# Patent

## Title
Method for producing polymers having a preselected activity

## Abstract

The present invention relates to a method for isolating from the immunological gene repertoire a gene coding for a receptor having the ability to bind a preselected ligand. Receptors produced by the gene isolated by the method, particularly catalytic receptors, are also contemplated.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application is a continuation of U.S. application Ser. No. 09/726,646, filed Nov. 28, 2000, which is a division of U.S. application Ser. No. 07/933,959 (now U.S. Pat. No. 6,291,159), filed Aug. 21, 1992, which is a continuation of Ser. No. 07/789,619 (now abandoned), filed Nov. 8, 1991, which is a continuation of Ser. No. 07/497,106 (now abandoned), filed Mar. 20, 1990, which is a continuation-in-part of Ser. No. 07/411,058 (now abandoned), filed Sep. 21, 1989, which is a continuation-in-part of Ser. No. 07/410,716 (now abandoned), filed Sep. 20, 1989, which is a continuation-in-part of Ser. No. 07/352,884 (now abandoned), filed May 17, 1989, which is a continuation-in-part of Ser. No. 07/352,927 (now abandoned), filed May 16, 1989; co-pending Ser. No. 09/726,646 is also a continuation-in-part of U.S. application Ser. No. 07/410,749 filed Sep. 20, 1989 (now abandoned) which is a continuation of Ser. No. 07/352,884 (now abandoned), filed May 17, 1989, the disclosures of which are hereby incorporated by reference herein.


TECHNICAL FIELD
The present invention relates to a method for producing polymers having a preselected activity.
BACKGROUND
Binding phenomena between ligands and receptors play many crucial roles in biological systems. Exemplary of such phenomena are the binding of oxygen molecules to deoxyhemoglobin to form oxyhemoglobin, and the binding of a substrate to an enzyme that acts upon it such as between a protein and a protease like trypsin. Still further examples of biological binding phenomena include the binding of an antigen to an antibody 1 and the binding of complement component C3 to the so-called CR1 receptor.
Many drugs and other therapeutic agents are also believed to be dependent upon binding phenomena. For example, opiates such as morphine are reported to bind to specific receptors in the brain. Opiate agonists and antagonists are reported to compete with drugs like morphine for those binding sites.
Ligands such as man-made drugs, like morphine and its derivatives, and those that are naturally present in biological systems such as endorphins and hormones bind to receptors that are naturally present in biological systems, and will be treated together herein. Such binding can lead to a number of the phenomena of biology, including particularly the hydrolysis of amide and ester bonds as where proteins are hydrolyzed into constituent polypeptides by an enzyme such as trypsin or papain or where a fat is cleaved into glycerine and three carboxylic acids, respectively. In addition, such binding can lead to formation of amide and ester bonds in the formation of proteins and fats, as well as to the formation of carbon to carbon bonds and carbon to nitrogen bonds.
An exemplary receptor-producing system in vertebrates is the immune system. The immune system of a mammal is one of the most versatile biological systems as probably greater than 1.0×107 receptor specificities, in the form of antibodies, can be produced. Indeed, much of contemporary biological and medical research is directed toward tapping this repertoire. During the last decade there has been a dramatic increase in the ability to harness the output of the vast immunological repertoire. The development of the hybridoma methodology by Kohler and Milstein has made it possible to produce monoclonal antibodies, i.e., a composition of antibody molecules of a single specificity, from the repertoire of antibodies induced during an immune response.
Unfortunately, current methods for generating monoclonal antibodies are not capable of efficiently surveying the entire antibody response induced by a particular immunogen. In an individual animal there are at least 5-10,000 different B-cell clones capable of generating unique antibodies to a small relatively rigid immunogens, such as, for example dinitrophenol. Further, because of the process of somatic mutation during the generation of antibody diversity, essentially an unlimited number of unique antibody molecules may be generated. In contrast to this vast potential for different antibodies, current hybridoma methodologies typically yield only a few hundred different monoclonal antibodies per fusion.
Other difficulties in producing monoclonal antibodies with the hybridoma methodology include genetic instability and low production capacity of hybridoma cultures. One means by which the art has attempted to overcome these latter two problems has been to clone the immunoglobulin-producing genes from a particular hybridoma of interest into a procaryotic expression system. See, for example, Robinson et al., PCT Publication No. WO 89/0099; Winter et al., European Patent Publication No. 0239400; Reading, U.S. Pat. No. 4,714,681; and Cabilly et al., European Patent Publication No. 0125023.
The immunologic repertoire of vertebrates has recently been found to contain genes coding for immunoglobulins having catalytic activity. Tramontano et al., Sci., 234:1566-1570 (1986); Pollack et al., Sci., 234:1570-1573 (1986); Janda et al., Sci., 241:1188-1191 (1988); and Janda et al., Sci., 244:437-440 (1989). The presence of, or the ability to induce the repertoire to produce, antibodies molecules capable of a catalyzing chemical reaction, i.e., acting like enzymes, had previously been postulated almost 20 years ago by W. P. Jencks in Catalysis in Chemistry and Enzymoloqy, McGraw-Hill, N.Y. (1969).
It is believed that one reason the art failed to isolate catalytic antibodies from the immunological repertoire earlier, and its failure to isolate many to date even after their actual discovery, is the inability to screen a large portion of the repertoire for the desired activity. Another reason is believed to be the bias of currently available screening techniques, such as the hybridoma technique, towards the production high affinity antibodies inherently designed for participation in the process of neutralization, as opposed to catalysis.
BRIEF SUMMARY OF THE INVENTION
The present invention provides a novel method for screening a larger portion of a conserved receptor coding gene repertoire for receptors having a preselected activity than has heretofore been possible, thereby overcoming the before-mentioned inadequacies of the hybridoma technique.
In one embodiment, a conserved receptor-coding gene library containing a substantial portion of the conserved receptor-coding gene repertoire is synthesized. In preferred embodiments, the conserved receptor-coding gene library contains at least about 103, preferably at least about 104 and more preferably at least about 105 different receptor-coding genes.
The gene library can be synthesized by either of two methods, depending on the starting material.
Where the starting material is a plurality of receptor-coding genes, the repertoire is subjected to two distinct primer extension reactions. The first primer extension reaction uses a first polynucleotide synthesis primer capable of initiating the first reaction by hybridizing to a nucleotide sequence conserved (shared by a plurality of genes) within the repertoire. The first primer extension produces of different conserved receptor-coding homolog compliments (nucleic acid strands complementary to the genes in the repertoire).
The second primer extension reaction produces, using the complements as templates, a plurality of different conserved receptor-coding DNA homologs. The second primer extension reaction uses a second polynucleotide synthesis primer that is capable of initiating the second reaction by hybridizing to a nucleotide sequence conserved among a plurality of the compliments.
Where the starting material is a plurality of compliments of conserved receptor-coding genes, the repertoire is subjected to the above-discussed second primer extension reaction. Of course, if both a repertoire of conserved receptor-coding genes and their complements are present, both approaches can be used in combination.
A conserved receptor-coding DNA homolog, i.e., a gene coding for a receptor capable of binding the preselected ligand, is then segregated from the library to produce the isolated gene. This is typically accomplished by operatively linking for expression a plurality of the different conserved receptor-coding DNA homologs of the library to an expression vector. The receptor-expression vectors so produces are introduced into a population of compatible host cells, i.e., cells capable of expressing a gene operatively linked for expression to the vector. The transformants are cultured under conditions for expressing the receptor corded for by the receptor-coding DNA homolog. The transformants are cloned and the clones are screened for expression of a receptor that binds the preselected ligand. Any of the suitable methods well known in the art for detecting the binding of a ligand to a receptor can be used. A transformant expressing the desired activity is then segregated from the population to produce the isolated gene.
In another embodiment, the present invention contemplates a gene library comprising an isolated admixture of at least about 103, preferably at least about 104 and more preferably at least 105 conserved receptor-coding DNA homologs, a plurality of which share a conserved antigenic determinant. Preferably, the homologs are present in a medium suitable for in vitro manipulation, such as water, phosphate buffered saline and the like, which maintains the biological activity of the homologs.
A receptor having a preselected activity, preferably catalytic activity, produced by a method of the present invention, preferably a monomer or dimer as described herein, is also contemplated.



BRIEF DESCRIPTION OF THE DRAWINGS
In the drawings forming a portion of this disclosure:
FIG. 1 Illustrates a schematic diagram of the immunoglobulin molecule showing the principal structural features. The circled area on the heavy chain represents the variable region (VH), a polypeptide containing a biologically active (ligand binding) portion of that region, and a gene coding for that polypeptide, are produced by the methods of the present invention. Sequences L03, L35, L47 and L48 (designated SEQ ID NO:22 and SEQ ID NOs:35-37) could not be classified into any predefined subgroups.
FIG. 2A Diagrammatic sketch of an H chain of human IgG (IgGl subclass). Numbering is from the N-terminus on the left to the C-terminus on the right. Note the presence of four domains, each containing an intrachain disulfide bond (S—S) spanning approximately 60 amino acid residues. The symbol CHO stands for carbohydrate. The V region of the heavy (H) chain (VH) resembles VL in having three hypervariable CDR (not shown).
FIG. 2B Diagrammatic sketch of a human K chain (Panel 1). Numbering is from the N-terminus on the left to the C-terminus on the right. Note the intrachain disulfide bond (S—S) spanning about the same number of amino acid residues in the VL and CL domains. Panel 2 shows the locations of the complementarity-determining regions (CDR) in the VL domain. Segments outside the CDR are the framework segments (FR).
FIG. 3-1-3-4 Amino acid sequence of the VH regions of 19 mouse monoclonal antibodies (SEQ ID NOs: 1-19) with specificity for phosphorylcholine. The designation HP indicates that the protein is the product of a hybridoma. The remainder are myeloma proteins. (From Gearhart et al., Nature, 291:29, 1981.)
FIG. 4 Illustrates the results obtained from PCR amplification of mRNA obtained from the spleen of a mouse immunized with FITC. Lanes R17-R24 correspond to amplification reactions with the unique 5′ primers (SEQ ID NOs:49-56, Table 1) and the 3′ primer (SEQ ID NOs:60-61, Table 1), R16 represents the PCR reaction with the 5′ primer containing inosine (SEQ ID NOs:57-58, Table 1) and 3′ primer (SEQ ID NOs:60-61, Table 1). Z and R9 are the amplification controls; control Z involves the amplification of VH from a plasmid (PLR2) and R9 represents the amplification from the constant regions of spleen mRNA using primers designated SEQ ID NO:59 and SEQ ID NO:62 (Table 1).
FIG. 5 Nucleotide sequences are clones from the cDNA library of the PCR amplified VH regions in Lambda ZAP. The N-terminal 110 bases are listed here and the underlined nucleotides represent CDR1 (complementary determining region) (SEQ ID NOs:20-37).
FIG. 6 The sequence of the synthetic DNA insert inserted into Lambda ZAP to produce Lambda Zap II VH (Panel A) (FIG. 6A-1 and FIG. 6A-2) and Lambda Zap VL (Panel B) (FIG. 6B-1 and FIG. 6B-2) (SEQ ID NOs:38-45) expression vectors. The various features required for this vector to express the VH and VL-coding DNA homologs include the Shine-Dalgarno ribosome binding site, a leader sequence to direct the expressed protein to the periplasm as described by Mouva et al., J. Biol. Chem., 255:27, 1980, and various restriction enzyme sites used to operatively link the VH and VL homologs to the expression vector. The VH expression-vector sequence also contains a short nucleic acid sequence that codes for amino acids typically found in variable regions heavy chain (VH Backbone). This VH Backbone is just upstream and in the proper reading as the VH DNA homologs that are operatively linked into the Xho I and Spe I. The VL DNA homologs are operatively linked into the sequence (Panel B) at the Nco I and Spe I restriction enzyme sites and thus the VH Backbone region is deleted when the VL DNA homologs are operatively linked into the VL vector.
FIG. 7 The major features of the bacterial expression vector Lambda Zap II VH (VH-expression vector) are shown. The synthetic DNA sequence from FIG. 6 is shown at the top along with the T3 polymerase promoter from Lambda Zap II. The orientation of the insert in Lambda Zap II is shown. The VH DNA homologs are inserted into the Xho I and Spe I restriction enzyme sites. The VH DNA are inserted into the Xho I and Spe I site and the read through transcription produces the decapeptide epitope (tag) that is located just 3′ of the cloning sites.
FIG. 8 The major features of the bacterial expression vector Lambda Zap II VL (VL expression vector) are shown. The synthetic sequence shown in FIG. 6 is shown at the top along with the T3 polymerase promoter from Lambda Zap II. The orientation of the insert in Lambda Zap II is shown. The VL DNA homologs are inserted into the phagemid that is produced by the in vivo excision protocol described by Short et al., Nucleic Acids Res., 16:7583-7600, 1988. The VL DNA homelogs are inserted into the Nco I and Spe I cloning sites of the phagemid.
FIG. 9 A modified bacterial expression vector Lambda Zap II VLII. This vector is constructed by inserting this synthetic DNA sequence (SEQ ID NO:46 and SEQ ID NO:106),








TGAATTCTAAACTAGTCGCCAAGGAGACAGTCATAATGAATCGAACTTAA



 


GATTTGATCAGCGGTTCCTCTGTCAGTATTACTTATACCTATTGCCTACG


 


GCAGCCGCTGGATTGTTATTACTCGCTGTATGGATAACGGATGCCGTCGG


 


CGACCTAACAATAATGAGCGACCCCAACCAGCCATGGCCGAGCTCGTCAG


 


TTCTAGAGTTAAGCGGCCGGGGTTGGTCGGTACCGGCTCGAGCAGTCAAG


 


ATCTCAATTCGCCGGCAGCT






into Lambda Zap II that has been digested with the restriction enzymes Sac I and Xho I. This sequence contains the Shine-Dalgarno sequence (Ribosome binding site), the leader sequence to direct the expressed protein to the periplasm and the appropriate nucleic acid sequence to allow the VL DNA homologs to be operatively linked into the SacI and Xba I restriction enzyme sites provided by this vector.

FIG. 10 The sequence of the synthetic DNA segment inserted into Lambda Zap II to produce the lambda VLII-expression vector. The various features and restriction endonuclease recognition sites are shown (SEQ ID NOs:47-48).
FIG. 11-1-11-3 The vectors for expressing VH and VL separately and in combination are shown. The various essential components of these vectors are shown. The light chain vector or VL expression vector can be combined with the VH expression vector to produce a combinatorial vector containing both VH and VL operatively linked for expression to the same promoter.
FIG. 12 The labeled proteins immunoprecipitated from E. coli containing a VH and a VL DNA homolog are shown. In lane 1, the background proteins immunoprecipitated from E. coli that do not contain a VH or VL DNA homolog are shown. Lane 2 contains the VH protein immunoprecipitated from E. coli containing only a VH DNA homolog. In lanes 3 and 4, the commigration of a VH protein a VL protein immunoprecipitated from E. coli containing both a VH and a VL DNA homolog is shown. In lane 5 the presence of VH protein and VL protein expressed from the VH and VL DNA homologs is demonstrated by the two distinguishable protein species. Lane 5 contains the background proteins immunoprecipitated by anti-E. coli antibodies present in mouse ascites fluid.
FIG. 13 The transition state analogue (formula 1) which induces antibodies for hydrolyzing carboxamide substrate (formula 2). The compound of formula 1 containing a glutaryl spacer and a N-hydroxysuccinimide-linker appendage is the form used to couple the hapten (formula 1) to protein carriers KLH and BSA, while the compound of formula 3 is the inhibitor. The phosphonamidate functionality is a mimic of the stereoelectronic features of the transition state for hydrolysis of the amide bond.
FIG. 14 PCR amplification of Fd and kappa regions from the spleen mRNA of a mouse immunized with NPN is illustrated. Amplification was performed as described in Example 17 using RNA cDNA hybrids obtained by the reverse transcription of the mRNA with primer specific for amplification of light chain sequences (Table 2) or heavy chain sequences (Table 1). Lanes F1-F8 represent the product of heavy chain amplification reactions with one of each of the eight 5′ primers (SEQ ID NOs:49-56, Table 1) and the unique 3′ primer (SEQ ID NO:81, Table 2). Light chain (k) amplifications with the 5′ primers (SEQ ID NOs:69-72, and SEQ ID NO:78, respectively, Table 2) and the appropriate 3′ primer (SEQ ID NO:79, Table 2) are shown in lanes F9-F13. A band of 700 bps is seen in all lanes indicating the successful amplification of Fd and k regions.
FIG. 15 The screening of phage libraries for antigen binding is depicted according to Example 17 C. Duplicate plaque lifts of Fab (filters A, B), heavy chain (filters E, F) and light chain (filters G, H) expression libraries were screened against 125I-labeled BSA conjugated with NPN at a density of approximately 30,000 plaques per plate. Filters C and D illustrate the duplicate secondary screening of a cored positive from a primary filter A (arrows) as discussed in the text.
Screening employed standard plaque lift methods. XL1 Blue cells infected with phage were incubated on 150 mm plates for 4 h at 37°, protein expression induced by overlay with nitrocellulose filters soaked in 10 mM isopropyl thiogalactoside (IPTG) and the plates incubated at 25° for 8 h. Duplicate filters were obtained during a second incubation employing the same conditions. Filters were then blocked in a solution of 1% BSA in PBS for 1 h before incubation with rocking at 25° for 1 h with a solution of 125I-labelled BSA conjugated to NPN (2×106 cpm ml−1; BSA concentration at 0.1 M; approximately 15 NPN per BSA molecule) in 1% BSA in PBS. Background was reduced by pre-centrifugation of stock radiolabelled BSA solution at 100,000 g for 15 min and pre-incubation of solutions with plaque lifts from plates containing bacteria infected with a phage having no insert. After labeling, filters were washed repeatedly with PBS/0.05% Tween 20 before development of autoradiographs overnight.
FIG. 16 The specificity of antigen binding as shown by competitive inhibition is illustrated according to Example 17C. Filter lifts from positive plaques were exposed to 125I-BSA-NPN in the presence of increasing concentrations of the inhibitor NPN.
In this study a number of phages correlated with NPN binding as in FIG. 15 were spotted (about 100 particles per spot) directly onto a bacterial lawns. The plate was then overlaid with an IPTG-soaked filter and incubated for 19 h at 25°. The filter were then blocked in 1% BSA in PBS prior to incubation in 125I-BSA-NPN as described previously in FIG. 15 except with the inclusion of varying amounts of NPN in the labeling solution. Other conditions and procedures were as in FIG. 15. The results for a phage of moderate affinity are shown in duplicate in the figure. Similar results were obtained for four other phages with some differences in the effective inhibitor concentration ranges.
FIG. 17 The characterization of an antigen binding protein is illustrated according to Example 17D. The concentrated partially purified bacterial supernate of an NPN-binding clone was separated by gel filtration and aliquots from each fraction applied to microtitre plates coated with BSA-NPN. Addition of either anti-decapeptide (—) or anti-kappa chain (—) antibodies conjugated with alkaline phosphatase was followed by color development. The arrow indicates the position of elution of a known Fab fragment. The results show that antigen binding is a property of 50 kD protein containing both heavy and light chains.



