 


2041
cagaataata ggttccgaaa taggcagggg gcattaactg tttatacggg cactgttact


 


2101
caaggcactg accccgttaa aacttattac cagtacactc ctgtatcatc aaaagccatg


 


2161
tatgacgctt actggaacgg taaattcaga gactgcgctt tccattctgg ctttaatgag


 


2221
gatttatttg tttgtgaata tcaaggccaa tcgtctgacc tgcctcaacc tcctgtcaat


 


2281
gctggcggcg gctctggtgg tggttctggt ggcggctctg agggtggtgg ctctgagggt


 


2341
ggcggttctg agggtggcgg ctctgaggga ggcggttccg gtggtggctc tggttccggt


 


2401
gattttgatt atgaaaagat ggcaaacgct aataaggggg ctatgaccga aaatgccgat


 


2461
gaaaacgcgc tacagtctga cgctaaaggc aaacttgatt ctgtcgctac tgattacggt


 


2521
gctgctatcg atggtttcat tggtgacgtt tccggccttg ctaatggtaa tggtgctact


 


2581
ggtgattttg ctggctctaa ttcccaaatg gctcaagtcg gtgacggtga taattcacct


 


2641
ttaatgaata atttccgtca atatttacct tccctccctc aatcggttga atgtcgccct


 


2701
tttgtctttg gcgctggtaa accatatgaa ttttctattg attgtgacaa aataaactta


 


2761
ttccgtggtg tctttgcgtt tcttttatat gttgccacct ttatgtatgt attttctacg


 


2821
tttgctaaca tactgcgtaa taaggagtct taatcatgcc agttcttttg ggtattccgt


 


2881
tattattgcg tttcctcggt ttccttctgg taactttgtt cggctatctg cttacttttc


 


2941
ttaaaaaggg cttcggtaag atagctattg ctatttcatt gtttcttgct cttattattg


 


3001
ggcttaactc aattcttgtg ggttatctct ctgatattag cgctcaatta ccctctgact


 


3061
ttgttcaggg tgttcagtta attctcccgt ctaatgcgct tccctgtttt tatgttattc


 


3121
tctctgtaaa ggctgctatt ttcatttttg acgttaaaca aaaaatcgtt tcttatttgg


 


3181
attgggataa ataatatggc tgtttatttt gtaactggca aattaggctc tggaaagacg


 


3241
ctcgttagcg ttggtaagat tcaggataaa attgtagctg ggtgcaaaat agcaactaat


 


3301
cttgatttaa ggcttcaaaa cctcccgcaa gtcgggaggt tcgctaaaac gcctcgcgtt


 


3361
cttagaatac cggataagcc ttctatatct gatttgcttg ctattgggcg cggtaatgat


 


3421
tcctacgatg aaaataaaaa cggcttgctt gttctcgatg agtgcggtac ttggtttaat


 


3481
acccgttctt ggaatgataa ggaaagacag ccgattattg attggtttct acatgctcgt


 


3541
aaattaggat gggatattat ttttcttgtt caggacttat ctattgttga taaacaggcg


 


3601
cgttctgcat tagctgaaca tgttgtttat tgtcgtcgtc tggacagaat tactttacct


 


3661
tttgtcggta ctttatattc tcttattact ggctcgaaaa tgcctctgcc taaattacat


 


3721
gttggcgttg ttaaatatgg cgattctcaa ttaagcccta ctgttgagcg ttggctttat


 


3781
actggtaaga atttgtataa cgcatatgat actaaacagg ctttttctag taattatgat


 


3841
tccggtgttt attcttattt aacgccttat ttatcacacg gtcggtattt caaaccatta


 


3901
aatttaggtc agaagatgaa attaactaaa atatatttga aaaagttttc tcgcgttctt


 


3961
tgtcttgcga ttggatttgc atcagcattt acatatagtt atataaccca acctaagccg


 


4021
gaggttaaaa aggtagtctc tcagacctat gattttgata aattcactat tgactcttct


 


4081
cagcgtctta atctaagcta tcgctatgtt ttcaaggatt ctaagggaaa attaattaat


 


4141
agcgacgatt tacagaagca aggttattca ctcacatata ttgatttatg tactgtttcc


 


4201
attaaaaaag gtaattcaaa tgaaattgtt aaatgtaatt aattttgttt tcttgatgtt


 


4261
tgtttcatca tcttcttttg ctcaggtaat tgaaatgaat aattcgcctc tgcgcgattt


 


4321
tgtaacttgg tattcaaagc aatcaggcga atccgttatt gtttctcccg atgtaaaagg


 


4381
tactgttact gtatattcat ctgacgttaa acctgaaaat ctacgcaatt tctttatttc


 


4441
tgttttacgt gcaaataatt ttgatatggt aggttctaac ccttccataa ttcagaagta


 


4501
taatccaaac aatcaggatt atattgatga attgccatca tctgataatc aggaatatga


 


