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  • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
  • C07K1/04—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length on carriers
  • C07K1/047—Simultaneous synthesis of different peptide species; Peptide libraries
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  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
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  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
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  • C07—ORGANIC CHEMISTRY
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  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
  • C07K16/18—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
  • C07K16/24—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against cytokines, lymphokines or interferons
  • C07K16/241—Tumor Necrosis Factors
  • C07K16/242—Lymphotoxin [LT]
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  • C07—ORGANIC CHEMISTRY
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  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
  • C07K16/18—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
  • C07K16/26—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against hormones ; against hormone releasing or inhibiting factors
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  • C07—ORGANIC CHEMISTRY
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  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
  • C07K16/18—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
  • C07K16/28—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
  • C07K16/2851—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the lectin superfamily, e.g. CD23, CD72
  • C07K16/2854—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the lectin superfamily, e.g. CD23, CD72 against selectins, e.g. CD62
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  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
  • C07K16/18—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
  • C07K16/28—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
  • C07K16/2896—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against molecules with a "CD"-designation, not provided for elsewhere
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  • C07—ORGANIC CHEMISTRY
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  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
  • C07K16/44—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material not provided for elsewhere, e.g. haptens, metals, DNA, RNA, amino acids
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  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
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  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
  • C12N15/1034—Isolating an individual clone by screening libraries
  • C12N15/1037—Screening libraries presented on the surface of microorganisms, e.g. phage display, E. coli display
• • C—CHEMISTRY; METALLURGY
  • C40—COMBINATORIAL TECHNOLOGY
  • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
  • C40B40/00—Libraries per se, e.g. arrays, mixtures
  • C40B40/02—Libraries contained in or displayed by microorganisms, e.g. bacteria or animal cells; Libraries contained in or displayed by vectors, e.g. plasmids; Libraries containing only microorganisms or vectors
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
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  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
  • C07K2317/21—Immunoglobulins specific features characterized by taxonomic origin from primates, e.g. man
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
  • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
  • C07K2317/565—Complementarity determining region [CDR]
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  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
  • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
  • C07K2317/622—Single chain antibody (scFv)
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  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2319/00—Fusion polypeptide

Definitions

• the present invention relates to synthetic DNA sequences which encode one or more collections of homologous proteins/(poly)peptides, and methods for generating and applying libraries of these DNA sequences.
• the invention relates to the preparation of a library of human-derived antibody genes by the use of synthetic consensus sequences which cover the structural repertoire of antibodies encoded in the human genome.
• the invention relates to the use of a single consensus antibody gene as a universal framework for highly diverse antibody libraries.
• the Winter invention does not provide a method for optimizing the binding affinities of antibody fragments further on, a process which would be functionally equivalent to the naturally occurring phenomenon of "affinity maturation", which is provided by the present invention. Furthermore, the Winter invention does not provide for artificial variable region genes, which represent a whole family of structurally similar natural genes, and which can be assembled from synthetic DNA oligonucleotides. Additionally, Winter does not enable the combinatorial assembly of portions of antibody variable regions, a feature which is provided by the present invention. Furthermore, this approach has the disadvantage that the genes of all antibodies obtained in the screening procedure have to be completely sequenced, since, except for the PCR priming regions, no additional sequence information about the library members is available. This is time and labor intensive and potentially leads to sequencing errors.
• the expressibility of the genes is important for the library quality as well, since the screening procedure relies in most cases on the display of the gene product on a phage surface, and efficient display relies on at least moderate expression of the gene.
• each gene is built up from modules which represent structural sub-elements on the protein/(poly)peptide level.
• the modules consist of "framework” and "CDR" modules.
• framework and CDR modules By creating separate framework and CDR modules, different combinatorial assembly possibilities are enabled.
• two or more artificial genes carry identical pairs of cleavage sites at the boundaries of each of the genetic sub-elements, pre-built libraries of sub-elements can be inserted in these genes simultaneously, without any additional information related to any particular gene sequence.