Single plaques of two NPN-positive clones (FIG. 15) were picked and the plasmid containing the heavy and light chain inserts excised. 500 ml cultures in L-broth were inoculated with 3 ml of a saturated culture containing the excised plasmids and incubated for 4 h at 37. Proteins synthesis was induced by the addition of IPTG to a final concentration of 1 mM and the cultures incubated for 10 h at 25°. 200 ml of cells supernate were concentrated to 2 ml and applied to a TSK-G4000 column. 50 μl aliquots from the eluted fractions were assayed by ELISA.
For ELISA analysis, microtitre plates were coated with BSA-NPN at 1 μg/ml, 50 μl samples mixed with 50 μl PBS-Tween 20 (0.05%)-BSA (0.1%) added and the plates incubated for 2 h at 25°. After washing with PBS-Tween 20-BSA, 50 μl of appropriate concentrations of a rabbit anti-decapeptide antibody (20) and a goat anti-mouse kappa light chain (Southern Biotech) antibody conjugated with alkaline phosphatase were added and incubated for 2 h at 25°. After further washing, 50 μl of p-nitrophenyl phosphate (1 mg/ml in 0.1M tris pH 9.5 containing 50 mM MgCl2) were added and the plates incubated for 15-30 min before reading the OD at 405 nm.
DETAILED DESCRIPTION OF THE INVENTION
A. Definitions
Nucleotide: a monomeric unit of DNA or RNA consisting of a sugar moiety (pentose), a phosphate, and a nitrogenous heterocyclic base. The base is linked to the sugar moiety via the glycosidic carbon (1′ carbon of the pentose) and that combination of base and sugar is a nucleoside. When the nucleoside contains a phosphate group bonded to the 3′ or 5′ position of the pentose it is referred to as a nucleotide.
Base Pair (bp): a partnership of adenine (A) with thymine (T), or of cytosine (C) with guanine (G) in a double stranded DNA molecule. In RNA, uracil (U) is substituted for thymine.
Nucleic Acid: a polymer of nucleotides, either single or double stranded.
Gene: a nucleic acid whose nucleotide sequence codes for a RNA or polypeptide. A gene can be either RNA or DNA.
Complementary Bases: nucleotides that normally pair up when DNA or RNA adopts a double stranded configuration.
Complementary Nucleotide Sequence: a sequence of nucleotides in a single-stranded molecule of DNA or RNA that is sufficiently complementary to that on another single strand to specifically hybridize to it with consequent hydrogen bonding.
Conserved: a nucleotide sequence is conserved with respect to a preselected (reference) sequence if it non-randomly hybridizes to an exact complement of the preselected sequence.
Hybridization: the pairing of substantially complementary nucleotide sequences (strands of nucleic acid) to form a duplex or heteroduplex by the establishment of hydrogen bonds between complementary base pairs. It is a specific, i.e. non-random, interaction between two complementary polynucleotide that can be competitively inhibited.
Nucleotide Analog: a purine or pyrimidine nucleotide that differs structurally from A, T, G, C, or U, but is sufficiently similar to substitute for the normal nucleotide in a nucleic acid molecule.
DNA Homolog: is a nucleic acid having a preselected conserved nucleotide sequence and a sequence coding for a receptor capable of binding a preselected ligand.
B. Methods
The present invention contemplates a method of isolating from a repertoire of conserved genes a gene coding for a receptor having a preselected activity, preferably a catalytic activity. The receptor can be a polypeptide, an RNA molecule, such as a transfer RNA, an RNA displaying enzymatic activity, and the like. Preferably, the receptor will be a polypeptide capable of binding a ligand, such as an enzyme, antibody molecule or immunologically active portion thereof, cellular receptor, or cellular adhesion protein coded for by one of the members of a family of conserved genes, i.e., genes containing a conserved nucleotide sequence of at least about 10 nucleotides in length.
Exemplary conserved gene families are those coding for immunoglobulins, major histocompatibility complex antigens of class I or II, lymphocyte receptors, integrins and the like.
Immunoglobulins
The immunoglobulins, or antibody molecules, are a large family of molecules that include several types of molecules, such as IgD, IgG, IgA, IgM and IgE. The antibody molecule is typically comprised of two heavy (H) and light (L) chains with both a variable (V) and constant (C) region present on each chain. Several different regions of an immunoglobulin contain conserved sequences useful for isolating an immunoglobulin repertoire. Extensive amino acid and nucleic acid sequence data displaying exemplary conserved sequences is compiled for immunoglobulin molecules by Kabat et al., in Sequences of Proteins of Immunological Interest, National Institutes of Health, Bethesda, Md., 1987.
The C region of the H chain defines the particular immunoglobulin type. Therefore the selection of conserved sequences as defined herein from the C region of the H chain results in the preparation of a repertoire of immunoglobulin genes having members of the immunoglobulin type of the selected C region.
The V region of the H or L chain typically comprises four framework (FR) regions each containing relatively lower degrees of variability that includes lengths of conserved sequences. The use of conserved sequences from the FR1 and FR4 (J region) framework regions of the chain is a preferred exemplary embodiment and is described herein in the Examples. Framework regions are typically conserved across several or all immunoglobulin types and thus conserved sequences contained therein are particularly suited for preparing repertoires having several immunoglobulin types.
Major Histocompatibility Complex
The major histocompatibility complex (MHC) is a large genetic locus that encodes an extensive family of proteins that include several classes of molecules referred to as class I, class II or class III MHC molecules. Paul et al., in Fundamental Immunology, Raven Press, NY, pp. 303-378 (1984).
Class I MHC molecules are a polymorphic group of transplantation antigens representing a conserved family in which the antigen is comprised of a heavy chain and a non-MHC encoded light chain. The heavy chain includes several regions, termed the N, C1, C2, membrane and cytoplasmic regions. Conserved sequences useful in the present invention are found primarily in the N, C1 and C2 regions and are identified as continuous sequences of “invariant residues” in Kabat et al., supra.
Class II MHC molecules comprise a conserved family of polymorphic antigens that participate in immune responsiveness and are comprised of an alpha and a beta chain. The genes coding for the alpha and beta chain each include several regions that contain conserved sequences suitable for producing MHC class II alpha or beta chain repertoires. Exemplary conserved nucleotide sequences include those coding for amino acid residues 26-30 of the A1 region, residues 161-170 of the A2 region and residues 195-206 of the membrane region, all of the alpha chain. Conserved sequences are also present in the B1, B2 and membrane regions of the beta chain at nucleotide sequences coding for amino acid residues 41-45, 150-162 and 200-209, respectively.
Lymphocyte Receptors and Cell Surface Antigens
Lymphocytes contain several families of proteins on their cell surfaces including the T-cell receptor, Thy-1 antigen and numerous T-cell surface antigens including the antigens defined by the monoclonal antibodies OKT4 (leu3), OKUT5/8 (leu2), OKUT3, OKUTI (leu1), OKT 11 (leu5) OKT6 and OKT9. Paul, supra at pp. 458-479.
The T-cell receptor is a term used for a family of antigen binding molecules found on the surface of T-cells. The T-cell receptor as a family exhibits polymorphic binding specificity similar to immunoglobulins in its diversity. The mature T-cell receptor is comprised of alpha and beta chains each having a variable (V) and constant (C) region. The similarities that the T-cell receptor has to immunoglobulins in genetic organization and function shows that T-cell receptor contains regions of conserved sequence. Lai et al., Nature, 331:543-546 (1988).
Exemplary conserved sequences include those coding for amino acid residues 84-90 of alpha chain, amino acid residues 107-115 of beta chain, and amino acid residues 91-95 and 111-116 of the gamma chain. Kabat et al., supra, p. 279.
Integrins and Adhesins
Adhesive proteins involved in cell attachment are members of a large family of related proteins termed integrins. Integrins are heterodimers comprised of a beta and an alpha subunit. Members of the integrin family include the cell surface glycoproteins platelet receptor GpIIb-IIIa, vitronectin, receptor (VnR) fibronectin receptor (FnR) and the leukocyte adhesion receptors LFA-1, Mac-1, Mo-1 and 60.3. Roushahti et al., Science, 238:491-497 (1987). Nucleic acid and protein sequence data demonstrates regions of conserved sequences exist in the members of these families particularly between the beta chain of GpIIb-IIIa VnR and FnR, and between the alpha subunit of VnR, Mac-1, LFA-1, Fnr and GpIIb-IIIa. Suzuki et al., Proc. Natl. Acad. Sci. USA, 83:8614-8618, 1986; Ginsberg et al., J. Bios. Chem., 262:5437-5440, 1987.
The following discussion illustrates the method of the present invention applied to isolating a conserved receptor-coding gene from the immunoglobulin gene repertoire. This discussion is not to be taken as limiting, but rather as illustrating application of principles that can be used to isolate a gene from any family of conserved genes coding for functionally related receptors.
Generally, the method combines the following elements:
1. Isolating nucleic acids containing a substantial portion of the immunological repertoire.
2. Preparing polynucleotide primers for cloning polynucleotide segments containing immunoglobulin VH and/or VL region genes.
3. Preparing a gene library containing a plurality of different VH and VL genes from the repertoire.
4. Expressing the VH and/or VL polypeptides in a suitable host, including prokaryotic and eukaryotic hosts, either separately or in the same cell, and either on the same or different expression vectors.
5. Screening the expressed polypeptides for the preselected activity, and segregating a VH-and/or VL-coding gene identified by the screening process.
A receptor produced by the present invention assumes a conformation having a binding site specific for as evidenced by its ability to be competitively inhibited, a preselected or predetermined ligand such as an antigen, enzymatic substrate and the like. In one embodiment, a receptor of this invention is a ligand binding polypeptide that forms an antigen binding site which specifically binds to a preselected antigen to form a complex having a sufficiently strong binding between the antigen and the binding site for the complex to be isolated. When the receptor is an antigen binding polypeptide its affinity or avidity is generally greater than 105-M−1 more usually greater than 106 and preferably greater than 108 M−1.
In another embodiment, a receptor of the subject invention binds a substrate and catalyzes the formation of a product from the substrate. While the topology of the ligand binding site of a catalytic receptor is probably more important for its preselected activity than its affinity (association constant or pKa) for the substrate, the subject catalytic receptors have an association constant for the preselected substrate generally greater than 103 M−1, more usually greater than 105 M−1 or 106 M−1 and preferably greater than 107 M−1.
Preferably the receptor produced by the subject invention is heterodimeric and is therefore normally comprised of two different polypeptide chains, which together assume a conformation having a binding affinity, or association constant for the preselected ligand that is different, preferably higher, than the affinity or association constant of either of the polypeptides alone, i.e., as monomers. One or both of the different polypeptide chains is derived from the variable region of the light and heavy chains of an immunoglobulin. Typically, polypeptides comprising the light (VL) and heavy (VH) variable regions are employed together for binding the preselected ligand.
A receptor produced by the subject invention can be active in monomeric as well as multimeric forms, either homomeric or heteromeric, preferably heterodimeric. A VH and VL ligand binding polypeptide produced by the present invention can be advantageously combined in the heterodimer to modulate the activity of either or to produce an activity unique to the heterodimer. The individual ligand binding polypeptides will be referred to as VH and VL and the heterodimer will be referred to as a Fv. However, it should be understood that a VH binding polypeptide may contain in addition to the VH, substantially or a portion of the heavy chain constant region. A VL binding polypeptide may contain in addition to the VL, substantially all or a portion of the light chain constant region. A heterodimer comprised of a VH binding polypeptide containing a portion of the heavy chain constant region and a VL binding containing substantially all of the light chain constant region is termed a Fab fragment. The production of Fab can be advantageous in some situations because the additional constant region sequences contained in a Fab as compared to a Fv could stabilize the VH and VL interaction. Such stabilization could cause the Fab to have higher affinity for antigen. In addition the Fab is more commonly used in the art and thus there are more commercial antibodies available to specifically recognize a Fab.
The individual VH and VL polypeptides will generally have fewer than 125 amino acid residues, more usually fewer than about 120 amino acid residues, while normally having greater than 60 amino acid residues, usually greater than about 95 amino acid residues, more usually greater than about 100 amino acid residues. Preferably, the VH will be from about 110 to about 125 amino acid residues in length while VL will be from about 95 to about 115 amino acid residues in length.
The amino acid residue sequences will vary widely, depending upon the particular idiotype involved. Usually, there will be at least two cysteines separated by from about 60 to 75 amino acid residues and joined by a disulfide bond. The polypeptides produced by the subject invention will normally be substantial copies of idotypes of the variable regions of the heavy and/or light chains of immunoglobulins, but in some situations a polypeptide may contain random mutations in amino acid residue sequences in order to advantageously improve the desired activity.
In some situations, it is desirable to provide for covalent cross linking of the VH and VL polypeptides, which can be accomplished by providing cysteine resides at the carboxyl termini. The polypeptide will normally be prepared free of the immunoglobulin constant regions, however a small portion of the J region may be included as a result of the advantageous selection of DNA synthesis primers. The D region will normally be included in the transcript of the VH.
In other situations, it is desirable to provide a peptide linker to connect the VL and the VH to form a single-chain antigen-binding protein comprised of a VH and a VL. This single-chain antigen-binding protein would be synthesized as a single protein chain. Such single-chain antigen-binding proteins have been described by Bird et al., Science, 242:423-426 (1988). The design of suitable peptide linker regions is described in U.S. Pat. No. 4,704,692 by Robert Landner.
Such a peptide linker could be designed as part of the nucleic acid sequences contained in the expression vector. The nucleic acid sequences coding for the peptide linker would be between the VH and VL DNA homologs and the restriction endonuclease sites used to operatively link the VH and VL DNA homologs to the expression vector.
Such a peptide linker could also be coded for nucleic acid sequences that are part of the polynucleotide primers used to prepare the various gene libraries. The nucleic acid sequence coding for the peptide linker can be made up of nucleic acids attached to one of the primers or the nucleic acid sequence coding for the peptide linker may be derived from nucleic acid sequences that are attached to several polynucleotide primers used to create the gene libraries.
Typically the C terminus region of the VH and VL polypeptides will have a greater variety of the sequences than the N terminus and, based on the present strategy, can be further modified to permit a variation of the normally occurring VH and VL chains. A synthetic polynucleotide can be employed to vary one or more amino in an hypervariable region.
1. Isolation of the Repertoire
To prepare a composition of nucleic acids containing a substantial portion of the immunological gene repertoire, a source of genes coding for the VH and/or VL polypeptides is required. Preferably the source will be a heterogeneous population of antibody producing cells, i.e. B lymphocytes (B cells), preferably rearranged B cells such as those found in the circulation or spleen of a vertebrate. (Rearranged B cells are those in which immunoglobulin gene translocation, i.e., rearrangement, has occurred as evidenced by the presence in the cell of mRNA with the immunoglobulin gene V, D and J region transcripts adjacently located thereon.)
In some cases, it is desirable to bias the repertoire for a preselected activity, such as by using as a source of nucleic acid cells (source cells) from vertebrates in anyone of various stages of age, health and immune response. For example, repeated immunization of a healthy animal prior to collecting rearranged B cells results in obtaining a repertoire enriched for genetic material producing a ligand binding polypeptide of high affinity. Conversely, collecting rearranged B cells from a healthy animal whose immune system has not been recently challenged results in producing a repertoire that is not biased towards the production of high affinity VH and/or VL polypeptides.
It should be noted the greater the genetic heterogeneity of the population of cells for which the nucleic acids are obtained, the greater the diversity of the immunological repertoire that will be made available for screening according to the method of the present invention. Thus, cells from different individuals, particularly those having an immunologically significant age difference, and cells from individuals of different strains, races or species can be advantageously combined to increase the heterogeneity of the repertoire.
Thus, in one preferred embodiment, the source cells are obtained from a vertebrate, preferably a mammal, which has been immunized or partially immunized with an antigenic ligand (antigen) against which activity is sought, i.e., a preselected antigen. The immunization can be carried out conventionally. Antibody titer in the animal can be monitored to determine the stage of immunization desired, which stage corresponds to the amount of enrichment or biasing of the repertoire desired. Partially immunized animals typically receive only one immunization and cells are collected therefrom shortly after a response is detected. Fully immunized animals display a peak titer, which is achieved with one or more repeated injections of the antigen into the host mammal, normally at 2 to 3 week intervals. Usually three to five days after the last challenge, the spleen is removed and the genetic repertoire of the spleenocytes, about 90% of which are rearranged B cells, is isolated using standard procedures. See, Current Protocols in Molecular Biology, Ausubel et al., eds., John Wiley & Sons, NY.
Nucleic acids coding for VH and VL polypeptides can be derived from cells producing IgA, IgD, IgE, IgG or IgM, most preferably from IgM and IgG, producing cells.
Methods for preparing fragments of genomic DNA from which immunoglobulin variable region genes can be cloned as a diverse population are well known in the art. See for example Herrmann et al., Methods In Enzymol., 152:180-183, (1987); Frischauf, Methods In Enzymol., 152:183-190 (1987); Frischauf, Methods In Enzymol., 152:190-199 (1987); and DiLella et al., Methods In Enzymol., 152:199-212 (1987). (The teachings of the references cited herein are hereby incorporated by reference.)
The desired gene repertoire can be isolated from either genomic material containing the gene expressing the variable region or the messenger RNA (mRNA) which represents a transcript of the variable region. The difficulty in using the genomic DNA from other than non-rearranged B lymphocytes is in juxtaposing the sequences coding for the variable region, where the sequences are separated by introns. The DNA fragment(s) containing the proper exons must be isolated, the introns excised, and the exons then spliced in the proper order and in the proper orientation. For the most part, this will be difficult, so that the alternative technique employing rearranged B cells will be the method of choice because the C D and J immuglobulin gene regions have translocated to become adjacent, so that the sequence is continuous (free of introns) for the entire variable regions.
Where mRNA is utilized the cells will be lysed under RNase inhibiting conditions. In one embodiment, the first step is to isolate the total cellular mRNA by hybridization to an oligo-dT cellulose column. The presence of mRNAs coding for the heavy and/or light chain polypeptides can then be assayed by hybridization with DNA single strands of the appropriate genes. Conveniently, the sequences coding for the constant portion of the VH and VL can be used as polynucleotide probes, which sequences can be obtained from available sources. See for example, Early and Hood, Genetic Engineering, Setlow and Hollaender, eds., Vol. 3, Plenum Publishing Corporation, New York, (1981), pages 157-188; and Kabat et al., Sequences of Immunological Interest, National Institutes of Health, Bethesda, Md., (1987).
In preferred embodiments, the preparation containing the total cellular mRNA is first enriched for the presence of VH and/or VL coding mRNA. Enrichment is typically accomplished by subjecting the total mRNA preparation or partially purified mRNA product thereof to a primer extension reaction employing a polynucleotide synthesis primer of the present invention.
2. Preparation of Polynucleotide Primers
The term “polynucleotide” as used herein in reference to primers, probes and nucleic acid fragments or segments to be synthesized by primer extension is defined as a molecule comprised of two or more deoxyribonucleotides or ribonucleotides, preferably more than 3. Its exact size will depend on many factors, which in turn depends on the ultimate conditions of use.
The term “primer” as used herein refers to a polynucleotide whether purified from a nucleic acid restriction digest or produced synthetically, which is capable of acting as a point of initiation of synthesis when placed under conditions in which synthesis of a primer extension product which is complimentary to a nucleic acid strand is induced, i.e., in the presence of nucleotides and an agent for polymerization such as DNA polymerase, reverse transcriptase and the like, and at a suitable temperature and pH. The primer is preferably single stranded for maximum efficiency, but may alternatively be double stranded. If double stranded, the primer is first treated to separate its strands before being used to prepare extension products. Preferably, the primer is a polydeoxyribonucleotide. The primer must be sufficiently long to prime the synthesis of extension products in the presence of the agents for polymerization. The exact lengths of the primers will depend on many factors, including temperature and the source of primer. For example, depending on the complexity of the target sequence, a polynucleotide primer typically contains 15 to 25 or more nucleotides, although it can contain fewer nucleotides. Short primer molecules generally require cooler temperatures to form sufficiently stable hybrid complexes with template.
The primers used herein are selected to be “substantially” complementary to the different strands of each specific sequence to be synthesized or amplified. This means that the primer must be sufficiently complementary to nonrandomly hybridize with its respective template strand. Therefore, the primer sequence may not reflect the exact sequence of the template. For example, a non-complementary nucleotide fragment can be attached to the 5′ end of the primer, with the remainder of the primer sequence being substantially complementary to the strand. Such noncomplementary fragments typically code for an endocuclease restriction site. Alternatively, noncomplementary bases or longer sequences can be interspersed into the primer, provided the primer sequence has sufficient complementarily with the sequence of the strand to be synthesized or amplified to non-randomly hybridize therewith and thereby form an extension product under polynucleotide synthesizing conditions.
The polynucleotide primers can be prepared using any suitable method, such as, for example, the phosphotriester on phosphodiester methods see Narang et al., Meth. Enzymol., 68:90, (1979); U.S. Pat. No. 4,356,270; and Brown et al., Meth. Enzmmol., 68:109, (1979).
The choice of a primer's nucleotide sequence depends on factors such as the distance on the nucleic acid from the region coding for the desired receptor, its hybridization site on the nucleic acid relative to any second primer to be used, the number of genes in the repertoire it is to hybridize to, and the like.
For example, to produce VH-coding DNA homologs by primer extension, the nucleotide sequence of a primer is selected to hybridize with a plurality of immunoglobulin heavy chain genes at a site substantially adjacent to the VH-coding region so that a nucleotide sequence coding for a functional (capable of binding) polypeptide is obtained. To hybridize to a plurality of different VH-coding nucleic acid strands, the primer must be a substantial complement of a nucleotide sequence conserved among the different strands. Such sites include nucleotide sequences in the constant region, any of the variable region framework regions, preferably the third framework region, leader region, promoter region, J region and the like.
If the VH-coding and VL-coding DNA homologs are to be produced by polymerase chain reaction (PCR) amplification, two primers must be used for each coding strand of nucleic acid to be amplified. The first primer becomes part of the nonsense (minus or complimentary) strand and hybridizes to a nucleotide sequence conserved among VH (plus) strands within the repertoire. To produce VH coding DNA homologs, first primers are therefore chosen to hybridize to (i.e. be complementary to) conserved regions within the J region, CH1 region, hinge region, CH2 region, or CH3 region of immunoglobulin genes and the like. To produce a VL coding DNA homolog, first primers are chosen to hybridize with (i.e. be complementary to) a conserved region within the J region or constant region of immunoglobulin light chain genes and the like. Second primers become part of the coding (plus) strand and hybridize to a nucleotide sequence conserved among minus strands. To produce the VH-coding DNA homologs, second primers are therefore chosen to hybridize with a conserved nucleotide sequence at the 5′ end of the VH-coding immunoglobulin gene such as in that area coding for the leader or first framework region. It should be noted that in the amplification of both VH-and VL-coding DNA homologs the conserved 5′ nucleotide sequence of the second primer can be complementary to a sequence exogenously added using terminal deoxynucleotidyl transferase as described by Loh et al., Sci. Vol 243:217-220 (1989). One or both of the first and second primers can contain a nucleotide sequence defining an endonuclease recognition site. The site can be heterologous to the immunoglobulin gene being amplified and typically appears at or near the 5′ end of the primer.
Primers of the present invention may also contain a DNA-dependent RNA polymerase promoter sequence or its complement. See for example, Krieg et al., Nucleic Acids Research, 12:7057-70 (1984): Studier et al., J. Mol. Biol., 189:113-130 (1986): and Molecular Cloning: A Laboratory Manual. Second Edition, Maniatis et al., eds., Cold Spring Harbor, N.Y. (1989).
When a primer containing a DNA-dependent RNA polymerase promoter is used the primer is hybridized to the polynucleotide strand to be amplified and the second polynucleotide strand of the DNA-dependent RNA polymerase promoter is completed using an inducing such as E. coli, DNA polymerase I, or the Klenow fragment of E. coli DNA polymerase I. The complementary RNA polynucleotide is then produced by adding a RNA-dependent RNA polymerase. The starting polynucleotide is amplified by alternating between the production of an RNA polynucleotide and DNA polynucleotide.
3. Preparing a Gene Library
The strategy used for cloning, i.e., substantially reproducing, the VH and/or VL genes contained within the isolated repertoire will depend, as is well known in the art, on the type, complexity, and purity of the nucleic acids making up the repertoire. Other factors include whether or not the genes are to be amplified and/or mutigenized.
In one strategy, the object is to clone the VH-and/or VL-coding genes from a repertoire comprised of polynucleotide coding strands, such as mRNA and/or the sense strand of genomic DNA. If the repertoire is in the form of double stranded genomic DNA, it is usually first denatured, typically by melting, into single strands. The repertoire is subjected to a first primary extension reaction by treating (contacting) the repertoire with a first polynucleotide synthesis primer having a preselected nucleotide sequence. The first primer is capable of initiating the first primer extension reaction by hybridizing to a nucleotide sequence, preferably at least about 10 nucleotides in length and more preferably at least about 20 nucleotides in length, conserved within the repertoire. The first primer is sometimes referred to herein as the “sense primer” because it hybridizes to the coding or sense strand of a nucleic acid. In addition, the second primer is sometimes referred to herein as the “anti-sense primer” because it hybridizes to a non-coding or anti-sense strand of a nucleic acid, i.e., a strand complementary to a coding strand.
The first primer extension is performed by mixing the first primer, preferably a predetermined amount thereof, with the nucleic acids of the repertoire, preferably a predetermined amount thereof, to form a first primer extension reaction admixture. The admixture is maintained under polynucleotide synthesizing conditions for a time period, which is typically predetermined, sufficient for the formation of a first primer extension reaction product, thereby producing a plurality of different VH-coding DNA homolog complements. The complements are then subjected to a second primer extension reaction by treating them with a second polynucleotide synthesis primer having a preselected nucleotide sequence. The second primer is capable of initiating the second reaction by hybridizing to a nucleotide sequence, preferably at least about 10 nucleotides in length and more preferably at least about 20 nucleotides in length, conserved among a plurality of different VH-coding gene complements such as those, for example, produced by the first primer extension reaction. This is accomplished by mixing the second primer, preferably a predetermined amount thereof, with the compliment nucleic acids, preferably a predetermined amount thereof, to form a second primer extension reaction admixture. The admixture is maintained under polynucleotide synthesizing conditions for a time period, which is typically predetermined, sufficient for the formation of a first primer extension reaction product, thereby producing a gene library containing a plurality of different VH-and/or VL-coding DNA homologs.