4561
tgataattcc gctccttctg gtggtttctt tgttccgcaa aatgataatg ttactcaaac


 


4621
ttttaaaatt aataacgttc gggcaaagga tttaatacga gttgtcgaat tgtttgtaaa


 


4681
gtctaatact tctaaatcct caaatgtatt atctattgac ggctctaatc tattagttgt


 


4741
tagtgctcct aaagatattt tagataacct tcctcaattc ctttcaactg ttgatttgcc


 


4801
aactgaccag atattgattg agggtttgat atttgaggtt cagcaaggtg atgctttaga


 


4861
tttttcattt gctgctggct ctcagcgtgg cactgttgca ggcggtgtta atactgaccg


 


4921
cctcacctct gttttatctt ctgctggtgg ttcgttcggt atttttaatg gcgatgtttt


 


4981
agggctatca gttcgcgcat taaagactaa tagccattca aaaatattgt ctgtgccacg


 


5041
tattcttacg ctttcaggtc agaagggttc tatctctgtt ggccagaatg tcccttttat


 


5101
tactggtcgt gtgactggtg aatctgccaa tgtaaataat ccatttcaga cgattgagcg


 


5161
tcaaaatgta ggtatttcca tgagcgtttt tcctgttgca atggctggcg gtaatattgt


 


5221
tctggatatt accagcaagg ccgatagttt gagttcttct actcaggcaa gtgatgttat


 


5281
tactaatcaa agaagtattg ctacaacggt taatttgcgt gatggacaga ctcttttact


 


5341
cggtggcctc actgattata aaaacacttc tcaggattct ggcgtaccgt tcctgtctaa


 


5401
aatcccttta atcggcctcc tgtttagctc ccgctctgat tctaacgagg aaagcacgtt


 


5461
atacgtgctc gtcaaagcaa ccatagtacg cgccctgtag cggcgcatta agcgcggcgg


 


5521
gtgtggtggt tacgcgcagc gtgaccgcta cacttgccag cgccctagcg cccgctcctt


 


5581
tcgctttctt cccttccttt ctcgccacgt tcgccggctt tccccgtcaa gctctaaatc


 


5641
gggggctccc tttagggttc cgatttagtg ctttacggca cctcgacccc aaaaaacttg


 


5701
atttgggtga tggttcacgt agtgggccat cgccctgata gacggttttt cgccctttga


 


5761
cgttggagtc cacgttcttt aatagtggac tcttgttcca aactggaaca acactcaacc


 


5821
ctatctcggg ctattctttt gatttataag ggattttgcc gatttcggaa ccaccatcaa


 


5881
acaggatttt cgcctgctgg ggcaaaccag cgtggaccgc ttgctgcaac tctctcaggg


 


5941
ccaggcggtg aagggcaatc agctgttgcc cgtctcactg gtgaaaagaa aaaccaccct


 


6001
ggatccaagc ttgcaggtgg cacttttcgg ggaaatgtgc gcggaacccc tatttgttta


 


6061
tttttctaaa tacattcaaa tatgtatccg ctcatgagac aataaccctg ataaatgctt


 


6121
caataatatt gaaaaaggaa gagtatgagt attcaacatt tccgtgtcgc ccttattccc


 


6181
ttttttgcgg cattttgcct tcctgttttt gctcacccag aaacgctggt gaaagtaaaa


 


6241
gatgctgaag atcagttggg cgcactagtg ggttacatcg aactggatct caacagcggt


 


6301
aagatccttg agagttttcg ccccgaagaa cgttttccaa tgatgagcac ttttaaagtt


 


6361
ctgctatgtg gcgcggtatt atcccgtatt gacgccgggc aagagcaact cggtcgccgc


 


6421
atacactatt ctcagaatga cttggttgag tactcaccag tcacagaaaa gcatcttacg


 


6481
gatggcatga cagtaagaga attatgcagt gctgccataa ccatgagtga taacactgcg


 


6541
gccaacttac ttctgacaac gatcggagga ccgaaggagc taaccgcttt tttgcacaac


 


6601
atgggggatc atgtaactcg ccttgatcgt tgggaaccgg agctgaatga agccatacca


 


6661
aacgacgagc gtgacaccac gatgcctgta gcaatggcaa caacgttgcg caaactatta


 


6721
actggcgaac tacttactct agcttcccgg caacaattaa tagactggat ggaggcggat


 


6781
aaagttgcag gaccacttct gcgctcggcc cttccggctg gctggtttat tgctgataaa


 


6841
tctggagccg gtgagcgtgg gtctcgcggt atcattgcag cactggggcc agatggtaag


 


6901
ccctcccgta tcgtagttat ctacacgacg gggagtcagg caactatgga tgaacgaaat


 


6961
agacagatcg ctgagatagg tgcctcactg attaagcatt ggtaactgtc agaccaagtt


 


7021
tactcatata tactttagat tgatttaaaa cttcattttt aatttaaaag gatctaggtg


 