• DNA cassettes encoding libraries of genetic sub-elements can be (i), pre-built, stored and reused and (ii), inserted in any of these sequences at the right position without knowing the actual sequence or having to determine the sequence of the individual library member.
• the limited number of consensus sequences used for creating the library allows to speed up the identification of binding antibodies after screening. After having identified the underlying consensus gene sequence, which could be done by sequencing or by using fingerprint restriction sites, just those part(s) comprising the random sequence(s) have to be determined. This reduces the probability of sequencing errors and of false-positive results.
• cleavage sites can be used only if they are unique in the vector system where the artificial genes have been inserted. As a result, the vector has to be modified to contain none of these cleavage sites.
• the construction of a vector consisting of basic elements like resistance gene and origin of replication, where cleavage sites have been removed, is of general interest for many cloning attempts. Additionally, these vector(s) could be part of a kit comprising the above mentioned artificial genes and pre-built libraries.
• the collection of artificial genes can be used for a rapid humanization procedure of non-human antibodies, preferably . of rodent antibodies.
• the amino acid sequence of the non-human, preferably rodent antibody is compared with the amino acid sequences encoded by the collection of artificial genes to determine the most homologous light and heavy framework regions. These genes are then used for insertion of the genetic sub-elements encoding the CDRs of the non-human, preferably rodent antibody.
• one aspect of the present invention is the use of a single consensus sequence as a universal framework for the creation of useful (poly)peptide libraries and antibody consensus sequences useful therefor.
• the present invention enables the creation of useful libraries of (poly)peptides.
• the invention provides for a method of setting up nucleic acid sequences suitable for the creation of said libraries.
• a collection of at least three homologous proteins is identified and then analyzed. Therefore, a database of the protein sequences is established where the protein sequences are aligned to each other. The database is used to define subgroups of protein sequences which show a high degree of similarity in both the sequence and, if information is available, in the structural arrangement.
• a (poly)peptide sequence comprising at least one consensus sequence which represents the members of this subgroup; the complete collection of (poly)peptide sequences represent therefore the complete structural repertoire of the collection of homologous proteins.
• These artificial (poly)peptide sequences are then analyzed, if possible, according to their structural properties to identify unfavorable interactions between amino acids within said (poly)peptide sequences or between said or other (poly)peptide sequences, for example, in multimeric proteins. Such interactions are then removed by changing the consensus sequence accordingly.
• the (poly)peptide sequences are then analyzed to identify sub- elements such as domains, loops, helices or CDRs.
• the amino acid sequence is backtranslated into a corresponding coding nucleic acid sequence which is adapted to the codon usage of the host planned for expressing said nucleic acid sequences.
• a set of cleavage sites is set up in a way that each of the sub-sequences encoding the sub-elements identified as described above, is flanked by two sites which do not occur a second time within the nucleic acid sequence. This can be achieved by either identifying a cleavage site already flanking a sub-sequence of by changing one or more nucleotides to create the cleavage site, and by removing that site from the remaining part of the gene.
• the cleavage sites should be common to all corresponding sub-elements or sub-sequences, thus creating a fully modular arrangement of the sub-sequences in the nucleic acid sequence and of the sub-elements in the corresponding (poly)peptide.
• the invention provides for a method which sets up two or more sets of (poly)peptides, where for each set the method as described above is performed, and where the cleavage sites are not only unique within each set but also between any two sets.
• This method can be applied for the creation of (poly)peptide libraries comprising for example two ⁇ -helical domains from two different proteins, where said library is screened for novel hetero-association domains.
• at least two of the sets as described above are derived from the same collection of proteins or at least a part of it. This describes libraries comprising for example, but not limited to, two domains from antibodies such as VH and VL, or two extracellular loops of transmembrane receptors.
• nucleic acid sequences set up as described above are synthesized. This can be achieved by any one of several methods well known to the practitioner skilled in the art, for example, by total gene synthesis or by PCR-based approaches.
• the nucleic acid sequences are cloned into a vector.