A plurality of first primer and/or a plurality of second primers can be used in each amplification, or an individual pair of first and second primers can be used. In any case, the amplification products of amplifications using the same or different combinations of first and second primers can be combined to increase the diversity of the gene library.
In another strategy, the object is to clone the VH-and/or VL-coding genes from a repertoire by providing a polynucleotide complement of the repertoire, such as the anti-sense strand of genomic dsDNA or the polynucleotide produced by subjecting mRNA to a reverse transcriptase reaction. Methods for producing such complements are well known in the art. The complement is subjected to a primer extension reaction similar to the above-described second primer extension reaction, i.e., a primer extension reaction using a polynucleotide synthesis primer capable of hybridizing to a nucleotide sequence conserved among a plurality of different VH-coding gene complements.
The primer extension reaction is performed using any suitable method. Generally it occurs in a buffered aqueous solution, preferably at a pH of 7-9, most preferably about 8. Preferably, a molar excess (for genomic nucleic acid, usually about 106:1 primer:template) of the primer is admixed to the buffer containing the template strand. A large molar excess is preferred to improve the efficiency of the process.
The deoxyribonucleotide triphosphates dATP, dCTP, dGTP, and dTTP are also admixed to the primer extension (polynucleotide synthesis) reaction admixture in adequate amounts and the resulting solution is heated to about 90 C -10° C. for about 1 to 10 minutes, preferably from 1 to 4 minutes. After this heating period the solution is allowed to cool to room temperature, which is preferable for primer hybridization. To the cooled mixture is added an appropriate agent for inducing or catalyzing the primer extension reaction, and the reaction is allowed to occur under conditions known in the art. The synthesis reaction may occur at from room temperature up to a temperature above which the inducing agent no longer functions efficiently. Thus, for example, if DNA polymerase is used as inducing agent, the temperature is generally no greater than about 40 C.
The inducing agent may be any compound or system which will function to accomplish the synthesis of primer extension products, including enzymes. Suitable enzymes for this purpose include, for example, E. coli, DNA polymerase I, Klenow fragment of E. coli DNA polymerase I, T4 DNA polymerase, other available DNA polymerases, reverse transcriptase, and other enzymes, including heat-stable enzymes, which will facilitate combination of the nucleotides in the proper manner to form the primer extension products which are complementary to each nucleic acid strand. Generally, the synthesis will be initiated at the 3′ end of each primer and proceed in the 5′ direction along the template strand, until synthesis terminates, producing molecules of different lengths. There may be inducing agents, however, which initiate synthesis at the 5′ end and proceed in the above direction, using the same process as described above.
The inducing agent also may be a compound or system which will function to accomplish the synthesis of RNA primer extension products, including enzymes. In preferred embodiments, the inducing agent may be a DNA-dependent RNA polymerase such as T7 RNA polymerase, T3 RNA polymerase or SP6 RNA polymerase. These RNA polymerases initiate synthesis from a promoter contained within a primer of the present invention. These polymerases produce a complementary RNA polynucleotide. The high turn over rate of the RNA polymerase amplifies the starting polynucleotide as has been described by Chamberlin et al., The Enzymes, ed., P. Boyer, PP. 87-108, Academic Press, New York (1982). Another advantage of T7 RNA polymerase is that mutations can be introduced into the polynucleotide synthesis by replacing a portion of cDNA with one or more mutagenic oligodeoxynucleotides (polynucleotides) and transcribing the partially-mismatched template directly as has been previously described by Joyce et al., Nucleic Acid Research, 17:711-722 (1989).
If the inducing agent is a DNA-dependent RNA polymerase and therefore incorporates ribonucleotide triphosphates, sufficient amounts of ATP, CTP, GTP, and UTP are admixed to the primer extension reaction admixture and the resulting solution is treated as described above.
The newly synthesized strand and its complementary nucleic acid strand form a double-stranded molecule which can be used in the succeeding steps of the process.
The first and/or second primer extension reaction discussed above can advantageously be used to incorporate into the receptor a preselected epitope useful in immunologically detecting and/or isolating a receptor. This is accomplished by utilizing a first and/or second polynucleotide synthesis primer or expression vector to incorporate a predetermined amino acid residue sequence into the amino acid residue sequence of the receptor.
After producing VH-and/or VL-coding DNA homologs for a plurality of different VH-and/or VL-coding genes within the repertoire, the homologs are typically amplified. While the VH and/or VL-coding DNA homologs can be amplified by classic techniques such as incorporation into an autonomously replicating vector, it is preferred to first amplify the DNA homologs by subjecting them to a polymerase chain reaction (PCR) prior to inserting them into a vector. In fact, in preferred strategies, the first and/or second primer extension reactions used to produce the gene library are the first and second primer extension reactions in a polymerase chain reaction.
PCR is carried out by cycling i.e., simultaneously performing in one admixture, the above described first and second primer extension reactions, each cycle comprising polynucleotide synthesis followed by denaturation of the double stranded polynucleotides formed. Methods and systems for amplifying a DNA homolog are described in U.S. Pat. Nos. 4,683,195 and 4,683,202, both to Mullis et al.
In preferred embodiments only one pair of first and second primers is used per amplification reaction. The amplification reaction products obtained from a plurality of different amplifications, each using a plurality of different primer pairs, are then combined.
However, the present invention also contemplates DNA homolog production via co-amplification (using two pairs of primers), and multiplex amplification (using up to about 8, 9 or 10 primer pairs).
The VH-and VL-coding DNA homologs produced by PCR amplification are typically in double-stranded form and have contiguous or adjacent to each of their termini a nucleotide sequence defining an endonuclease restriction site. Digestion of the VH-and VL-coding DNA homologs having restriction sites at or near their termini with one or more appropriate endonucleases results in the production of homologs having cohesive termini of predetermined specificity.
In preferred embodiments, the PCR process is used not only to amplify the VH-and/or VL-coding DNA homologs of the library, but also to induce mutations within the library and thereby provide a library having a greater heterogeneity. First, it should be noted that the PCR processes itself is inherently mutagenic due to a variety of factors well known in the art. Second, in addition to the mutation inducing variations described in the above referenced U.S. Pat. No. 4,683,195, other mutation inducing PCR variations can be employed. For example, the PCR reaction admixture, i.e., the combined first and second primer extension reaction admixtures, can be formed with different amounts of one or more of the nucleotides to be incorporated into the extension product. Under such conditions, the PCR reaction proceeds to produce nucleotide substitutions within the extension product as a result of the scarcity of a particular base. Similarly, approximately equal molar amounts of the nucleotides can be incorporated into the initial PCR reaction admixture in an amount to efficiently perform X number of cycles, and then cycling the admixture through a number of cycles in excess of X, such as, for instance, 2×. Alternatively, mutations can be induced during the PCR reaction by incorporating into the reaction admixture nucleotide derivatives such as inosine, not normally found in the nucleic acids of the repertoire being amplified. During subsequent in vivo amplification, the nucleotide derivative will be replaced with a substitute nucleotide thereby inducing a point mutation.
4. Expressing the VH and/or VL DNA Homologs.
The VH-and/or VL-coding DNA homologs contained within the library produced by the above-described method can be operatively linked to a vector for amplification and/or expression.
As used herein, the term “vector” refers to a nucleic acid molecule capable of transporting between different genetic environments another nucleic acid to which it has been operatively linked. One type of preferred vector is an episome, i.e., a nucleic acid molecule capable of extra-chromosomal replication. Preferred vectors are those capable of autonomous replication and/or expression of nucleic acids to which they are linked. Vectors capable of directing the expression of genes to which they are operatively linked are referred to herein as “expression vectors”.
The choice of vector to which a VH-and/or VL-coding DNA homolog is operatively linked depends directly, as is well known in the art, on the functional properties desired, e.g., replication or protein expression, and the host cell to be transformed, these being limitations inherent in the art of constructing recombinant DNA molecules.
In preferred embodiments, the vector utilized includes a procaryotic replicon i.e., a DNA sequence having the ability to direct autonomous replication and maintenance of the recombinant DNA molecule extra chromosomally in a procaryotic host cell, such as a bacterial host cell, transformed therewith. Such replicons are well known in the art. In addition, those embodiments that include a procaryotic replicon also include a gene whose expression confers a selective advantage, such as drug resistance, to a bacterial host transformed therewith. Typical bacterial drug resistance genes are those that confer resistance to ampicillin or tetracycline.
Those vectors that include a procaryotic replicon can also include a procaryotic promoter capable of directing the expression (transcription and translation) of the VH-and/or VL-coding homologs in a bacterial host cell, such as E. coli transformed therewith. A promoter is an expression control element formed by a DNA sequence that permits binding of RNA polymerase and transcription to occur. Promoter sequences compatible with bacterial hosts are typically provided in plasmid vectors containing convenience restriction sites for insertion of a DNA segment of the present invention. Typical of such vector plasmids are pUC8, pUC9, pBR322, and pBR329 available from BioRad Laboratories, (Richmond, Calif.) and pPL and pKK223 available from Pharmacia, (Piscataway, N.J.).
Expression vectors compatible with eucaryotic cells, preferably those compatible with vertebrate cells, can also be used. Eucaryotic cell expression vectors are well known in the art and are available from several commercial sources. Typically, such vectors are provided containing convenient restriction sites for insertion of the desired DNA homologue. Typical of such vectors are pSVL and pKSV-10 (Pharmacia), pBPV-1/PML2d (International Biotechnologies, Inc.), and pTDT1 (ATCC, No. 31255).
In preferred embodiments, the eucaryotic cell expression vectors used include a selection marker that is effective in an eucaryotic cell, preferably a drug resistant selection marker. A preferred drug resistance marker is the gene whose expression results in neomycin resistance, i.e., the neomycin phosphotransferase (neo) gene. Southern et al., J. Mol. Appl. Genet., 1:327-341 (1982).
The use of retroviral expression vectors to express the genes of the VH and/or VL-coding DNA homologs is also contemplated. As used herein, the term “retroviral expression vector” refers to a DNA molecule that includes a promoter sequences derived from the long terminal repeat (LTR) region of a retrovirus genome.
In preferred embodiments, the expression vector is typically a retroviral expression vector that is preferably replication-incompetent in eucaryotic cells. The construction and use of retroviral vectors has been described by Sorge et al., Mol. Cel. Biol., 4:1730-1737 (1984).
A variety of methods have been developed to operatively link DNA to vectors via complementary cohesive termini. For instance, complementary cohesive termini can be engineered into the VH-and/or VL-coding DNA homologs during the primer extension reaction by use of an appropriately designed polynucleotide synthesis primer, as previously discussed. The vector, and DNA homolog if necessary, is cleaved with a restriction endonuclease to produce termini complementary to those of the DNA homolog. The complementary cohesive termini of the vector and the DNA homolog are then operatively linked (ligated) to produce a unitary double stranded DNA molecule.
In preferred embodiments, the VH-coding and VL-coding DNA homologs of diverse libraries are randomly combined in vitro for polycistronic expression from individual vectors. That is, a diverse population of double stranded DNA expression vectors is produced wherein each vector expresses, under the control of a single promoter, one VH-coding DNA homolog and one VL-coding DNA homolog, the diversity of the population being the result of different VH-and VL-coding DNA homolog combinations.
Random combination in vitro can be accomplished using two expression vectors distinguished from one another by the location on each of a restriction site common to both. Preferably the vectors are linear double stranded DNA, such as a Lambda Zap derived vector as described herein. In the first vector, the site is located between a promoter and a polylinker, i.e., 5 terminal (upstream relative to the direction of expression) to the polylinker but 3 terminal (downstream relative to the direction of expression). In the second vector, the polylinker is located between a promoter and the restriction site, i.e., the restriction site is located 3 terminal to the polylinker, and the polylinker is located 3 terminal to the promoter.
In preferred embodiments, each of the vectors defines a nucleotide sequence coding for a ribosome binding and a leader, the sequence being located between the promoter and the polylinker, but downstream (3 terminal) from the shared restriction site if that site is between the promoter and polylinker. Also preferred are vectors containing a stop codon downstream from the polylinker, but upstream from any shared restriction site if that site is downstream from the polylinker. The first and/or second vector can also define a nucleotide sequence coding for a peptide tag. The tag sequence is typically located downstream from the polylinker but upstream from any stop codon that may be present.
In preferred embodiments, the vectors contain selectable markers such that the presence of a portion of that vector, i.e. a particular lambda arm, can be selected for or selected against. Typical selectable markers are well known to those skilled in the art. Examples of such markers are antibiotic resistance genes, genetically selectable markers, mutation suppressors such as amber suppressors and the like. The selectable markers are typically located upstream of the promoter and/or downstream of the second restriction site. In preferred embodiments, one selectable marker is located upstream of the promoter on the first vector containing the VH-coding DNA homologs. A second selectable marker is located downstream of the second restriction site on the vector containing the VL-coding DNA homologs. This second selectable marker may be the same or different from the first as long as when the VH-coding vectors and the VL-coding vectors are randomly combined via the first restriction site the resulting vectors containing both VH and VL and both selectable markers can be selected.
Typically the polylinker is a nucleotide sequence that defines one or more, preferably at least two, restriction sites, each unique to the vector and preferably not shared by the other vector, i.e., if it is on the first vector, it is not on the second vector. The polylinker restriction sites are oriented “to permit ligation of VH-or VL-coding DNA homologs into the vector in same reading frame as any leader, tag or stop codon sequence present.
Random combination is accomplished by ligating VH-coding DNA homologs into the first vector, typically at a restriction site or sites within the polylinker. Similarly, VL-coding DNA homologs are ligated into the second vector, thereby creating two diverse populations of expression vectors. It does not matter which type of DNA homolog, i.e., VH or VL, is ligated to which vector, but it is preferred, for example, that all VH-coding DNA homologs are ligated to either the first or second vector, and all of the VL-coding DNA homologs are ligated to the other of the first or second vector. The members of both populations are then cleaved with an endonuclease at the shared restriction site, typically by digesting both populations with the same enzyme. The resulting product is two diverse populations of restriction fragments where the members of one have cohesive termini complementary to the cohesive termini of the members of the other. The restriction fragments of the two populations are randomly ligated to one another, i.e., a random, interpopulation ligation is performed, to produce a diverse population of vectors each having a VH-coding and VL-coding DNA homolog located in the same reading frame and under the control of second vector's promoter. Of course, subsequent recombinations can be effected through cleavage at the shared restriction site, which is typically reformed upon ligation of members from the two populations, followed by subsequent religations.
The resulting construct is then introduced into an appropriate host to provide amplification and/or expression of the VH-and/or VL-coding DNA homologs, either separately or in combination. When coexpressed within the same organism, either on the same or the different vectors, a functionally active Fv is produced. When the VH and VL polypeptides are expressed in different organisms, the respective polypeptides are isolated and then combined in an appropriate medium to form a Fv. Cellular hosts into which a VH-and/or VL-coding DNA homolog-containing construct has been introduced are referred to herein as having been “transformed” or as “transformants”.
The host cell can be either procaryotic or eucaryotic. Bacterial cells are preferred procaryotic host cells and typically are a strain of E. coli such as, for example, the E. coli strain DH5 available from Bethesda Research Laboratories, Inc., Bethesda, Md. Preferred eucaryotic host cells include yeast and mammalian cells, preferably vertebrate cells such as those from a mouse, rat, monkey or human cell line.
Transformation of appropriate cell hosts with a recombinant DNA molecule of the present invention is accomplished by methods that typically depend on the type of vector used. With regard to transformation of procaryotic host cells, see, for example, Cohen et al., Proceedings National Academy of Science, USA, Vol. 69, P. 2110 (1972); and Maniatis et al., Molecular Cloning, a Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1982). With regard to the transformation of vertebrate cells with retroviral vectors containing rDNAs, see for example, Sorge et al., Mol. Cell. Biol., 4:1730-1737 (1984); Graham et al., Virol., 52:456 (1973); and Wigler et al., Proceedings National Academy of Sciences, USA, Vol. 76, P. 1373-1376 (1979).
5. Screening For Expression of VH and/or VL Polypeptides
Successfully transformed cells, i.e., cells containing a VH-and/or VL-coding DNA homolog operatively linked to a vector, can be identified by any suitable well known technique for detecting the binding of a receptor to a ligand or the presence of a polynucleotide coding for the receptor, preferably its active site. Preferred screening assays are those where the binding of ligand by the receptor produces a detectable signal, either directly or indirectly. Such signals include, for example, the production of a complex, formation of a catalytic reaction product, the release or uptake of energy, and the like. For example, cells from a population subjected to transformation with a subject rDNA can be cloned to produce monoclonal colonies. Cells form those colonies can be harvested, lysed and their DNA content examined for the presence of the rDNA using a method such as that described by Southern, J. Mol. Biol., 98:503 (1975) or Berent et al., Biotech. 3:208 (1985).
In addition to directly assaying for the presence of a VH-and/or VL-coding DNA homolog, successful transformation can be confirmed by well known immunological methods, especially when the VH and/or VL polypeptides produced contain a preselected epitope. For example, samples of cells suspected of being transformed are assayed for the presence of the preselected epitope using an antibody against the epitope.
6. VH-And/Or VL-Coding Gene Libraries
The present invention contemplates a gene library, preferably produced by a primer extension reaction or combination of primer extension reactions as described herein, containing at least about 103, preferably at least about 104 and more preferably at least about 105 different VH-and/or VL-coding DNA homologs. The homologs are preferably in an isolated form, that is, substantially free of materials such as, for example, primer extension reaction agents and/or substrates, genomic DNA segments, and the like.
In preferred embodiments, a substantial portion of the homologs present in the library are operatively linked to a vector, preferably operatively linked for expression to an expression vector.
Preferably, the homologs are present in a medium suitable for in vitro manipulation, such as water, water containing buffering salts, and the like. The medium should be compatible with maintaining the biological activity of the homologs. In addition, the homologs should be present at a concentration sufficient to allow transformation of a host cell compatible therewith at reasonable frequencies.
It is further preferred that the homologs be present in compatible host cells transformed therewith.
C. Expression Vectors
The present invention also contemplates various expression vectors useful in performing, inter alia, the methods of the present invention. Each of the expression vectors is a novel derivative of Lambda Zap.
1. Lambda Zap II
Lambda Zap II is prepared by replacing the Lambda S gene of the vector Lambda Zap with the Lambda S gene from the Lambda gt10 vector, as described in Example 6.
2. Lambda Zap II VH 
Lambda Zap II VH is prepared by inserting the synthetic DNA sequences illustrated in FIG. 6A (SEQ ID NOs:38-41) into the above-described Lambda Zap II vector. The inserted nucleotide sequence advantageously provides a ribosome binding site (Shine-Dalgamo sequence) to permit proper imitation of mRNA translation into protein, and a leader sequence to efficiently direct the translated protein to the periplasm. The preparation of Lambda Zap II VH is described in more detail in Example 9, and its features illustrated in FIGS. 6A and 7.
3. Lambda Zap II VL 
Lambda Zap II VL is prepared as described in Example 12 by inserting into Lambda Zap II the synthetic DNA sequence illustrated in FIG. 6B (SEQ ID NOs: 42-45). Important features of Lambda Zap II VL are illustrated in FIG. 8.
4. Lambda Zap II VL II
Lambda Zap II VL II is prepared as described in Example 11 by inserting into Lambda Zap II the synthetic DNA sequence illustrated in FIG. 10 (SEQ ID NOs:47-48).
The above-described vectors are compatible with E. coli hosts, i.e., they can express for secretion into the periplasm proteins coded for by genes to which they have been operatively linked for expression.
EXAMPLES
The following examples are intended to illustrate, but not limit, the scope of the invention.
1. Polynucleotide Selection
The nucleotide sequences encoding the immunoglobulin protein CDR's are highly variable. However, there are several regions of conserved sequences that flank the VH domains. For instance, contain substantially conserved nucleotide sequences, i.e., sequences that will hybridize to the same primer sequence. Therefore, polynucleotide synthesis (amplification) primers that hybridize to the conserved sequences and incorporate restriction sites into the DNA homolog produced that are suitable for operatively linking the synthesized DNA fragments to a vector were constructed. More specifically, the DNA homologs were inserted into Lambda ZAP II vector (Stratagene Cloning System, San Diego, Calif.) at the Xho I and EcoR I sites. For amplification of the VH domains, the 3′ primer (SEQ ID NO:60 in Table 1), was designed to be complementary to the mRNA in the JH region. In all cases, the 5′ primers (SEQ ID NOs:49-56, Table 1) were chosen to be complementary to the first strand cDNA in the conserved N-terminus region (antisense strand). Initially amplification was performed with a mixture of 32 primers that were degenerate at five positions (SEQ ID NO:105, Table 1). Hybridoma mRNA could be amplified with mixed primers, but initial attempts to amplify mRNA from spleen yielded variable results. Therefore, several alternatives to amplification using the mixed 5′ primers were compared.
The first alternative was to construct multiple unique primers, eight of which are shown in Table 1, corresponding to individual members of the mixed primer pool. The individual primers designated SEQ ID NOs:49-56 of Table 1 were constructed by incorporating either of the two possible nucleotides at three of the five degenerate positions.
The second alternative was to construct a primer containing inosine (SEQ ID NOs:57-58, Table 1) at four of the variable positions based on the published work of Takahashi, et al., Proc. Natl. Acad. Sci. (U.S.A.), 82:1931-1935, (1985) and Ohtsuka et al., J. Biol. Chem., 260: 2605-2608, (1985). This primer has the advantage that it is not degenerate and, at the same time minimizes the negative effects of mismatches at the unconserved positions as discussed by Martin et al., Nuc. Acids Res., 13:8927 (1985). However, it was not known if the presence of inosine nucleotides would result in incorporation of unwanted sequences in the cloned VH regions. Therefore, inosine was not included at the one position that remains in the amplified fragments after the cleavage of the restriction sites. As a result, inosine was not in the cloned insert.
Additional, VH amplification primers including the unique 3′ primer were designed to be complementary to a portion of the first constant region domain of the gamma 1 heavy chain mRNA (SEQ ID NOs:64-65, Table 1). These primers will produce DNA homologs containing polynucleotides coding for amino acids from the VH and the first constant region domains of the heavy chain. These DNA homologs can therefore be used to produce Fab fragments rather than an Fv.
As a control for amplification from spleen or hybridoma mRNA, a set of primers hybridizing to a highly conserved region within the constant region IgG, heavy chain gene were constructed. The 5′ primer (SEQ ID NO:59, Table 1) is complementary to the cDNA in the CH2 region whereas the 3′ primer (SEQ ID NO:62, Table 1) is complementary to the mRNA in the CH3 region. It is believed that no mismatches were present between these primers and their templates.
The nucleotide sequences encoding the VL CDRs are highly variable. However, there are several regions of conserved sequences that flank the VL CDR domains including the JL VL framework regions and VL leader/promotor. Therefore, amplification primers that hybridize to the conserved sequences and incorporate restriction sites that allowing cloning the amplified fragments into the pBluescript SK-vector cut with Nco I and Spe I were constructed. For amplification of the VL CDR domains, the 3′ primer (SEQ ID NO:63 in Table 1), was designed to be complementary to the mRNA in the JL regions. The 5′ primer (SEQ ID NO:64, Table 1) was chosen to be complementary to the first strand cDNA in the conserved N-terminus region (antisense strand).
A second set of amplification primers for amplification of the VL CDR domains the 5′ primers (SEQ ID NOs:67-74 in Table 2) were designed to be complementary to the first strand cDNA in the conserved N-terminus region. These primers also introduced a Sac I restriction endonuclease site to allow the VL DNA homolog to be cloned into the VLII-expression vector. The 3′ VL amplification primer (SEQ ID NO:75 in Table 2) was designed to be complementary to the mRNA in the JL regions and to introduce the Xba I restriction endonuclease site required to insert the VL DNA homolog into the VL II-expression vector.
Additional 3′ VL amplification primers were designed to hybridize to the constant region of either kappa or lambda mRNA (SEQ ID NO:76 and SEQ ID NO:77 in Table 2). These primers allow a DNA homolog to be produced containing polynucleotide sequences coding for constant region amino acids of either kappa or lambda chain. These primers make it possible to produce an Fab fragment rather than an Fv.
The primers used for amplification of kappa light chain sequences for construction of Fabs are shown at least in Table 2. Amplification with these primers was performed in 5 separate reactions, each containing one of the 5′ primers (SEQ ID NOs:69-72, and SEQ ID NO:78) and one of the 3′ primers (SEQ ID NO:79). The remaining 3 primer (SEQ ID NO:75) has been used to construct Fv fragments. The 5′ primers contain a Sac I restriction site and the 3′ primers contain a Xba I restriction site.
The primers used for amplification of heavy chain Fd fragments for construction of Fabs are shown at least in Table 1. Amplification was performed in eight separate reactions, each containing one of the 5′ primers (SEQ ID NOs:49-56) and one of the 3′ primers (SEQ ID NO:64). The remaining 5′ primers that have been used for amplification in a single reaction are either a degenerate primer (SEQ ID NO:105) or a primer that incorporates inosine at four degenerate positions (SEQ ID NOs:57-58, Table 1, and SEQ ID NOs:83-84, Table 2). The remaining 3′ primer (SEQ ID NO:80, Table 2) has been used to construct Fv fragments. Many of the 5′ primers incorporate a Xho I site, and the 3′ primers include a Spe I restriction site.
VL amplification primers designed to amplify human light chain variable regions of both the lambda and kappa isotypes are also shown in Table 2.
All primers and synthetic polynucleotides used herein and shown on Tables 1-4 were either purchased from Research Genetics in Huntsville, Ala. or synthesized on an Applied Biosystems DNA synthesizer, model 381A, using the manufacturer's instruction.