7081
aagatccttt ttgataatct catgaccaaa atcccttaac gtgagttttc gttccactgt


 


7141
acgtaagacc cccaagcttg tcgactgaat ggcgaatggc gctttgcctg gtttccggca


 


7201
ccagaagcgg tgccggaaag ctggctggag tgcgatcttc ctgacgctcg agcgcaacgc


 


7261
aattaatgtg agttagctca ctcattaggc accccaggct ttacacttta tgcttccggc


 


7321
tcgtatgttg tgtggaattg tgagcggata acaatttcac acaggaaaca gctatgacca


 


7381
tgattacgcc aagctttgga gccttttttt tggagatttt caacatgaaa tacctattgc


 


7441
ctacggcagc cgctggattg ttattactcg cGGCCcagcc GGCCatggcc gaagttcaat


 


7501
tgttagagtc tggtggcggt cttgttcagc ctggtggttc tttacgtctt tcttgcgctg


 


7561
cttccggatt cactttctct tcgtacgcta tgtcttgggt tcgccaagct cctggtaaag


 


7621
gtttggagtg ggtttctgct atctctggtt ctggtggcag tacttactat gctgactccg


 


7681
ttaaaggtcg cttcactatc tctagagaca actctaagaa tactctctac ttgcagatga


 


7741
acagcttaag ggctgaggac actgcagtct actattgcgc taaagcctat cgtccttctt


 


7801
atcatgacat atggggtcaa ggtactatgg tcaccgtctc tagtgcctcc accaagggcc


 


7861
catcggtctt cccgctagca ccctcctcca agagcacctc tgggggcaca gcggccctgg


 


7921
gctgcctggt caaggactac ttccccgaac cggtgacggt gtcgtggaac tcaggcgccc


 


7981
tgaccagcgg cgtccacacc ttcccggctg tcctacagtc ctcaggactc tactccctca


 


8041
gcagcgtagt gaccgtgccc tccagcagct tgggcaccca gacctacatc tgcaacgtga


 


8101
atcacaagcc cagcaacacc aaggtggaca agaaagttga gcccaaatct tgtgcggccg


 


8161
cacatcatca tcaccatcac ggggccgcag aacaaaaact catctcagaa gaggatctga


 


8221
atggggccgc agaggctagc tctgctagtg gcgacttcga ctacgagaaa atggctaatg


 


8281
ccaacaaagg cgccatgact gagaacgctg acgagaatgc tttgcaaagc gatgccaagg


 


8341
gtaagttaga cagcgtcgcg accgactatg gcgccgccat cgacggcttt atcggcgatg


 


8401
tcagtggttt ggccaacggc aacggagcca ccggagactt cgcaggttcg aattctcaga


 


8461
tggcccaggt tggagatggg gacaacagtc cgcttatgaa caactttaga cagtaccttc


 


8521
cgtctcttcc gcagagtgtc gagtgccgtc cattcgtttt cggtgccggc aagccttacg


 


8581
agttcagcat cgactgcgat aagatcaatc ttttccgcgg cgttttcgct ttcttgctat


 


8641
acgtcgctac tttcatgtac gttttcagca ctttcgccaa tattttacgc aacaaagaaa


 


8701
gctagtgatc tcctaggaag cccgcctaat gagcgggctt tttttttctg gtatgcatcc


 


8761
tgaggccgat actgtcgtcg tcccctcaaa ctggcagatg cacggttacg atgcgcccat


 


8821
ctacaccaac gtgacctatc ccattacggt caatccgccg tttgttccca cggagaatcc


 


8881
gacgggttgt tactcgctca catttaatgt tgatgaaagc tggctacagg aaggccagac


 


8941
gcgaattatt tttgatggcg ttcctattgg ttaaaaaatg agctgattta acaaaaattt


 


9001
aatgcgaatt ttaacaaaat attaacgttt acaatttaaa tatttgctta tacaatcttc


 


9061
ctgtttttgg ggcttttctg attatcaacc ggggtacata tgattgacat gctagtttta


 


9121
cgattaccgt tcatcgattc tcttgtttgc tccagactct caggcaatga cctgatagcc


 


9181
tttgtagatc tctcaaaaat agctaccctc tccggcatta atttatcagc tagaacggtt


 


9241
gaatatcata ttgatggtga tttgactgtc tccggccttt ctcacccttt tgaatcttta


 


9301
cctacacatt actcaggcat tgcatttaaa atatatgagg gttctaaaaa tttttatcct


 


9361
tgcgttgaaa taaaggcttc tcccgcaaaa gtattacagg gtcataatgt ttttggtaca


 


9421
accgatttag ctttatgctc tgaggcttta ttgcttaatt ttgctaattc tttgccttgc


 


9481
ctgtatgatt tattggatgt t
















TABLE 35





DNA sequence of pMID21: 5957 bp (SEQ ID NO: 895)

