TABLE 1







SEQ ID
5′ AGGT(C/G)(C/A)A(G/A)CT(G/T)CTCGAGTC(T/A)GG 3′
degenerate 5′ primer for the amplification of



NO:105

variable heavy chain region (VH)


 


SEQ ID
5′ AGGTCCAGCTGCTCGAGTCTGG 3′
Unique 5′ primer for the amplification of VH


NO:49


 


SEQ ID
5′ AGGTCCAGCTGCTCGAGTCAGG 3′
′′


NO:50


 


SEQ ID
5′ AGGTCCAGCTTCTCGAGTCTGG 3′
′′


NO:51


 


SEQ ID
5′ AGGTCCAGCTTCTCGAGTCAGG 3′
′′


NO:52


 


SEQ ID
5′ AGGTCCAACTGCTCGAGTCTGG 3′
′′


NO:53


 


SEQ ID
5′ AGGTCCAACTGCTCGAGTCAGG 3′
′′


NO:54


 


SEQ ID
5′ AGGTCCAACTTCTCGAGTCTGG 3′
′′


NO:55


 


SEQ ID
5′ AGGTCCAACTTCTCGAGTCAGG 3′
′′


NO:56



 


SEQ ID
5′ AGGTIIAICTICTCGAGTC(T/A) 3′
5′ degenerate primer containing inosine at 4


NOs:57-

degenerate positions


58



 


SEQ ID
5′ GCCCAAGGATGTGCTCACC 3′
5′ primer for amplification in the CH2 region


NO:59

of mouse IgG1


 


SEQ ID
5′ CTATTAGAATTCAACGGTAACAGTGGTGCCTTGGCCCCA 3′
3′ primer for amplification of VH


NO:60


 


SEQ ID
5′ CTATTAACTAGTAACGGTAACAGTGGTGCCTTGGCCCCA 3′
3′ primer for amplification of VH using 3′


NO:61

Spe I site


 


SEQ ID
5′ CTCAGTATGGTGGTTGTGC 3′
3′ primer for amplification in the CH3 region


NO:62

of mouse IgGI


 


SEQ ID
5′ GCTACTAGTTTTGATTTCCACCTTGG 3′
3′ primer for amplification of VL


NO:63


 


SEQ ID
5′ CAGCCATGGCCGACATCCAGATG 3′
5′ primer for amplification of VL


NO:64


 


SEQ ID
5′ AATTTTACTAGTCACCTTGGTGCTGCTGGC 3′
Unique 3′ primer for amplification of VH


NO:65

Including part of the mouse gamma 1 first




constant


 


SEQ ID
5′ TATGCAACTAGTACAACCACAATCCCTGGGCACAATTTT 3′
Unique 3′ primer for amplification of VH


NO:66

including part of mouse gamma 1 first




constant region and hinge region.



















TABLE 2







SEQ ID
5′ CCAGTTCCGAGCTCGTTGTGACTCAGGAATCT 3′
Unique 5′ primer for the amplification of VL



NO:67


 


SEQ ID
5′ CCAGTTCCGAGCTCGTGTTGACGCAGCCGCCC 3′
Unique 5′ primer for the amplification of VL


NO:68


 


SEQ ID
5′ CCAGTTCCGAGCTCGTGCTCACCCAGTCTCCA 3′
′′


NO:69


 


SEQ ID
5′ CCAGTTCCGAGCTCCAGATGACCCAGTCTCCA 3′
′′


NO:70


 


SEQ ID
5′ CCAGATGTGAGCTCGTGATGACCCAGACTCCA 3′
′′


NO:71


 


SEQ ID
5′ CCAGATGTGAGCTCGTCATGACCCAGTCTCCA 3′
′′


NO:72


 


SEQ ID
5′ CCAGATGTGAGCTCTTGATGACCCAAACTCAA 3′
′′


NO:73


 


SEQ ID
5′ CCAGATGTGAGCTCGTGATAACCCAGGATGAA 3′
′′


NO:74


 


SEQ ID
5′ GCAGCATTCTAGAGTTTCAGCTCCAGCTTGCC 3′
Unique 3′ primer for VL amplification


NO:75


 


SEQ ID
5′ CCGCCGTCTAGAACACTCATTCCTGTTGAAGCT 3′
Unique 3′ primer for VL amplification including the


NO:76

kappa constant region


 


SEQ ID
5′ CCGCCGTCTAGAACATTCTGCAGGAGACAGACT 3′
Unique 3′ primer for VL amplification including the


NO:77

lambda constant region


 


SEQ ID
5′ CCAGTTCCGAGCTCGTGATGACACAGTCTCCA 3′
Unique 5′ primer for VL amplification


NO:78


 


SEQ ID
5′ GCGCCGTCTAGAATTAACACTCATTCCTGTTGAA 3′
Unique 3′ primer for VL amplification


NO:79


 


SEQ ID
5′ CTATTAACTAGTAACGGTAACAGTGGTGCCTTGCCCCA 3′
′′


NO:80


 


SEQ ID
5′ AGGCTTACTAGTACAATCCCTGGGCACAAT 3′
′′


NO:81


 


SEQ ID
5′ GCCGCTCTAGAACACTCATTCCTGTTGAA 3′
′′


NO:82


 


SEQ ID
5′ AGGTIIAICTICTCGAGTCTGC 3′
Degenerate of 5′ primer containing inosine at 4


NO:83

degenerate positions


 


SEQ ID
5′ AGGTIIAICTICTCGAGTCAGC 3′
′′


NO:84









2. Production of a VH Coding Repertoire Enriched in FITC Binding Proteins
Fluorescein isothiocyanate (FITC) was selected as a ligand for receptor binding. It was further decided to enrich by immunization the immunological gene repertoire, i.e., VH-and VL-coding gene repertoires, for genes coding for anti-FITC receptors. This was accomplished by linking FITC to keyhole limpet hemocyanin (KLH) using the techniques described in Antibodies A Laboratory Manual, Harlow and Lowe, eds., Cold Spring Harbor, N.Y., (1988). Briefly, 10.0 milligrams (mg) of keyhole limpet hemocyanin and 0.5 mg of FITC were added to 1 ml of buffer containing 0.1 M sodium carbonate at pH 9.6 and stirred for 18 to 24 hours at 4 degrees C. (4 C). The unbound FITC was removed by gel filtration through Sephadex G-25.
The KLH-FITC conjugate was prepared for injection into mice by adding 100 μg of the conjugate to 250 μl of phosphate buffered saline (PBS). An equal volume of complete Freund's adjuvant was added and emulsified the entire solution for 5 minutes. A 129 G1×+ mouse was injected with 300 μl of the emulsion. Injections were given subcutaneously at several sites using a 21 gauge needle. A second immunization with KLH-FITC was given two weeks later. This injection was prepared as follows: fifty μg of KLH-FITC were diluted in 250 μL of PBS and an equal volume of alum was admixed to the KLH-FITC solution. The mouse was injected intraperitoneally with 500 μl of the solution using a 23 gauge needle. One month later the mice were given a final injection of 50 μg of the KLH-FITC conjugate diluted to 200 μl in PBS. This injection was given intravenously in the lateral tail vein using a 30 gauge needle. Five days after This final injection the mice were sacrificed and total cellular RNA was isolated from their spleens.
Hybridoma PCP 8D11 producing an antibody immunospecific for phosphonate ester was cultured in DMEM media (Gibco Laboratories, Grand Island, N.Y.) containing 10 percent fetal calf serum supplemented with penicillin and streptomycin. About 5×108 hybridoma cells were harvested and washed twice in phosphate buffered saline. Total cellular RNA was prepared from these isolated hybridoma cells.
3. Preparation of a VH-Coding Gene Repertoire
Total cellular RNA was prepared from the spleen of a single mouse immunized with KLH-FITC as described in Example 2 using the RNA preparation methods described by Chomczynski et al., Anal Biochem., 162:156-159 (1987) using the manufacturer1s instructions and the RNA isolation kit produced by Stratagene Cloning Systems, La Jolla, Calif. Briefly, immediately after removing the spleen from the immunized mouse, the tissue was homogenized in 10 ml of a denaturing solution containing 4.0 M guanine isothiocyanate, 0.25 M sodium citrate at pH 7.0, and 0.1 M 2-mercaptoethanol using a glass homogenizer. One ml of sodium acetate at a concentration of 2 M at pH 4.0 was admixed with the homogenized spleen. One ml of phenol that had been previously saturated with H20 was also admixed to the denaturing solution containing the homogenized spleen. Two ml of a chloroform:isoamyl alcohol (24:1 v/v) mixture was added to this homogenate. The homogenate was mixed vigorously for ten seconds and maintained on ice for 15 minutes. The homogenate was then transferred to a thick-walled 50 ml polypropylene centrifuged tube (Fisher Scientific Company, Pittsburg, Pa.). The solution was centrifuged at 10,000×g for 20 minutes at 4 C. The upper RNA-containing aqueous layer was transferred to a fresh 50 ml polypropylene centrifuge tube and mixed with an equal volume of isopropyl alcohol. This solution was maintained at −20 C for at least one hour to precipitate the RNA. The solution containing the precipitated RNA was centrifuged at 10,000×g for twenty minutes at 4 C. The pelleted total cellular RNA was collected and dissolved in 3 ml of the denaturing solution described above. Three ml of isopropyl alcohol was added to the resuspended total cellular RNA and vigorously mixed. This solution was maintained at −20 C for at least 1 hour to precipitate the RNA. The solution containing the precipitated RNA was centrifuged at 10,000×g for ten minutes at 4 C. The pelleted RNA washed once with a solution containing 75% ethanol. The pelleted RNA was dried under vacuum for 15 minutes and then resuspended in dimethylpyrocarbonate (DEPC) treated (DEPC—H2O)H2O.
Messenger RNA (mRNA) enriched for sequences containing long poly A tracts was prepared from the total cellular RNA using methods described in Molecular Cloning A Laboratory Manual, Maniatias et al., eds., Cold Spring Harbor Laboratory, New York, (1982). Briefly, one half of the total RNA isolated from a single immunized mouse spleen prepared as described above was resuspended in one ml of DEPC—H20 and maintained at 65 C for five minutes. One ml of 2× high salt loading buffer consisting of 100 mM Tris-HCl, 1 M sodium chloride, 2.0 mM disodium ethylene diamine tetraacetic acid (EDTA) at pH 7.5, and 0.2% sodium dodecyl sulfate (SDS) was added to the resuspended RNA and the mixture allowed to cool to room temperature. The mixture was then applied to an oligo-dT (Collaborative Research Type 2 or Type 3) column that was previously prepared by washing the oligo-dT with a solution containing 0.1 M sodium hydroxide and 5 mM EDTA and then equilibrating the column with DEPC—H20. The eluate was collected in a sterile polypropylene tube and reapplied to the same column after heating the eluate for 5 minutes at 65 C. The oligo dT column was then washed with 2 ml of high salt loading buffer consisting of 50 mM Tris-HCl at pH 7.5, 500 mM sodium chloride, 1 mM EDTA at pH 7.5 and 0.1% SDS. The oligo dT column was then washed with 2 ml of 1× medium salt buffer consisting of 50 mM Tris-HCl at pH 7.5, 100 mM sodium chloride 1 mM EDTA and 0.1% SDS. The messenger RNA was eluted from the oligo dT column with 1 ml of buffer consisting of 10 mM Tris-HCl at pH 7.5, 1 mM EDTA at pH 7.5 and 0.05% SDS. The messenger RNA was purified by extracting this solution with phenol/chloroform followed by a single extraction with 100% chloroform. The messenger RNA was concentrated by ethanol precipitation and resuspended in DEPC H2O.
The messenger RNA isolated by the above process contains a plurality of different VH coding polynucleotides, i.e., greater than about 104 different VH-coding genes.
4. Preparation of a Single VH Coding Polynucleotide
Polynucleotides coding for a single VH were isolated according to Example 3 except total cellular RNA was extracted from monoclonal hybridoma cells prepared in Example 2. The polynucleotides isolated in this manner code for a single VH.
5. DNA Homolog Preparation
In preparation for PCR amplification, mRNA prepared according to the above examples was used as a template for cDNA synthesis by a primer extension reaction. In a typical 50 μl transcription reaction, 5-10 μg of spleen or hybridoma mRNA in water was first hybridized (annealed) with 500 ng (50.0 μmol) of the 3′ VH primer (SEQ ID NO:60, Table 1), at 65 C for five minutes. Subsequently, the mixture was adjusted to 1.5 mM dATP, dCTP, dGTP and dTTP, 40 mM Tris-HCl at pH 8.0, 8 mM MgCl2, 50 mM NaCl, and 2 mM spermidine. Moloney-Murine Leukemia virus Reverse transcriptase (Stratagene Cloning Systems), 26 units, was added and the solution was maintained for 1 hour at 37 C.
PCR amplification was performed in a 100 μl reaction containing the products of the reverse transcription reaction (approximately 5 μg of the cDNA/RNA hybrid), 300 ng of 3′ VH primer (SEQ ID NO:60 of Table 1), 300 ng each of the 5′ VH primers (SEQ ID NOs:49-58 of Table 1) 200 mM of a mixture of dNTP's, 50 mM KCl, 10 mM Tris-HCl pH 8.3, 15 mM MgCl2, 0.1% gelatin and 2 units of Taq DNA polymerase. The reaction mixture was overlaid with mineral oil and subjected to 40 cycles of amplification. Each amplification cycle involved denaturation at 92 C for 1 minute, annealing at 52 C for 2 minutes and polynucleotide synthesis by Primer extension (elongation) at 72 C for 1.5 minutes. The amplified VH-coding DNA homolog containing samples were extracted twice with phenol/chloroform, once with chloroform, ethanol precipitated and were stored at −70 C in 10 mM Tris-HCl, (pH, 7.5) and 1 mM EDTA.
Using unique 5′ primers (SEQ ID NOs:49-56, Table 1), efficient VH-coding DNA homolog synthesis and amplification from the spleen mRNA was achieved as shown in FIG. 3, lanes R17-R24. The amplified cDNA (VH-coding DNA homolog) is seen as a major band of the expected size (360 bp). The intensities of the amplified VH-coding polynucleotide fragment in each reaction appear to be similar, indicating that all of these primers are about equally efficient in initiating amplification. The yield and quality of the amplification with these primers was reproducible.
The primer containing inosine also synthesized amplified VH-coding DNA homologs from spleen mRNA reproducibly, leading to the production of the expected sized fragment, of an intensity similar to that of the other amplified cDNAs (FIG. 4, lane R16). This result indicated that the presence of inosine also permits efficient DNA homolog synthesis and amplification. Clearly indicating how useful such primers are in generating a plurality of VH-coding DNa homologs. Amplification products obtained from the constant region primers (SEQ ID NO:59 and SEQ ID NO:62, Table 1) were more intense indicating that amplification was more efficient, possibly because of a higher degree of homology between the template and primers (FIG. 4, Lane R9). Based on these results, a VH-coding gene library was constructed from the products of eight amplifications, each performed with a different 5′ primer. Equal portions of the products from each primer extension reaction were mixed and the mixed product was then used to generate a library of VH-coding DNA homolog-containing vectors.
DNA homologs of the VL were prepared from the purified mRNA prepared as described above. In preparation for PCR amplification, mRNA prepared according to the above examples was used as a template for cDNA synthesis. In a typical 50 μl transcription reaction, 5-10 μg of spleen or hybridoma mRNA in water was first annealed with 300 ng (50.0 μmol) of the 3′ VL primer (SEQ ID NO:63, Table 1), at 65 C for five minutes. Subsequently, the mixture was adjusted to 1.5 mM dATP, dCTP, dGTP, and dTTP, 40 mM Tris-HCl at pH 8.0, 8 mM MgCl2, 50 mM NaCl, and 2 mM spermidine. Moloney-Murine Leukemia virus reverse transcriptase (Stratagene Cloning Systems), 26 units, was added and the solution was maintained for 1 hour at 37 C. The PCR amplification was performed in a 100 μl reaction containing approximately 5 μg of the cDNA/RNA hybrid produced as described above, 300 ng of the 3′ VL primer (SEQ ID NO:63 of Table 1), 300 ng of the 5′ VL primer (SEQ ID NO:64 of Table 1), 200 mM of a mixture of dNTP's, 50 mM KCl, 10 mM Tris-HCl pH 8.3, 15 mM MgCl2, 0.1% gelatin and 2 units of Taq DNA polymerase. The reaction mixture was overlaid with mineral oil and subjected to 40 cycles of amplification. Each amplification cycle involved denaturation at 92 C for 1 minute, annealing at 52 C for 2 minutes and elongation at 72 C for 1.5 minutes. The amplified samples were extracted twice with phenol/chloroform, once with chloroform, ethanol precipitated and were stored at −70 C in 10 mM Tris-HCl at 7.5 and 1 mM EDTA.
6. Inserting DNA Homoloas Into Vectors
In preparation for cloning a library enriched in VH sequences, PCR amplified products (2.5 mg/30 μl of 150 mM NaCl, 8 mM Tris-HCl (pH 7.5), 6 mM MgSO4, 1 mM DTT, 200 mg/ml bovine serum albumin (BSA) at 37 C were digested with restriction enzymes Xho I (125 units) and EcoR I (10 U) and purified on a 1% agarose gel. In cloning experiments which required a mixture of the products of the amplification reactions, equal volumes (50 μl, 1-10 μg concentration) of each reaction mixture were combined after amplification but before restriction digestion. After gel electrophoresis of the digested PCR amplified spleen mRNA, the region of the gel containing DNA fragments of approximately 350 bps was excised, electroeluted into a dialysis membrane, ethanol precipitated and resuspended in 10 mM Tris-HCl pH 7.5 and 1 mM EDTA to a final concentration of 10 ng/μl. Equimolar amounts of the insert were then ligated overnight at 5 C to 1 μg of Lambda ZAPTM II vector (Stratagene Cloning Systems, La Jolla, Calif.) previously cut by EcoR I and Xho I. A portion of the ligation mixture (1 μg) was packaged for 2 hours at room temperature using Gigapack Gold packaging extract (Stratagene Cloning Systems, La Jolla, Calif.), and the packaged material was plated on XL1-blue host cells. The library was determined to consist of 2×107 VH homologs with less than 30% non-recombinant background.
The vector used above, Lambda Zap II is a derivative of the original Lambda Zap (ATCC # 40,298) that maintains all of the characteristics of the original Lambda Zap including 6 unique cloning sites, fusion protein expression, and the ability to rapidly excise the insert in the form of a phagemid (Bluescript SK-), but lacks the SAM 100 mutation, allowing growth on many Non-Sup F strains, including XL1-Blue. The Lambda Zap II was constructed as described in Short et al., Nucleic Acids Res., 16:7583-7600, 1988, by replacing the Lambda S gene contained in a 4254 base pair (bp) DNA fragment produced by digesting Lambda Zap with the restriction enzyme NcoI. This 4254 bp DNA fragment was replaced with the 4254 bp DNA fragment containing the Lambda S gene isolated from Lambda gt10 (ATCC # 40,179) after digesting the vector with the restriction enzyme NcoI. The 4254 bp DNA fragment isolated from lambda gt10 was ligated into the original Lambda Zap vector using T4 DNA ligase and standard protocols for such procedures described in Current Protocols in Molecular Biology, Ausubel et al., eds., John Wiley and Sons, New York, 1987.
In preparation of cloning a library enriched in VL sequences, 2 μg of PCR amplified products (2.5 mg/30 μl of 150 mM NaCl, 8 mM Tris-HCL (pH 7.5), 6 mM Mg S04, 1 mM DTT, 200 mg/ml BSA. 37 C) were digested with restriction enzymes Nco I (30 units) and Spe I (45 units). The digested PCR amplified products were purified on a 1% agarose gel using standard electroelution technique described in Molecular Cloning A Laboratory Manual, Maniatis et al., eds., Cold spring Harbor, N.Y., (1982). Briefly, after gel electroelution of the digested PCR amplified product the region of the gel containing the VL-coding DNA fragment of the appropriate size was excised, electroelution into a dialysis membrane, ethanol precipitated and resuspended at a final concentration of 10 ng per ml in a solution containing 10 mM Tris-HCL at pH 7.5 and 1 mM EDTA.
An equal molar amount of DNA representing a plurality of different VL-coding DNA homologs was ligated to a pBluescript SK-phagemid vector that had been previously cut with Nco I and Spe I. A portion of the ligation mixture was transformed using the manufacturer's instructions into Epicuian Coli XL 1-Blue competent cells (Stratagene Cloning Systems, La Jolla, Calif.). The transformant library was determined to consist of 1.2×103 colony forming units/μg Of VL homologs with less than 3% non-recombinant background.
7. Sequencing of Plasmids from the VH-coding cDNA Library
To analyze the Lambda Zap II phage clones the clones were excised from Lambda Zap into plasmids according to the manufacture's instructions (Stratagene Cloning System, La Jolla, Calif.). Briefly, phage plaques were cored from the agar plates and transferred to sterile microfuge tubes containing 500 μl a buffer containing 50 mM Tris-HCl at pH 7.5, 100 mM NaCl, 10 mM MgSO4, and 0.01% gelatin and 20 μl of chloroform.
For excisions, 200 μl of the phage stock, 200 μl of XL1-Blue cells (A600=1.00) and 1 μl of R408 helper phage (1×1011 pfu/ml) were incubated at 37 C for 15 minutes. The excised plasmids were infected into XL1-Blue cells and plated onto LB plates containing ampicillin. Double stranded DNA was prepared from the phagemid containing cells according to the methods described by Holmes et al., Anal. Biochem., 114:193, (1981). Clones were first screened for DNA inserts by restriction digests with either Pvu II or Bgl I and clones containing the putative VH insert were sequenced using reverse transcriptase according to the general method described by Sanger et al., Proc. Natl. Acad. Sci., USA, 74:5463-5467, (1977) and the specific modifications of this method provided in the manufacturer's instructions in the AMV reverse transcriptase 35S-dATP sequencing kit from Stratagene Cloning Systems, La Jolla, Calif.
8. Characterization of the Cloned VH Repertoire
The amplified products which had been digested with Xho I and EcoR I and cloned into Lambda ZAP, resulted in a cDNA library with 9.0×105 pfu's. In order to confirm that the library consisted of a diverse population of VH-coding DNA homologs, the N-terminal 120 bases of 18 clones, selected at random from the library, were excised and sequenced (FIG. 5). To determine if the clones were of VH gene origin, the cloned sequences were compared with known VH sequences and VL sequences. The clones exhibited from 80 to 90% homology with sequences of known heavy chain origin and little homology with sequences of light chain origin when compared with the sequences available in Sequences of Proteins of Immunological Interest by Kabot et al., 4th ed., U.S. Dept. of Health and Human Sciences, (1987). This demonstrated that the library was enriched for the desired VH sequence in preference to other sequences, such as light chain sequences.
The diversity of the population was assessed by classifying the sequenced clones into predefined subgroups (FIG. 5). Mouse VH sequences are classified into eleven subgroups (FIG. 5). Mouse VH sequences are classified into eleven subgroups [I (A,B,), II (A,B,C), III (A,B,C,D,) V (A,B)] based on framework amino acid sequences described in Sequences of Proteins of Immunological Interest by Kabot et al., 4th ed., U.S. Dept. of Health and Human Sciences, (1987); Dildrop, Immunology Today, 5:84, (1984); and Brodeur et al., Eur. J. Immunol., 14; 922, (1984). Classification of the sequenced clones demonstrated that the cDNA library contained VH sequences of at least 7 different subgroups. Further, a pairwise comparison of the homology between the sequenced clones showed that no two sequences were identical at all positions, suggesting that the population is diverse to the extent that it is possible to characterize by sequence analysis.
Six of the clones (SEQ ID NOs:27-31, FIG. 5) belong to the subclass III B and had very similar nucleotide sequences. This may reflect a preponderance of mRNA derived from one or several related variable genes in stimulated spleen, but the data does not permit ruling out the possibility of a bias in the amplification process.
9. VH-Expression Vector Construction
The main criterion used in choosing a vector system was the necessity of generating the largest number of Fab fragments which could be screened directly. Bacteriophage lambda was selected as the expression vector for three reasons. First, in vitro packaging of phage DNA is the most efficient method of reintroducing DNA into host cells. Second, it is possible to detect protein expression at the level of single phage plaques. Finally, the screening of phage libraries typically involve less difficulty with nonspecific binding. The alternative, plasmid cloning vectors, are only advantageous in the analysis of clones after they have been identified. This advantage is not lost in the present system because of the use of lambda zap, thereby permitting a plasmid containing the heavy chain, light chain, or Fab expressing inserts to be excised.
To express the plurality of VH-coding DNA homologs in an E. coli host cell, a vector was constructed that placed the VH-coding DNA homologs in the proper reading frame, provided a ribosome binding site as described by Shine et al., Nature, 254:34, 1975, provided a leader sequence directing the expressed protein to the periplasmic space, provided a polynucleotide sequence that coded for a known epitope (epitope tag) and also provided a polynucleotide that coded for a spacer protein between the VH-coding DNA homolog and the polynucleotide coding for the epitope tag. A synthetic DNA sequence containing all of the above polynucleotides and features was constructed by designing single stranded polynucleotide segments of 20-40 bases that would hybridize to each other and form the double stranded synthetic DNA sequence shown in FIG. 6. The individual single-stranded polynucleotides (SEQ ID NOs:85-96) are shown in Table 3.
Polynucleotides designated SEQ ID NOs:86-87, SEQ ID NOs:93-94, SEQ ID NO:96, and SEQ ID NOs:90-92 were kinased by adding 1 μl of each polynucleotide (0.1 μg/μl) and 20 units of T4 polynucleotide kinase to a solution containing 70 mM Tris-HCl at pH 7.6, 10 mM MgCl2, 5 mM DTT, 10 mM 2ME, 500 micrograms per ml of BSA. The solution was maintained at 37 C for 30 minutes and the reaction stopped by maintaining the solution at 65 C for 10 minutes. The two end polynucleotides 20 ng of polynucleotides designated SEQ ID NO:85 and SEQ ID NO:95, were added to the above kinasing reaction solution together with 1/10 volume of a solution containing 20.0 mM Tris-HCl at pH 7.4, 2.0 mM MgCl2 and 50.0 mM NaCl. This solution was heated to 70 C for 5 minutes and allowed to cool to room temperature, approximately 25 C, over 1.5 hours in a 500 ml beaker of water. During this time period all 10 polynucleotides annealed to form the double stranded synthetic DNA insert shown in FIG. 6A. The individual polynucleotides were covalently linked to each other to stabilize the synthetic DNA insert by adding 40 μg of the above reaction to a solution containing 50 mM Tris-HCl at pH 7.5, 7 mM MgCl2, 1 mM DTT, 1 mM adenosine triphosphate (ATP) and 10 units of T4 DNA ligase. This solution was maintained at 37 C for 30 minutes and then the T4 DNA ligase was inactivated by maintaining the solution at 65 C for 10 minutes. The end polynucleotides were kinased by mixing 52 μl of the above reaction, 4 μl of a solution containing 10 mM ATP and 5 units of T4 polynucleotide kinase. This solution was maintained at 37 C for 30 minutes and then the T4 polynucleotide kinase was inactivated by maintaining the solution at 65 C for 10 minutes. The completed synthetic DNA insert was ligated directly into a lambda Zap II vector that had been previously digested with the restriction enzymes Not I and Xho I. The ligation mixture was packaged according to the manufacture's instructions using Gigapack II Gold packing extract available from Stratagene Cloning Systems, La Jolla, Calif. The packaged ligation mixture was plated on XL1 blue cells (Stratagene Cloning Systems, San Diego, Calif.). Individual lambda Zap II plaques were cored and the inserts excised according to the in vivo excision protocol provided by the manufacturer, Stratagene cloning Systems, La Jolla, Calif. This in vivo excision protocol moves the cloned insert from the lambda Zap II vector into a plasmid vector to allow easy manipulation and sequencing. The accuracy of the above cloning steps was confirmed by sequencing the insert using the Sanger dideoxide method described in by Sanger et al., Proc. Natl. Acad. Sci. USA, 74:5463-5467, (1977) and using the manufacture's instructions in the AMV Reverse Transcriptase 35S-ATP sequencing kit from Stratagene Cloning Systems, La Jolla, Calif. The sequence of the resulting VH expression vector is shown in FIG. 6A and FIG. 7.