1
gacgaaaggg cctcgtgata cgcctatttt tataggttaa tgtcatgata ataatggttt



 


61
cttagacgtc aggtggcact tttcggggaa atgtgcgcgg aacccctatt tgtttatttt


 


121
tctaaataca ttcaaatatg tatccgctca tgagacaata accctgataa atgcttcaat


 


181
aatattgaaa aaggaagagt atgagtattc aacatttccg tgtcgccctt attccctttt


 


241
ttgcggcatt ttgccttcct gtttttgctc acccagaaac gctggtgaaa gtaaaagatg


 


301
ctgaagatca gttgggtgcc cgagtgggtt acatcgaact ggatctcaac agcggtaaga


 


361
tccttgagag ttttcgcccc gaagaacgtt ttccaatgat gagcactttt aaagttctgc


 


421
tatgtggcgc ggtattatcc cgtattgacg ccgggcaaga gcaactcggt cgccgcatac


 


481
actattctca gaatgacttg gttgagtact caccagtcac agaaaagcat cttacggatg


 


541
gcatgacagt aagagaatta tgcagtgctg ccataaccat gagtgataac actgcggcca


 


601
acttacttct gacaacgatc ggaggaccga aggagctaac cgcttttttg cacaacatgg


 


661
gggatcatgt aactcgcctt gatcgttggg aaccggagct gaatgaagcc ataccaaacg


 


721
acgagcgtga caccacgatg cctgtagcaa tggcaacaac gttgcgcaaa ctattaactg


 


781
gcgaactact tactctagct tcccggcaac aattaataga ctggatggag gcggataaag


 


841
ttgcaggacc acttctgcgc tcggcccttc cggctggctg gtttattgct gataaatctg


 


901
gagccggtga gcgtgggtct cgcggtatca ttgcagcact ggggccagat ggtaagccct


 


961
cccgtatcgt agttatctac acgacgggga gtcaggcaac tatggatgaa cgaaatagac


 


1021
agatcgctga gataggtgcc tcactgatta agcattggta actgtcagac caagtttact


 


1081
catatatact ttagattgat ttaaaacttc atttttaatt taaaaggatc taggtgaaga


 


1141
tcctttttga taatctcatg accaaaatcc cttaacgtga gttttcgttc cactgagcgt


 


1201
cagaccccgt agaaaagatc aaaggatctt cttgagatcc tttttttctg cgcgtaatct


 


1261
gctgcttgca aacaaaaaaa ccaccgctac cagcggtggt ttgtttgccg gatcaagagc


 


1321
taccaactct ttttccgaag gtaactggct tcagcagagc gcagatacca aatactgttc


 


1381
ttctagtgta gccgtagtta ggccaccact tcaagaactc tgtagcaccg cctacatacc


 


1441
tcgctctgct aatcctgtta ccagtggctg ctgccagtgg cgataagtcg tgtcttaccg


 


1501
ggttggactc aagacgatag ttaccggata aggcgcagcg gtcgggctga acggggggtt


 


1561
cgtgcataca gcccagcttg gagcgaacga cctacaccga actgagatac ctacagcgtg


 


1621
agctatgaga aagcgccacg cttcccgaag ggagaaaggc ggacaggtat ccggtaagcg


 


1681
gcagggtcgg aacaggagag cgcacgaggg agcttccagg gggaaacgcc tggtatcttt


 


1741
atagtcctgt cgggtttcgc cacctctgac ttgagcgtcg atttttgtga tgctcgtcag


 


1801
gggggcggag cctatggaaa aacgccagca acgcggcctt tttacggttc ctggcctttt


 


1861
gctggccttt tgctcacatg ttctttcctg cgttatcccc tgattctgtg gataaccgta


 


1921
ttaccgcctt tgagtgagct gataccgctc gccgcagccg aacgaccgag cgcagcgagt


 


1981
cagtgagcga ggaagcggaa gagcgcccaa tacgcaaacc gcctctcccc gcgcgttggc


 


2041
cgattcatta atgcagctgg cacgacaggt ttcccgactg gaaagcgggc agtgagcgca


 


2101
acgcaattaa tgtgagttag ctcactcatt aggcacccca ggctttacac tttatgcttc


 


2161
cggctcgtat gttgtgtgga attgtgagcg gataacaatt tcacacagga aacagctatg


 


2221
accatgatta cgccaagctt tggagccttt tttttggaga ttttcaacgt gaaaaaatta


 


2281
ttattcgcaa ttcctttagt tgttcctttc tattctcaca gtgcacaggt ccaactgcag


 


2341
gagctcgaga tcaaacgtgg aactgtggct gcaccatctg tcttcatctt cccgccatct


 


2401
gatgagcagt tgaaatctgg aactgcctct gttgtgtgcc tgctgaataa cttctatccc


 


2461
agagaggcca aagtacagtg gaaggtggat aacgccctcc aatcgggtaa ctcccaggag


 