TABLE 3







SEQ ID NO:85
5′ GGCCGCAAATTCTATTTCAAGGAGACAGTCAT




3′


 


SEQ ID NO:86
5′ AATGAAATACCTATTGCCTACGGCAGCCGCTGGA



TT 3′


 


SEQ ID NO:87
5′ GTTATTACTCGCTGCCCAACCAGCCATGGCCC



3′


 


SEQ ID NO:88
5′ AGGTGAAACTGCTCGAGAATTCTAGACTAGGTTA



ATAG 3′


 


SEQ ID NO:89
5′ TCGACTATTAACTAGTCTAGAATTCTCGAG 3′


 


SEQ ID NO:90
5′ CAGTTTCACCTGGGCCATGGCTGGTTGGG 3′


 


SEQ ID NO:91
5′ CAGCGAGTAATAACAATCCAGCGGCTGCCGTAGG



CAATAG 3′


 


SEQ ID NO:92
5′ GTATTTCATTATGACTGTCTCCTTGAAATAGAAT



TTGC 3′


 


SEQ ID NO:93
5′ AGGTGAAACTGCTCGAGATTTCTAGACTAGTTAC



CCGTAC 3′


 


SEQ ID NO:94
5′ GACGTTCCGGACTACGGTTCTTAATAGAATTCG



3′


 


SEQ ID NO:95
5′ TCGACGAATTCTATTAAGAACCGTAGTC 3′


 


SEQ ID NO:96
5′ CGGAACGTCGTACGGGTAACTAGTCTAGAAATCT



CGAG 3′









10. VL Expression Vector Construction
To express the plurality of VL coding polynucleotides in an E. coli host cell, a vector was constructed that placed the VL coding polynucleotide in the proper reading frame, provided a ribosome binding site as described by Shine et al., Nature, 254:34, (1975), provided a leader sequence directing the expressed protein to the periplasmic space and also provided a polynucleotide that coded for a spacer protein between the VL polynucleotide and the polynucleotide coding for the epitope tag. A synthetic DNA sequence containing all of the above polynucleotides and features was constructed by designing single stranded polynucleotide segments of 20-40 bases that would hybridize to each other and form the double stranded synthetic DNA sequence shown in FIG. 6B. The individual single-stranded polynucleotides (SEQ ID NOs:85-92) are shown in Table 3.
Polynucleotides designated SEQ ID NOs:86-88 and SEQ ID NOs:90-92 were kinased by adding 1 μl of each polynucleotide and 20 units of T4 polynucleotide kinase to a solution containing 70 mM Tris-HCl at pH 7.6, 10 mM MgCl2, 5 mM DDT, 10 mM 2ME, 500 micrograms per ml of BSA. The solution was maintained at 37 C for 30 minutes and the reaction stopped by maintaining the solution at 65 C for 10 minutes. The two end polynucleotides 20 ng of polynucleotides designated SEQ ID NO:85 and SEQ ID NO:89 were added to the above kinasing reaction solution together with 1/10 volume of a solution containing 20.0 mM Tris-HCl at pH 7.4, 2.0 mM MgCl2 and 50.0 mM NaCl. This solution was heated to 70 C for 5 minutes and allowed to cool to room temperature, approximately 25 C, over 1.5 hours in a 500 ml beaker of water. During this time period all the polynucleotides annealed to form the double stranded synthetic DNA insert. The individual polynucleotides were covalently linked to each other to stabilize the synthetic DNA insert with adding 40 μl of the above reaction to a solution containing 50 μl Tris-HCl at pH 7.5, 7 mM MgCl2, 1 mM DTT, 1 mM ATP and 10 units of T4 DNA ligase. This solution was maintained at 37 C for 30 minutes and then the T4 DNA ligase was inactivated by maintaining the solution at 65 C for 10 minutes. The end polynucleotides were kinased by mixing 52 μl of the above reaction, 4 μl of a solution recontaining 10 mM ATP and 5 units of T4 polynucleotide kinase. This solution was maintained at 37 C for 30 minutes and then the T4 polynucleotide kinase was inactivated by maintaining the solution at 65 C for 10 minutes. The completed synthetic DNA insert was ligated directly into a lambda Zap II vector that had been previously digested with the restriction enzymes Not I and Xho I. The ligation mixture was packaged according to the manufacture's instructions using Gigapack II Gold packing extract available from Stratagene Cloning Systems, La Jolla, Calif. The packaged ligation mixture was plated on XL1-Blue cells (Stratagene Cloning Systems, La Jolla, Calif.). Individual lambda Zap II plaques were cored and the inserts excised according to the in vivo excision protocol provided by the manufacturer, Stratagene Cloning Systems, La Jolla, Calif. and described in Short et al., Nucleic Acids Res., 16:7583-7600, 1988. This in vivo excision protocol moves the cloned insert from the lambda Zap II vector into a phagemid vector to allow easy manipulation and sequencing and also produces the phagemid version of the VL expression vectors. The accuracy of the above cloning steps was confirmed by sequencing the insert using the Sanger dideoxide method described by Sanger et al., Proc. Natl. Acad. Aci. USA, 74:5463-5467, (1977) and using the manufacturer's instructions in the AMV reverse transcriptase 35S-dATP sequencing kit from Stratagene Cloning Systems, La Jolla, Calif. The sequence of the resulting VL expression vector is shown in FIG. 6 and FIG. 8.
The VL expression vector used to construct the VL library was the phagemid produced to allow the DNA of the VL expression vector to be determined. The phagemid was produced, as detailed above, by the in vivo excision process from the Lambda Zap VL expression vector (FIG. 8). The phagemid version of this vector was used because the Nco I restriction enzyme site is unique in this version and thus could be used to operatively linked the VL DNA homologs into the expression vector.
11. VLII-Expression Vector Construction
To express the plurality of VL-coding DNA homologs in an E. coli host cell, a vector was constructed that placed the VL-coding DNA homologs in the proper reading frame, provided a ribosome binding site as described by Shine et al., Nature, 254:34, 1975, provided the Pel B gene leader sequence that has been previously used to successfully secrete Fab fragments in E. coli by Lei et al., J. Bac., 169:4379 (1987) and Better et al., Science, 240:1041 (1988), and also provided a polynucleotide containing a restriction endonuclease site for cloning. A synthetic DNA sequence containing all of the above polynucleotides and features was constructed by designing single stranded polynucleotide segments of 20-60 bases that would hybridize to each other and form the double stranded synthetic DNA sequence shown in FIG. 10. The sequence of each individual single-stranded polynucleotides (SEQ ID NOs:97-104) within the double stranded synthetic DNA sequence is shown in Table 4.
Polynucleotides designated SEQ ID NOs:98-103 were kinased by adding 1 μl (0.1 ug/μl) of each polynucleotide and 20 units of T4 polynucleotide kinase to a solution containing 70 mM Tris-HCl at pH 7.6, 10 mM magnesium chloride (MgCl), 5 mM dithiothreitol (DTT), 10 mM 2-mercaptoethanol (2ME), 500 micrograms per ml of bovine serum albumin. The solution was maintained at 37 C for 30 minutes and the reaction stopped by maintaining the solution at 65 C for 10 minutes. The 20 ng each of the two end polynucleotides, SEQ ID NO:97 and SEQ ID NO:104, were added to the above kinasing reaction solution together with 1/10 volume of a solution containing 20.0 mM Tris-HCl at pH 7.4, 2.0 mM MgCl and 15.0 mM sodium chloride (NaCl). This solution was heated to 70 C for 5 minutes and allowed to cool to room temperature, approximately 25 C, over 1.5 hours in a 500 ml beaker of water. During this time period all 8 polynucleotides annealed to form the double stranded synthetic DNA insert shown in FIG. 9. The individual polynucleotides were covalently linked to each other to stabilize the synthetic DNA insert by adding 40 μl of the above reaction to a solution containing 50 ml Tris-HCl at pH 7.5, 7 ml MgCl, 1 mm DTT, 1 mm ATP and 10 units of T4 DNA ligase. This solution was maintained at 37 C for 30 minutes and then the T4 DNA ligase was inactivated by maintaining the solution at 65 C for 10 minutes. The end polynucleotides were kinased by mixing 52 μl of the above reaction, 4 μl of a solution containing 10 mM ATP and 5 units of T4 polynucleotide kinase. This solution was maintained at 37 C for 30 minutes and then the T4 polynucleotide kinase was inactivated by maintaining the solution at 65 C for 10 minutes. The completed synthetic DNA insert was ligated directly into a lambda Zap II vector that had been previously digested with the restriction enzymes Not I and Xho I. The ligation mixture was packaged according to the manufacture's instructions using Gigapack II Gold packing extract available from Stratagene Cloning systems, La Jolla, Calif. The packaged ligation mixture was plated on XL1 blue cells (Stratagene Cloning Systems, San Diego, Calif.). Individual lambda Zap II plaques were cored and the inserts excised according to the in vivo excision protocol provided by the manufacturer, Stratagene Cloning Systems, La Jolla, Calif. This in vivo excision protocol moves the cloned insert from the lambda Zap II vector into a plasmid vector to allow easy manipulation and sequencing. The accuracy of the above cloning steps was confirmed by sequencing the insert using the manufacture's instructions in the AMV Reverse Transcriptase 35S-dATP sequencing kit from Stratagene Cloning Systems, La Jolla, Calif. The sequence of the resulting VLII-expression vector is shown in FIG. 9 and FIG. 11.