2521
agtgtcacag agcaggacag caaggacagc acctacagcc tcagcagcac cctgacgctg


 


2581
agcaaagcag actacgagaa acacaaagtc tacgcctgcg aagtcaccca tcagggcctg


 


2641
agttcaccgg tgacaaagag cttcaacagg ggagagtgtt aataaggcgc gcctaaccat


 


2701
ctatttcaag gaacagtctt aatgaaaaag cttttattca tgatcccgtt agttgtaccg


 


2761
ttcgtggccc agccggcctc tgctgaagtt caattgttag agtctggtgg cggtcttgtt


 


2821
cagcctggtg gttctttacg tctttcttgc gctgcttccg gagcttcaga tctgtttgcc


 


2881
tttttgtggg gtggtgcaga tcgcgttacg gagatcgacc gactgcttga gcaaaagcca


 


2941
cgcttaactg ctgatcaggc atgggatgtt attcgccaaa ccagtcgtca ggatcttaac


 


3001
ctgaggcttt ttttacctac tctgcaagca gcgacatctg gtttgacaca gagcgatccg


 


3061
cgtcgtcagt tggtagaaac attaacacgt tgggatggca tcaatttgct taatgatgat


 


3121
ggtaaaacct ggcagcagcc aggctctgcc atcctgaacg tttggctgac cagtatgttg


 


3181
aagcgtaccg tagtggctgc cgtacctatg ccatttgata agtggtacag cgccagtggc


 


3241
tacgaaacaa cccaggacgg cccaactggt tcgctgaata taagtgttgg agcaaaaatt


 


3301
ttgtatgagg cggtgcaggg agacaaatca ccaatcccac aggcggttga tctgtttgct


 


3361
gggaaaccac agcaggaggt tgtgttggct gcgctggaag atacctggga gactctttcc


 


3421
aaacgctatg gcaataatgt gagtaactgg aaaacaccgg caatggcctt aacgttccgg


 


3481
gcaaataatt tctttggtgt accgcaggcc gcagcggaag aaacgcgtca tcaggcggag


 


3541
tatcaaaacc gtggaacaga aaacgatatg attgttttct caccaacgac aagcgatcgt


 


3601
cctgtgcttg cctgggatgt ggtcgcaccc ggtcagagtg ggtttattgc tcccgatgga


 


3661
acagttgata agcactatga agatcagctg aaaatgtacg aaaattttgg ccgtaagtcg


 


3721
ctctggttaa cgaagcagga tgtggaggcg cataaggagt tctagagaca actctaagaa


 


3781
tactctctac ttgcagatga acagcttaag tctgagcatt cggtccgggc aacattctcc


 


3841
aaactgacca gacgacacaa acggcttacg ctaaatcccg cgcatgggat ggtaaagagg


 


3901
tggcgtcttt gctggcctgg actcatcaga tgaaggccaa aaattggcag gagtggacac


 


3961
agcaggcagc gaaacaagca ctgaccatca actggtacta tgctgatgta aacggcaata


 


4021
ttggttatgt tcatactggt gcttatccag atcgtcaatc aggccatgat ccgcgattac


 


4081
ccgttcctgg tacgggaaaa tgggactgga aagggctatt gccttttgaa atgaacccta


 


4141
aggtgtataa cccccagcag ctagccatat tctctcggtc accgtctcaa gcgcctccac


 


4201
caagggccca tcggtcttcc cgctagcacc ctcctccaag agcacctctg ggggcacagc


 


4261
ggccctgggc tgcctggtca aggactactt ccccgaaccg gtgacggtgt cgtggaactc


 


4321
aggcgccctg accagcggcg tccacacctt cccggctgtc ctacagtcta gcggactcta


 


4381
ctccctcagc agcgtagtga ccgtgccctc ttctagcttg ggcacccaga cctacatctg


 


4441
caacgtgaat cacaagccca gcaacaccaa ggtggacaag aaagttgagc ccaaatcttg


 


4501
tgcggccgca catcatcatc accatcacgg ggccgcagaa caaaaactca tctcagaaga


 


4561
ggatctgaat ggggccgcag aggctagttc tgctagtaac gcgtcttccg gtgattttga


 


4621
ttatgaaaag atggcaaacg ctaataaggg ggctatgacc gaaaatgccg atgaaaacgc


 


4681
gctacagtct gacgctaaag gcaaacttga ttctgtcgct actgattacg gtgctgctat


 


4741
cgatggtttc attggtgacg tttccggcct tgctaatggt aatggtgcta ctggtgattt


 


4801
tgctggctct aattcccaaa tggctcaagt cggtgacggt gataattcac ctttaatgaa


 


4861
taatttccgt caatatttac cttccctccc tcaatcggtt gaatgtcgcc cttttgtctt


 


4921
tggcgctggt aaaccatatg aattttctat tgattgtgac aaaataaact tattccgtgg


 


4981
tgtctttgcg tttcttttat atgttgccac ctttatgtat gtattttcta cgtttgctaa


 