TABLE 4







SEQ ID NO:97
5′ TGAATTCTAAACTAGTCGCCAAGGAGACAGTCAT




3′


 


SEQ ID NO:98
5′ AATGAAATACCTATTGCCTACGGCAGCCGCTGGA



TT 3′


 


SEQ ID NO:99
5′ GTTATTACTCGCTGCCCAACCAGCCATGGCC 3′


 


SEQ ID NO:100
5 I GAGCTCGTCAGTTCTAGAGTTAAGCGGCCG 3′


 


SEQ ID NO:101
5′ GTATTTCATTATGACTGTCTCCTTGGCGACTAG-



TTTAGAATTCAAGCT 3′


 


SEQ ID NO:102
5′ CAGCGAGTAATAACAATCCAGCGGCTGCCGTAGG



CAATAG 3′


 


SEQ ID NO:103
5′ TGACGAGCTCGGCCATGGCTGGTTGGG 3′


 


SEQ ID NO:104
5′ TCGACGGCCGCTTAACTCTAGAAC 3′









12. VH+VL Library Construction
To prepare an expression library enriched in VH sequences, DNA homologs enriched in VH sequences were prepared according to Example 6 using the same set of 5′ primers but with primer designated SEQ ID NO:61 (Table 1) as the 3′ primer. These homologs were then digested with the restriction enzymes Xho I and Spe I and purified on a 1% agarose gel using the standard electroelution technique described in Molecular Cloning A Laboratory Manual, Maniatis et al., eds., Cold Spring Harbor, N.Y., (1982). These prepared VI! DNA homologs were then directly inserted into the VH expression vector that had been previously digested with Xho I and Spe I.
The ligation mixture containing the VH DNA homologs were packaged according to the manufacturers specifications using Gigapack Gold II packing Extract (Stratagene Cloning Systems, La Jolla, Calif.). The expression libraries were then ready to be plated on XL-1 Blue cells.
To prepare a library enriched in VL sequences, PCR amplified products enriched in VL sequences were prepared according to Example 6. These VL DNA homologs were digested with restriction enzymes Nco I and Spe I. The digested VL DNA homologs were purified on a 1% agarose gel using standard electroelusion techniques described in Molecular Cloning A Laboratory Manual, Maniatis et al., eds., Cold Spring Harbor, N.Y. (1982). The prepared VL DNA homologs were directly inserted into the VL expression vector that had been previously digested with the restriction enzymes Nco I and Spe I. The ligation mixture containing the VL DNA homologs were transformed into XL-1 blue competent cells using the manufacturer's instructions (Stratagene Cloning Systems, La Jolla, Calif.).
13. Inserting V1 Coding DNA Homoloqs into V1 Expression Vector
In preparation for cloning a library enriched in VL sequences, PCR amplified products (2.5 μg/30 μl of 150 mM NaCl, 8 mM Tris-HCl (pH 7.5), 6 mM MgSO4, 1 mM DTT, 200 μg/ml BSA at 37 C were digested with restriction enzymes Sac I (125 units) and Xba I (125 units) and purified on a 1% agarose gel. In cloning experiments which required a mixture of the products of the amplification reactions, equal volumes (50 μl, 1-10 ug concentration) of each reaction mixture were combined after amplification but before restriction digestion. After gel electrophoresis of the digested PCR amplified spleen mRNA, the region of the gel containing DNA fragments of approximate 350 bps was excised, electroeluted into a dialysis membrane, ethanol precipitated and resuspended in a TE solution containing 10 mM Tris-HCl pH 7.5 and 1 mM EDTA to a final concentration of 50 ng/ul.
The VLII-expression DNA vector was prepared for cloning by admixing 100 μg of this DNA to a solution containing 250 units each of the restriction endonucleases Sac 1 and Xba 1 (both from Boehringer Mannheim, Indianapolis, Ind.) and a buffer recommended by the manufacturer. This solution was maintained at 37 from 1.5 hours. The solution was heated at 65 C for 15 minutes top inactivate the restriction endonucleases. The solution was chilled to 30 C and 25 units of heat-killable (HK) phosphatase (Epicenter, Madison, Wis.) and CaCl2 were admixed to it according to the manufacturer's specifications. This solution was maintained at 30 C for 1 hour. The DNA was purified by extracting the solution with a mixture of phenol and chloroform followed by ethanol precipitation. The VLII expression vector was now ready for ligation to the VL DNA homologs prepared in the above examples.
DNA homologs enriched in VL sequences were prepared according to Example 5 but using a 5′ light chain primer and the 3′ light chain primer shown in Table 2. Individual amplification reactions were carried out using each 5′ light chain primer in combination with the 3′ light chain primer. These separate VL homolog containing reaction mixtures were mixed and digested with the restriction endonucleases Sac I and Xba I according to Example 6. The VL homologs were purified on a 1% agarose gel using the standard electroelution technique described in Molecular Cloning A Laboratory Manual, Maniatis et al., eds., Cold spring Harbor, N.Y., (1982). These prepared VL DNA homologs were then directly inserted into the Sac I-Xba cleaved VLII-expression vector that was prepared above by ligating 3 moles of VL DNA homolog inserts with each mole of the VLII-expression vector overnight at 5 C. 3.0×105 plague forming units were obtained after packaging the DNA with Gigapack II Bold (stratagene Cloning Systems; La Jollaj CA) and 50% were recombinants.
14. Randomly Combining VH and VL DNA Homologs on the Same Expression Vector
The VLII-expression library prepared in Example 13 was amplified and 500 μg of VLII-expression library phage DNA prepared from the amplified phage stock using the procedures described in Molecular cloning: A Laboratory Manual, Maniatis et al., eds., Cold Spring Harbor Laboratory, Cold Spring Harbor; NY (1982), 50 μg of this VLII-expression library phage DNA was maintained in a solution containing 100 units of MLuI restriction endonuclease (Boehringer Mannheim, Indianapolis, Ind.) in 200 μl of a buffer supplied by the endonuclease manufacturer for 1.5 hours at 37 C. The solution was then extracted with a mixture of phenol and chloroform. The DNA was then ethanol precipitated and resuspended in 100 μl of water. This solution was admixed with 100 units of the restriction endonuclease EcoR I (Boehringer Mannheim, Indianapolis, Ind.) in a final volume of 200 μl of buffer containing the components specified by the manufacturer. This solution was maintained at 37 C for 1.5 hours and the solution was then extracted with a mixture of phenol and chloroform. The DNA was ethanol precipitated and the DNA resuspended in TE.
The VH expression library prepared in Example 12 was amplified and 500 μg of VH expression library phage DNA prepared using the methods detailed above. 50 μg of the VH expression library phage DNA was maintained in a solution containing 100 units of Hind III restriction endonuclease (Boehringer Mannheim, Indianapolis, Ind.) in 200 μl of a buffer supplied by the endonuclease manufacturer for 1.5 hours at 37 C. The solution was then extracted with a mixture of phenol and chloroform saturated with 0.1 M Tris-HCl at pH 7.5. The DNA was then ethanol precipitated and resuspended in 100 μl of water. This solution was admixed with 100 units of the restriction endonuclease EcoR I (Boehringer Mannheim, Indianapolis, Ind.) in a final volume of 200 μl of buffer containing the components specified by the manufacturer. This solution was maintained at 37 C for 1.5 hours and the solution was then extracted with a mixture of phenol and chloroform. The DNA was ethanol precipitated and the DNA resuspended in TE.
The restriction digested VH and VLII-expression Libraries were ligated together. The ligation reaction consisted of 1 μg of VH and 1 μg of VLII phage library DNA in a 10 μl reaction using the reagents supplied in a ligation kit purchased from Stratagene Cloning Systems (La Jolla, Calif.). After ligation for 16 hr at 4 C, 1 μl of the ligated the phage DNA was packaged with Gigapack Gold II packaging extract and plated on XL 1-blue cells prepared according to the manufacturers instructions. A portion of the 3×106 clones obtained were used to determine the effectiveness of the combination. The resulting VH and VL expression vector is shown in FIG. 11.
Clones containing both VH and VL were excised from the phage to pBluescript using the in vitro excision protocol described by Short et al., Nucleic Acid Research, 16:7583-7600 (1988). Clones chosen for excision expressed the decapepetide tag and did not cleave X-gal in the presence of 2 mM IPTG thus remaining white. Clones with these characteristics represented 30% of the library. 50% of the clones chosen for excision contained a VH and VL as determined by restriction analysis. Since approximately 30% of the clones in the VH library expressed the decapeptide tag and 50% of the clones in the VLII library contained a VL sequence it was anticipated that no more than 15% of the clones in the combined library would contain both VH and VL clones. The actual number obtained was 15% of the library indicating that the process of combination was very efficient.
15. Segregating DNA Homologs for a VH Antigen Binding Protein
To segregate the individual clones containing DNA homologs that code for a VH antigen binding protein, the titre of the VH expression library prepared according to Example 11 was determined. This library titration was performed using methods well known to one skilled in the art. Briefly, serial dilutions of the library were made into a buffer containing 100 mM NaCl, 50 mM Tris-HCl at pH 7.5 and 10 mM MgSO4. Ten μl of each dilution was added to 200 μl of exponentially growing E. coli cells and maintained at 37 C for 15 minutes to allow the phage to absorb to the bacterial cells. Three ml of top agar consisting of 5 g/L NaCl, 2 g/L of MgSO4, 5 g/L yeast extract, 10 g/L NZ amine (casein hydrolysate) and 0.7% melted, 50 C agarose. The phage, the bacteria and the top agar were mixed and then evenly distributed across the surface of a prewarmed bacterial agar plate (5 g/L NaCl, 2 g/L MgSO4, 5 g/L yeast extract, 10 g/L NZ amine (casein hydrolysate) and 15 g/L Difco agar. The plates were maintained at 37 C for 12 to 24 hours during which time period the lambda plaques developed on the bacterial lawn. The lambda plaques were counted to determine the total number of plaque forming units per ml in the original library.
The titred expression library was then plated out so that replica filters could be made from the library. The replica filters will be used to later segregate out the individual clones in the library that are expressing the antigens binding proteins of interest. Briefly, a volume of the titred library that would yield 20,000 plaques per 150 millimeter plate was added to 600 μl of exponentially growing E. coli cells and maintained at 37 C for 15 minutes to allow the phage to absorb to the bacterial cells. Then 7.5 ml of top agar was admixed to the solution containing the bacterial cells and the absorbed phage and the entire mixture distributed evenly across the surface of a prewarmed bacterial agar plate. This process was repeated for a sufficient number of plates to plate out a total number of plaques at least equal to the library size. These plates were then maintained at 37 C for 5 hours. The plates were then overlaid with nitrocellulose filters that had been pretreated with a solution containing 10 mM isopropyl-beta-D-thiogalactopyranosid (IPTG) and maintained at 37 C for 4 hours. The orientation of the nitrocellulose filters in relation to the plate were marked by punching a hole with a needle dipped in waterproof ink through the filter and into the bacterial plates at several locations. The nitrocellulose filters were removed with forceps and washed once in a TBST solution containing 20 mM Tris-HCl at pH 7.5, 150 mM NaCl and 0.05% monolaurate (tween-20). A second nitrocellulose filter that had also been soaked in a solution containing 10 mM IPTG was reapplied to the bacterial plates to produce duplicate filters. The filters were further washed in a fresh solution of TBST for 15 minutes. Filters were then placed in a blocking solution consisting of 20 mM Tris-HCl at pH 7.5, 150 mM NaCl and 1% BSA and agitated for 1 hour at room temperature. The nitrocellulose filters were transferred to a fresh blocking solution containing a 1 to 500 dilution of the primary antibody and gently agitated for at least 1 hour at room temperature. After the filters were agitated in the solution containing the primary antibody the filters were washed 3 to 5 times in TBST for 5 minutes each time to remove any of the residual unbound primary antibody. The filters were transferred into a solution containing fresh blocking solution and a 1 to 500 to a 1 to 1,000 dilution of alkaline phosphatase conjugated secondary antibody. The filters were gently agitated in the solution for at least 1 hour at room temperature. The filters were washed 3 to 5 times in a solution of TBST for at least 5 minutes each time to remove any residual unbound secondary antibody. The filters were washed once in a solution containing 20 mM Tris-HCl at pH 7.5 and 150 mM NaCl. The filters were removed from this solution and the excess moisture blotted from them with filter paper. The color was developed by placing the filter in a solution containing 100 mM Tris-HCl at pH 9.5, 100 mM NaCl, 5 mM MgCl2, 0.3 mg/ml of nitro Blue Tetrazolium (NBT) and 0.15 mg/ml of 5-bromo-4-chloro-3-indolyl-phosphate (BCIP) for at least 30 minutes at room temperature. The residual color development solution was rinsed from the filter with a solution containing 20 mM Tris-HCl at pH 7.5 and 150 mM NaCl. The filter was then placed in a stop solution consisting of 20 mM Tris-HCl at pH 2.9 and 1 mM EDTA. The development of an intense purple color indicates at positive result. The filters are used to locate the phage plaque that produced the desired protein. That phage plaque is segregated and then grown up for further analysis.
Several different combinations of primary antibodies and second antibodies were used. The first combination used a primary antibody immunospecific for a decapeptide that will be expressed only if the VH antigen binding protein is expressed in the proper reading frame to allow read through translation to include the decapeptide epitope covalently attached to the VH antigen binding protein. This decapeptide epitope and an antibody immunospecific for this decapeptide epitope was described by Green et al., Cell 28:477 (1982) and Niman et al., Proc. Nat. Acad. Sci. U.S.A. 80:4949 (1983). The sequence of decapeptide recognized is shown in FIG. 11. A functional equivalent of the monoclonal antibody that is immunospecific for the decapeptide can be prepared according to the methods of Green et ale and Niman et ale The secondary antibody used with this primary antibody was a goat antimouse IgG (Fisher Scientific). This antibody was immunospecific for the constant region of mouse IgG and did not recognize any portion of the variable region of heavy chain. This particular combination of primary and secondary antibodies when used according to the above protocol determined that between 25% and 30% of the clones were expressing the decapeptide and therefore these clones were assumed to also be expressing a VH antigen binding protein.
In another combination the anti-decapeptide mouse monoclonal was used as the primary antibody and an affinity purified goat anti-mouse IgG, commercially available as part of the picoBlue immunoscreening kit from Stratagene Cloning System, La Jolla, Calif., was use as the secondary antibody. This combination resulted in a large number of false positive clones because the secondary antibody also immunoreacted with the VH of the heavy chain Therefore this antibody reacted with all clones expressing any VH protein and this combination of primary and secondary antibodies did not specifically detect clones with the VH polynucleotide in the proper reading frame and thus allowing expressing of the decapeptide.
Several combinations of primary and secondary antibodies are used where the primary antibody is conjugated to fluorescein isothiocyanate (FITC) and thus the immunospecificity of the antibody was not important because the antibody is conjugated to the preselected antigen (FITC) and it is that antigen that should be bound by the VH antigen binding proteins produced by the clones in the expression library. After this primary antibody has bound by virtue that is FITC conjugated mouse monoclonal antibody p2 5764 (ATCC #HB-9505). The secondary antibody used with this primary antibody is a goat anti-mouse IgG (Fisher Scientific, Pittsburg, Pa.) conjugated to alkaline phosphatase. Using the method described in Antibodies A Laboratory Manual, Harlow and Lowe, eds., Cold Springing Harbor, N.Y., (1988). If a particular clone in the VH expression, library, expresses a VH binding protein that binds the FITC covalently coupled to the primary antibody, the secondary antibody binds specifically and when developed the alkaline phosphate causes a distinct purple color to form.
The second combination of antibodies of the type uses a primary antibody that is FITC conjugated rabbit anti-human IgG (Fisher Scientific, Pittsburg, Pa.). The secondary antibody used with this primary antibody is a goat anti-rabbit IgG conjugated to alkaline phosphatase using the methods described in Antibodies A Laboratory Manual, Harlow and Lane, eds., Cold Spring Harbor, N.Y., (1988). If a particular clone in the VH expression library expresses a VH binding protein that binds the FITC conjugated to the primary antibody, the secondary antibody binds specifically and when developed the alkaline phosphatase causes a distinct purple color to form.
Another primary antibody was the mouse monoclonal antibody p2 5764 (ATCC # HB-9505) conjugated to both FITC and 125I. The antibody would be bound by any VH antigen binding proteins expressed. Then because the antibody is also labeled with 125I, an autoradiogram of the filter is made instead of using a secondary antibody that is conjugated to alkaline phosphatase. This direct production of an autoradiogram allows segregation of the clones in the library expressing a VH antigen binding protein of interest.
16. Segregating DNA Homologs for a VH and VL that form an Antigen Binding Fv 
To segregate the individual clones containing DNA homologs that code for a VH and a VL that form an antigen binding Fv the VH and VL expression library was titred according to Example 15. The titred expression library was then screened for the presence of the decapeptide tag expressed with the VH using the methods described in Example 15. DNA was then prepared from the clones to express the decapeptide tag. This DNA was digested with the restriction endonuclease Pvu II to determine whether these clones also contained a VL DNA homolog. The slower migration of a PvuII restriction endonuclease fragment indicated that the particular clone contained both a VH and a VL DNA homolog.
The clones containing both a VH and a VL DNA homolog were analyzed to determine whether these clones produced an assembled Fv protein molecule from the VH and VL DNA homologs.
The FV protein fragment produced in clones containing both VH and VL was visualized by immune precipitation of radiolabeled protein expressed in the clones. A 50 ml culture of LB broth (5 g/L yeast extract, 10 g/L and tryptone 10 g/L NaCl at pH 7.0) containing 100 μg/μl of ampicillin was inoculated with E. Coli harboring a plasmid contain a VH and a VL. The culture was maintained at 37 C with shaking until the optical density measured at 550 nm was 0.5 culture then was centrifuged at 3,000 g for 10 minutes and resuspended in 50 ml of M9 media (6 g/L Na2HPO4, 3 g/L KH2PO4, 0.5 g/L NaCl, 1 g/L NH4Cl, 2 g/L glucose, 2 mM MgSO4 and 0.1 mMgSO4 CaCl2 supplemented with amino acids without methionine or cysteine. This solution was maintained at 37 C for 5 minutes and then 0.5 mCi of 35S as HSO4− (New England Nuclear, Boston, Mass.) was added and the solution was further maintained at 37 C for an additional 2 hours. The solution was then centrifuged at 3000×g and the supernatant discarded. The resulting bacterial cell pellet was frozen and thawed and then resuspended in a solution containing 40 mM Tris pH 8.0, 100 mM sucrose and 1 mM EDTA. The solution was centrifuged at 10000 xg for 10 minutes and the resulting pellet discarded. The supernatant was admixed with 10 μl of anti-decapeptide monoclonal antibody and maintained for 30-90 minutes on ice. 40 μl of protein G coupled to sepharose beads (Pharmacia, Piscataway, N.J.) was admixed to the solution and the added solution maintained for 30 minutes on ice to allow an immune precipitate to form. The solution was centrifuged at 10,000×g for 10 minutes and the resulting pellet was resuspended in 1 ml of a solution containing 100 mM Tris-HCl at pH 7.5 and centrifuged at 10,000×g for 10 minutes. This procedure was repeated twice. The resulting immune precipitate pellet was loaded onto a PhastGel Homogenous 20 gel (Pharmacia, Piscataway, N.J.) according to the manufacturer's directions. The gel was dried and used to expose X-ray film.
The resulting autoradiogram is shown in FIG. 12. The presence of assembled Fv molecules can be seen by the presence of VL that was immunoprecipitated because it was attached to the VH-decapeptide tag recognized by the precipitating antibody.
17. Generation of a Large Combinatorial Library of the Immunoglobulin Repertoire in Phage
Vectors suitable for expression of VH, VL, Fv and Fab sequences are diagrammed in FIGS. 7 and 9. As previously discussed, the vectors were constructed by modification of Lambda Zap by inserting synthetic oligonucleotides into the multiple cloning site. The vectors were designed to be antisymmetric with respect to the Not I and EcoR I restriction sites which flank the cloning and expression sequences. As described below, this antisymmetry in the placement of restriction sites in a linear vector like bacteriophage is the essential feature of the system which allows a library expressing light chains to be combined with one expressing heavy chains to construct combinatorial Fab expression libraries. Lambda Zap II VLII (FIG. 9) is designed to serve as a cloning vector for light chain fragments and Lambda Zap II VH (FIG. 7) is designed to serve as a cloning vector for heavy chain sequences in the initial step of library construction. These vectors are engineered to efficiently clone the products of PCR amplification with specific restriction sites incorporated at each end.
A. PCR Amplification of Antibody Fragments
The PCR amplification of mRNA isolated from spleen cells with oligonucleotides which incorporate restriction sites into the ends of the amplified product can be used to clone and express heavy chain sequences including Fd and kappa chain sequences. The oligonucleotide primers used for these amplifications are presented in Tables 1 and 2. The primers are analogous to those which have been successfully used in Example 5 for amplification of VH sequences. The set of 5′ primers for heavy chain amplification were identical to those previously used to amplify VH and those for light chain amplification were chosen on similar principles, Sastry et al., Proc. Natl. Acad. Sci. USA, 8G: 5728 (1989) and Orland et al., Proc Natl. Acad. Sci. USA, 8G:3833 (1989). The unique 3′ primers of heavy (IgG1) and light (k) chain sequences were chosen to include the cysteines involved in heavy-light chain disulfide bond formation. At this stage no primer was constructed to amplify lambda light chains since they constitute only a small fraction of murine antibodies. In addition, Fv fragments have been constructed using a 3′ primer which is complementary to the mRNA in the J (joining) region (amino acid 128) and a set of unique 5′ primers which are complementary to the first strand cDNA in the conserved N-terminal region of the processed protein. Restriction endonuclease recognition sequences are incorporated into the primers to allow for the cloning of the amplified fragment into a lambda phage vector in a predetermined reading frame for expression.
B. Library Construction
The construction of a combinatorial library was accomplished in two steps. In the first step, separate heavy and light chain libraries were constructed in Lambda Zap II VH and Lambda Zap II VL II respectively. In the second step, these two libraries were combined at the antisyrometric EcoR1 sites present in each vector. This resulted in a library of clones each of which potentially co-expresses a heavy and a light chain. The actual combinations are random and do not necessarily reflect the combinations present in the B-cell population in the parent animal. Lambda Zap II VH expression vector has been used to create a library of heavy chain sequences from DNA obtained by PCR amplification of mRNA isolated from the spleen of a 129 Gix+mouse previously immunized with p-nitrophenyl phosphonamidate (NPN) antigen 1 according to formula I (FIG. 13) conjugated to keyhole limpet hemocyanin (KLH).
The NPN-KLH conjugate was prepared by admixture of 250 μl of a solution containing 2.5 mg of NPN according to formula 1 (FIG. 13) in dimethylformamide with 75011 of a solution containing 2 mg of KLH in 0.01 M sodium phosphate buffer (pH 7.2). The two solutions were admixed by slow addition of the NPN solution to the KLH solution while the KLH solution was being agitated by a rotating stirring bar. Thereafter the admixture was maintained at 4° for 1 hour with the same agitation to allow conjugation to proceed. The conjugated NPN-KLH was isolated from the nonconjugated NPN and KLH by gel filtration through Sephadex G-25. The isolated NPN-KLH conjugate was used in mouse immunizations as described in Example 2.
The spleen mRNA resulting from the above immunizations was isolated and used to create a primary library of VH gene sequences using the Lambda Zap II VH expression vector. The primary library contains 1.3×106 pfu and has been screened for the expression of the decapeptide tag to determine the percentage of clones expressing Fd sequences. The sequence for this peptide is only in frame for expression following the cloning of a Fd (or VH) fragment into the vector. At least 80% of the clones in the library express Fd fragments based on immuno-detection of the decapeptide tag.
The light chain library was constructed in the same way as the heavy chain and shown to contain 2.5×106 members. Plaque screening, using an anti-kappa chain antibody, indicated that 60% of the library contained expressed light chain inserts. This relatively small percentage of inserts probably resulted from incomplete dephosphorylation of vector after cleavage with Sac I and Xba I.
Once obtained, the two libraries were used to construct a combinatorial library by crossing them at the EcoR I site. To accomplish the cross, DNA was first purified from each library. The light chain library was cleaved with MluI restriction endonuclease, the resulting 5′ ends dephosphorylated and the product digested with EcoR I. This process cleaved the left arm of the vector into several pieces but the right arm containing the light chain sequences, remained intact. In a parallel fashion, the DNA of heavy chain library was cleaved with HindIII, dephosphorylated and cleaved with EcoR I, destroying the right arm but leaving the left arm containing the heavy chain sequences intact. The DNA's so prepared were then combined and ligated. After ligation only clones which resulted from combination of a right arm of light chain-containing clones and a left arm of heavy chain-containing clones reconstituted a viable phage. After ligation and packaging, 2.5×107 clones were obtained. This is the combinatorial Fab expression library that was screened to identify clones having affinity for NPN. To determine the frequency the phage clones which co-express the light and heavy chain fragments, duplicate lifts of the light chain, heavy chain and combinatorial libraries were screened as above for light and heavy chain expression. In this study of approximately 500 recombinant phage approximately 60% co-expressed light and heavy chain proteins.
C. Antigen Binding
All three libraries, the light chain, the heavy chain and Fab were screened to determine if they contained recombinant phage that expressed antibody fragments binding NPN. In a typical procedure 30,000 phage were plated and duplicate lifts with nitrocellulose screened for binding to NPN coupled to 125I labeled BSA (FIG. 15). Duplicate screens of 80,000 recombinant phage from the light chain library and a similar number from the heavy chain library did not identify any clones which bound the antigen. In contrast, the screen of a similar number of clones from the Fab expression library identified many phage plaques that bound NPN (FIG. 15). This observation indicates that under conditions where many heavy chains in combination with light chains bind to antigen the same heavy or light chains alone do not. Therefore, in the case of NPN, it is believed that there are many heavy and light chains that only bind antigen when they are combined with specific light and heavy chains respectively.
To assess the ability to screen large numbers of clones and obtain a more quantitative estimate of the frequency of antigen binding clones in the combinatorial library, one million phage plaques were screened and approximately 100 clones which bound to antigen were identified. For six clones which were believed to bind NPN, a region of the plate containing the positive and approximately 20 surrounding bacteriophage plaques was “cored”, replated, and screened with duplicate lifts (FIG. 15). As expected, approximately one in twenty of the phage specifically bind to antigen. “Cores” of regions of the plated phage believed to be negative did not give positives on replating.
To determine the specificity of the antigen-antibody interaction, antigen binding was competed with free unlabeled antigen as shown in FIG. 16. competition studies showed that individual clones could be distinguished on the basis of antigen affinity. The concentration of free haptens required for complete inhibition of binding varied between 10-100×109 M suggesting that the expressed Fab fragments had binding constants in the nanomolar range.
D. Composition of the Clones and their Expressed Products
In preparation for characterization of the protein products able to bind NPN as described in Example 18 C, a plasmid containing the heavy and light chain genes was excised from the appropriate “cored” bacteriophage plaque using M13 mp 8 helper phage. Mapping of the excised plasmid demonstrated a. restriction pattern consistent with incorporation of heavy and light chain sequences. The protein products of one of the clones was analyzed by ELISA and western blotting to establish the composition of the NPN binding protein. A bacterial supernate following IPTG induction was concentrated and subjected to gel filtration. Fractions in the molecular weight range 40-60 kD were pooled, concentrated and subjected to a further gel filtration separation. As illustrated in FIG. 17, ELISA analysis of the eluting fractions demonstrated that NPN binding was associated with a protein of molecular weight about 50 kD which immunological detection showed contained both heavy and light chains. A Western blot (not shown) of a concentrated bacterial supernate preparation under non-reducing conditions was developed with anti-decapeptide antibody. This revealed a protein band of molecular weight of 50 kD. Taken together these results are consistent with NPN binding being a function of Fab fragments in which heavy and light chains are covalently linked.
E. Comparison of the Properties of the In Vivo Repertoire Versus the Phage Combinatorial Library
In this example a relatively restricted library was prepared because only a limited number of primers were used for PCR amplification of Fd sequences. The library is expected to contain only clones expressing kappa/gammal sequences. However, this is not an inherent limitation of the method since additional primers can be added to amplify any antibody class or subclass. Despite this restriction we were able to isolate a large number of antigen binding clones.
A central issue arising from this work is how a phage library prepared as described herein compares with the in vivo antibody repertoire in terms of size, characteristics of diversity, and ease of access.
The size of the mammalian antibody repertoire is difficult to judge but a figure of the order of 106-108 different antigen specificities is often quoted. with some of the reservations discussed below, a phage library of this size or larger can readily be constructed by a modification of the current method. In fact once an initial combinatorial library has been constructed, heavy and light chains can be shuffled to obtain libraries of exceptionally large numbers.
In principle, the diversity characteristics of the naive (unimmunized) in vivo repertoire and corresponding phage library are expected to be similar in that both involve a random combination of heavy and light chains. However, different factors will act to restrict the diversity expressed by an in vivo repertoire and phage library. For example a physiological modification such as tolerance will restrict the expression of certain antigenic specificities from the in vivo repertoire but these specificities may still appear in the phage library. On the other hand, bias in the cloning process may introduce restrictions into the diversity of the phage library. For example the representation of mRNA for sequences expressed by stimulated B-cells can be expected to predominate over those of unstimulated cells because of higher levels of expression. Different source tissues (e.g., peripheral blood, bone marrow or regional lymph nodes) and different PCR primers (e.g., ones expected to amplify different antibody classes) may result in libraries with different diversity characteristics.
Another difference between in vivo repertoire and phage library is that antibodies isolated from the former may have benefited from affinity maturation due to somatic mutations after combination of heavy and light chains whereas the latter randomly combines the matured heavy and light chains. Given a large enough phage library derived from a particular in vivo repertoire, the original matured heavy and light chains will be recombined. However, since one of the potential benefits of this new technology is to obviate the need for immunization by the generation of a single highly diverse “generic” phage library, it would be useful to have methods to optimize sequences to compensate for the absence of somatic mutation and clonal selection. Three procedures are made readily available through the methods of the present invention. First, saturation mutagenesis may be performed on the CDR's and the resulting Fabs can be assayed for increased function. Second, a heavy or a light chain of a clone which binds antigen can be recombined with the entire light or heavy chain libraries respectively in a procedure identical to the one used to construct the combinatorial library. Third, iterative cycles of the two above procedures can be performed to further optimize the affinity or catalytic properties of the immunoglobulin. It should be noted that the latter two procedures are not permitted in B-cell clonal selection which suggests that the methods described here may actually increase the ability to identify optimal sequences.
Access is the third area where it is of interest to compare the in vivo antibody repertoire and phage library. In practical terms the phage library is much easier to access. The screening methods allow one to survey at least 50,000 clones per plate so that 106 antibodies can be readily examined in a day. This factor alone should encourage the replacement of hybridoma technology with the methods described here. The most powerful screening methods utilize selection which may be accomplished by incorporating selectable markers into the antigen such as leaving groups necessary for replication of auxotrophic bacterial strains or toxic substituents susceptible to catalytic inactivation. There are also further advantages related to the fact that the in vivo antibody repertoire can only be accessed via immunization which is a selection on the basis of binding affinity. The phage library is not similarly restricted. For example, the only general method to identify antibodies with catalytic properties has been by pre-selection on the basis of affinity of the antibody to a transition state analogue. No such restrictions apply to the in vitro library where catalysis can, in principle, be assayed directly. The ability to directly assay large numbers of antibodies for function may allow selection for catalysts in reactions where a mechanism is not well defined or synthesis of the transition state analog is difficult. Assaying for catalysis directly eliminates the bias of the screening procedure for reaction mechanisms pejorative to a synthetic analog and therefore simultaneous exploration of multiple reaction pathways for a given chemical transformation are possible.
The methods disclosed herein describe generation of Fab fragments which are clearly different in a number of important respects from intact (whole) antibodies. There is undoubtedly a loss of affinity in having monovalent Fab antigen binders but this can be compensated by selection of suitably tight binders. For a number of applications such as diagnostics and biosensors it may be preferable to have monovalent Fab fragments. For applications requiring Fc effector functions, the technology already exists for extending the heavy chain gene and expressing the glycosylated whole antibody in mammalian cells.
The ideas presented here address the bottle neck in the identification and evaluation of antibodies. It is now possible to construct and screen at least three orders of magnitude more clones with mono-specificity than previously possible. The potential applications of the method should span basic research and applied sciences.
The foregoing is intended as illustrative of the present invention but not limiting. Numerous variations and modifications can be effected without departing from the true spirit and scope of the invention.