5041
catactgcgt aataaggagt cttaatgaaa cgcgtgatga gaattcactg gccgtcgttt


 


5101
tacaacgtcg tgactgggaa aaccctggcg ttacccaact taatcgcctt gcagcacatc


 


5161
cccctttcgc cagctggcgt aatagcgaag aggcccgcac cgatcgccct tcccaacagt


 


5221
tgcgcagcct gaatggcgaa tggcgcctga tgcggtattt tctccttacg catctgtgcg


 


5281
gtatttcaca ccgcatacgt caaagcaacc atagtacgcg ccctgtagcg gcgcattaag


 


5341
cgcggcgggt gtggtggtta cgcgcagcgt gaccgctaca cttgccagcg ccttagcgcc


 


5401
cgctcctttc gctttcttcc cttcctttct cgccacgttc gccggctttc cccgtcaagc


 


5461
tctaaatcgg gggctccctt tagggttccg atttagtgct ttacggcacc tcgaccccaa


 


5521
aaaacttgat ttgggtgatg gttcacgtag tgggccatcg ccctgataga cggtttttcg


 


5581
ccctttgacg ttggagtcca cgttctttaa tagtggactc ttgttccaaa ctggaacaac


 


5641
actcaactct atctcgggct attcttttga tttataaggg attttgccga tttcggtcta


 


5701
ttggttaaaa aatgagctga tttaacaaaa atttaacgcg aattttaaca aaatattaac


 


5761
gtttacaatt ttatggtgca gtctcagtac aatctgctct gatgccgcat agttaagcca


 


5821
gccccgacac ccgccaacac ccgctgacgc gccctgacgg gcttgtctgc tcccggcatc


 


5881
cgcttacaga caagctgtga ccgtctccgg gagctgcatg tgtcagaggt tttcaccgtc


 


5941
atcaccgaaa cgcgcga
















TABLE 40





pLCSK23 (SEQ ID NO: 896)

















1
GACGAAAGGG CCTGCTCTGC CAGTGTTACA ACCAATTAAC CAATTCTGAT TAGAAAAACT



 


61
CATCGAGCAT CAAATGAAAC TGCAATTTAT TCATATCAGG ATTATCAATA CCATATTTTT


 


121
GAAAAAGCCG TTTCTGTAAT GAAGGAGAAA ACTCACCGAG GCAGTTCCAT AGGATGGCAA


 


181
GATCCTGGTA TCGGTCTGCG ATTCCGACTC GTCCAACATC AATACAACCT ATTAATTTCC


 


241
CCTCGTCAAA AATAAGGTTA TCAAGTGAGA AATCACCATG AGTGACGACT GAATCCGGTG


 


301
AGAATGGCAA AAGCTTATGC ATTTCTTTCC AGACTTGTTC AACAGGCCAG CCATTACGCT


 


361
CGTCATCAAA ATCACTCGCA TCAACCAAAC CGTTATTCAT TCGTGATTGC GCCTGAGCGA


 


421
GACGAAATAC GCGATCGCTG TTAAAAGGAC AATTACAAAC AGGAATTGAA TGCAACCGGC


 


481
GCAGGAACAC TGCCAGCGCA TCAACAATAT TTTCACCTGA ATCAGGATAT TCTTCTAATA


 


541
CCTGGAATGC TGTTTTCCCG GGGATCGCAG TGGTGAGTAA CCATGCATCA TCAGGAGTAC


 


601
GGATAAAATG CTTGATGGTC GGAAGAGGCA TAAATTCCGT CAGCCAGTTT AGTCTGACCA


 


661
TCTCATCTGT AACATCATTG GCAACGCTAC CTTTGCCATG TTTCAGAAAC AACTCTGGCG


 


721
CATCGGGCTT CCCATACAAT CGATAGATTG TCGCACCTGA TTGCCCGACA TTATCGCGAG


 


781
CCCATTTATA CCCATATAAA TCAGCATCCA TGTTGGAATT TAATCGCGGC CTCGAGCAAG


 


841
ACGTTTCCCG TTGAATATGG CTCATAACAC CCCTTGTATT ACTGTTTATG TAAGCAGACA


 


901
GTTTTATTGT TCATGATGAT ATATTTTTAT CTTGTGCAAT GTAACATCAG AGATTTTGAG


 


961
ACACAACGTG GCTTTCCCCC CCCCCCCCTG CAGGTCTCGG GCTATTCCTG TCAGACCAAG


 


1021
TTTACTCATA TATACTTTAG ATTGATTTAA AACTTCATTT TTAATTTAAA AGGATCTAGG


 


1081
TGAAGATCCT TTTTGATAAT CTCATGACCA AAATCCCTTA ACGTGAGTTT TCGTTCCACT


 


1141
GAGCGTCAGA CCCCGTAGAA AAGATCAAAG GATCTTCTTG AGATCCTTTT TTTCTGCGCG


 


1201
TAATCTGCTG CTTGCAAACA AAAAAACCAC CGCTACCAGC GGTGGTTTGT TTGCCGGATC


 


1261
AAGAGCTACC AACTCTTTTT CCGAAGGTAA CTGGCTTCAG CAGAGCGCAG ATACCAAATA


 


1321
CTGTTCTTCT AGTGTAGCCG TAGTTAGGCC ACCACTTCAA GAACTCTGTA GCACCGCCTA


 


1381
CATACCTCGC TCTGCTAATC CTGTTACCAG TGGCTGCTGC CAGTGGCGAT AAGTCGTGTC


 


1441
TTACCGGGTT GGACTCAAGA CGATAGTTAC CGGATAAGGC GCAGCGGTCG GGCTGAACGG


 


1501
GGGGTTCGTG CATACAGCCC AGCTTGGAGC GAACGACCTA CACCGAACTG AGATACCTAC


 


1561
AGCGTGAGCT ATGAGAAAGC GCCACGCTTC CCGAAGGGAG AAAGGCGGAC AGGTATCCGG


 


1621
TAAGCGGCAG GGTCGGAACA GGAGAGCGCA CGAGGGAGCT TCCAGGGGGA AACGCCTGGT


 


1681
ATCTTTATAG TCCTGTCGGG TTTCGCCACC TCTGACTTGA GCGTCGATTT TTGTGATGCT


 


1741
CGTCAGGGGG GCGGAGCCTA TGGAAAAACG CCAGCAACGC GGCCTTTTTA CGGTTCCTGG


 


1801
CCTTTTGCTG GCCTTTTGCT CACATGTTCT TTCCTGCGTT ATCCCCTGAT TCTGTGGATA


 


1861
ACCGTATTAC CGCCTTTGAG TGAGCTGATA CCGCTCGCCG CAGCCGAACG ACCGAGCGCA


 


1921
GCGAGTCAGT GAGCGAGGAA GCGGAAGAGC GCCCAATACG CAAACCGCCT CTCCCCGCGC


 


1981
GTTGGCCGAT TCATTAATGC AGCTGGCACG ACAGGTTTCC CGACTGGAAA GCGGGCAGTG


 


2041
AGCGCAACGC AATTAATGTG AGTTAGCTCA CTCATTAGGC ACCCCAGGCT TTACACTTTA


 


2101
TGCTTCCGGC TCGTATGTTG TGTGGAATTG TGAGCGGATA ACAATTTCAC ACAGGAAACA


 


2161
GCTATGACCA TGATTACGCC AAGCTTTGGA GCCTTTTTTT TGGAGATTTT CAACATGAAG


 


2221
AAGCTCCTCT TTGCTATCCC GCTCGTCGTT CCTTTTGTGG CCCAGCCGGC CATGGCCGAC


 


2281
ATCCAGATGA CCCAGTCTCC ATCCTCCCTG TCTGCATCTG TAGGAGACAG AGTCACCATC


 


2341
ACTTGCCGGG CAAGTCAGAG CATTAGCAGC TATTTAAATT GGTATCAGCA GAAACCAGGG


 


2401
AAAGCCCCTA AGCTCCTGAT CTATGCTGCA TCCAGTTTGC AAAGTGGGGT CCCATCAAGG


 


2461
TTCAGTGGCA GTGGATCTGG GACAGATTTC ACTCTCACCA TCAGCAGTCT GCAACCTGAA


 


2521
GATTTTGCAA CTTACTACTG TCAACAGAGT TACAGTACCC CTTTCACTTT CGGCCCTGGG


 


2581
ACCAAAGTGG ATATCAAACG TGGtACcGTG GCTGCACCAT CTGTCTTCAT CTTCCCGCCA


 


2641
TCTGATGAGC AGTTGAAATC TGGAACTGCC TCTGTTGTGT GCCTGCTGAA TAACTTCTAT


 


2701
CCCAGAGAGG CCAAAGTACA GTGGAAGGTG GATAACGCCC TCCAATCGGG TAACTCCCAG


 


2761
GAGAGTGTCA CAGAGCAGGA CAGCAAGGAC AGCACCTACA GCCTCAGCAG CACCCTGACG


 


2821
CTGAGCAAAG CAGACTACGA GAAACACAAA GTCTACGCCT GCGAAGTCAC CCATCAGGGC


 


2881
CTGAGTTCAC CGGTGACAAA GAGCTTCAAC AGGGGAGAGT GTGCGGCCGC TGGTAAGCCT


 


2941
ATCCCTAACC CTCTCCTCGG TCTCGATTCT ACGTGATAAC TTCACCGGTC AACGCGTGAT


 


3001
GAGAATTCAC TGGCCGTCGT TTTACAACGT CGTGACTGGG AAAACCCTGG CGTTACCCAA


 


3061
CTTAATCGCC TTGCAGCACA TCCCCCTTTC GCCAGCTGGC GTAATAGCGA AGAGGCCCGC


 