## Claims

1. A method of modifying the binding affinity of an antibody to an antigen, said method comprising providing an antibody comprising a heavy chain variable domain and a first light chain variable domain, which binds to said antigen, providing a nucleic acid encoding said heavy chain variable domain of said antibody, recombining the nucleic acid encoding said heavy chain variable domain with a library of at least 103 different light chain variable domain encoding nucleic acids, expressing said recombined nucleic acids in a host cell, and selecting an antibody having a modified binding affinity to said antigen relative to the antibody comprising said first light chain variable domain, wherein said antibody having modified binding affinity is encoded by said heavy chain variable domain encoding nucleic acid recombined with a second light chain variable domain encoding nucleic acid.

2. The method of claim 1 wherein said heavy chain variable domain is isolated from a subject immunized with an antigen and said library of at least 103 different light chain variable domain encoding nucleic acids is isolated from a subject not immunized with said antigen.

3. The method of claim 1 wherein said heavy chain variable domain and second light chain variable domain encoding nucleic acids encode an antibody with an increased affinity to said antigen relative to the antibody comprising the heavy chain variable domain and said first light chain variable domain.

4. A method of modifying the binding affinity of an antibody to an antigen, said method comprising providing an antibody comprising a light chain variable domain and a first heavy chain variable domain, which binds to said antigen, providing a nucleic acid encoding said light chain variable domain of said antibody, recombining the nucleic acid encoding said light chain variable domain with a library of at least 103 different heavy chain variable domain encoding nucleic acids, expressing said recombined nucleic acids in a host cell, and selecting an antibody having a modified binding affinity to said antigen relative to the antibody comprising said first heavy chain variable domain, wherein said antibody having modified binding affinity is encoded by said light chain variable domain encoding nucleic acid recombined with a second heavy chain variable domain encoding nucleic acid.

5. The method of claim 4 wherein said light chain variable domain is isolated from a subject immunized with an antigen and said library of at least 103 different heavy chain variable domain encoding nucleic acids is isolated from a subject not immunized with said antigen.

6. The method of claim 4 wherein said light chain variable domain and second heavy chain variable domain encoding nucleic acids encode an antibody with an increased affinity to said antigen relative to the antibody comprising the light chain variable domain and first heavy chain variable domain.

7. A method of isolating an antibody with modified binding affinity, comprising performing the method of claim 1 and recovering the antibody.

8. A method of isolating an antibody with modified binding affinity, comprising performing the method of claim 4 and recovering the antibody.