3121
ACCGATCGCC CTTCCCAACA GTTGCGCAGC CTGAATGGCG AATGGCGCCT GATGCGGTAT


 


3181
TTTCTCCTTA CGCATCTGTG CGGTATTTCA CACCGCATAC GTCAAAGCAA CCATAGTCTC


 


3241
AGTACAATCT GCTCTGATGC CGCATAGTTA AGCCAGCCCC GACACCCGCC AACACCCGCT


 


3301
GACGCGCCCT GACAGGCTTG TCTGCTCCCG GCATCCGCTT ACAGACAAGC TGTGACCGTC


 


3361
TCCGGGAGCT GCATGTGTCA GAGGTTTTCA CCGTCATCAC CGAAACGCGC GA









REFERENCES
The contents of all cited references including literature references, issued patents, published or non-published patent applications cited throughout this application as well as those listed below are hereby expressly incorporated by reference in their entireties. In case of conflict, the present application, including any definitions herein, will control.

    U.S. Published Application 2005-0119455A1
    Sidhu et al., J Mol Biol. 2004 338:299-310.


EQUIVALENTS
A number of embodiments of the invention have been described. Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, other embodiments are within the scope of the following claims.

## Claims

1. A method of diversifying a library, the method comprising
(i) obtaining a focused library of DNA plasmids or genetic packages comprising the DNA plasmids, the focused library comprising a plurality of variegated DNA molecules, each of which comprises a DNA sequence that encodes an antibody heavy chain variable domain having both frame work (FW) regions and complementary determining regions (CDR), wherein each antibody heavy chain variable domain comprises antibody heavy chain FW1, antibody heavy chain CDR1, antibody heavy chain FW2, antibody heavy chain CDR2, antibody heavy chain FW3, antibody heavy chain CDR3 and antibody heavy chain FW4 in a DNA molecule arranged in the orientation of FW1-CDR1-FW2-CDR2-FW3-CDR3-FW4, wherein the plurality of the variegated DNA molecules collectively encode a population of HC CDR3 regions that contain CDR3 regions having
(a) 3, 4, or 5 amino acids in length,
(b) 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34 or 35 amino acids in length, or
(c) 6 to 20 amino acids in length, inclusive,

wherein the HC CDR3 regions in the focused library contain greater than 40% Tyr (Y) or Ser (S) residues,
wherein the HC CDR3 of the focused library comprises amino acids from a diversified D region or fragment thereof or an extended JH region,
wherein the variegated DNA molecules each comprise a human germline VH gene as the FW1, FW2 and FW3 regions, and
wherein the diversity of the focused library is biased towards the natural diversity of heavy chain CDR3s of found in the human antibody family antibodies, both in sequence and in length; and
(ii) mutagenizing the focused library of DNA plasmids or genetic packages to produce a diversified library.

2. The method of claim 1, wherein the mutagenizing comprises error-prone PCR.

3. The method of claim 1, wherein the mutagenizing comprises wobbling.

4. The method of claim 1, wherein the mutagenizing comprises dobbling.

5. The method of claim 1, wherein the HC CDR3s of the focused library comprise a D region or a fragment thereof.

6. The method of claim 5, wherein the D region is selected from the group consisting of D2-2(RF 2), D2-8(RF 2), D2-15(RF 2), D2-21(RF 2), D3-16(RF 2), D3-22 (RF 2), D3-3 (RF-2), D3-9 (RF 2), D3-10 (RF 2), D1-26 (RF 3), D4-11 (RF 2), D4-4 (RF 2), D5-5 (RF 3), D5-12 (RF 3), D5-18 (RF 3), D6-6 (RF1), D6-13 (RF 1), and D6-19 (RF 1).

7. The method of claim 5, wherein the D region comprises one or more cysteine (Cys) residues and the one or more Cys residues are held constant.

8. The method of claim 5, wherein the HC CDR3s comprise one or more filling codons between FR3 and the D region and each filling codon is individually NNK, TMY, TMT, or TMC.

9. The method of claim 5, wherein the HC CDR3s comprise one or more filling codons between the D region and JH and each filling codon is individually NNK, TMY, TMT, or TMC.

10. The method of claim 1, wherein the plurality of variegated DNA molecules comprises diversity in the HC CDR1, or HC CDR2.

11. The method of claim 10, wherein the focused library further comprises a plurality of variegated DNA molecules, each of which encodes a light chain and the library comprises diversity in the light chains.

12. The method of claim 1, wherein greater than 50% of the population of HC CDR3 regions in (a) are 3, 4, or 5 amino acids in length.

13. The method of claim 1, wherein the population of HC CDR3 regions set forth in (b) contain CDR3 regions having 23, 24, or 25 amino acids in length.

14. The method of claim 1, wherein the population of HC CDR3 regions set forth in (b) contain CDR3 regions having 33, 34, or 35 amino acids in length.