• the vector could be a sequencing vector, an expression vector or a display (e.g. phage display) vector, which are well known to those skilled in the art.
• Any vector could comprise one nucleic acid sequence, or two or more nucleic sequences, either in different or the same operon. In the last case, they could either be cloned separately or as contiguous sequences.
• the removal of unfavorable interactions as described above leads to enhanced expression of the modified (poly)peptides.
• one or more sub-sequences of the nucleic acid sequences are replaced by different sequences. This can be achieved by excising the sub-sequences using the conditions suitable for cleaving the cleavage sites adjacent to or at the end of the sub--sequence, for example, by using a restriction enzyme at the corresponding restriction site under the conditions well known to those skilled in the art, and replacing the sub-sequence by a different sequence compatible with the cleaved nucleic acid sequence.
• the different sequences replacing the initial sub-sequence(s) are genomic or rearranged genomic sequences, for example in grafting CDRs from non-human antibodies onto consensus antibody sequences for rapid humanization of non-human antibodies.
• the different sequences are random sequences, thus replacing the sub-sequence by a collection of sequences to introduce variability and to create a library.
• the random sequences can be assembled in various ways, for example by using a mixture of mononucleotides or preferably a mixture of trinucleotides (Virnekas et al., 1 994) during automated oligonucleotide synthesis, by error-prone PCR or by other methods well known to the practitioner in the art.
• the random sequences may be completely randomized or biased towards or against certain codons according to the amino acid distribution at certain positions in known protein sequences. Additionally, the collection of random sub-sequences may comprise different numbers of codons, giving rise to a collection of sub-elements having different lengths.
• the invention provides for the expression of the nucleic acid sequences from a suitable vector and under suitable conditions well known to those skilled in the art.
• the (poly)peptides expressed from said nucleic acid sequences are screened and, optionally, optimized. Screening may be performed by using one of the methods well known to the practitioner in the art, such as phage-display, selectively infective phage, polysome technology to screen for binding, assay systems for enzymatic activity or protein stability.
• (Poly)peptides having the desired property can be identified by sequencing of the corresponding nucleic acid sequence or by amino acid sequencing or mass spectrometry.
• the nucleic acid sequences encoding the initially selected (poly)peptides can optionally be used without sequencing. Optimization is performed by repeating the replacement of sub-sequences by different sequences, preferably by random sequences, and the screening step one or more times.
• the desired property the (poly)peptides are screened for is preferably, but not exclusively, selected from the group of optimized affinity or specificity for a target molecule, optimized enzymatic activity, optimized expression yields, optimized stability and optimized solubility.
• the cleavage sites flanking the sub-sequences are sites recognized and cleaved by restriction enzymes, with recognition and cleavage sequences being either identical or different, the restricted sites either having blunt or sticky ends.
• the length of the sub-elements is preferably, but not exclusively ranging between 1 amino acid, such as one residue in the active site of an enzyme or a structure-determining residue, and 150 amino acids, as for whole protein domains. Most preferably, the length ranges between 3 and 25 amino acids, such as most commonly found in CDR loops of antibodies.
• the nucleic acid sequences could be RNA or, preferably, DNA.
• the (poly)peptides have an amino acid pattern characteristic of a particular species. This can for example be achieved by deducing the consensus sequences from a collection of homologous proteins of just one species, most preferably from a collection of human proteins. Since the (poly)peptides comprising consensus sequences are artificial, they have to be compared to the protein sequence(s) having the closest similarity to ensure the presence of said characteristic amino acid pattern.
• the invention provides for the creation of libraries of (poly)peptides comprising at least part of members or derivatives of the immunoglobulin superfamily, preferably of member or derivatives of the immnoglobuli ⁇ s.
• the invention provides for the creation of libraries of human antibodies, wherein said (poly)peptides are or are derived from heavy or light chain variable regions wherein said structural sub-elements are framework regions (FR) 1 , 2, 3, or 4 or complementary determining regions (CDR) 1 , 2, or 3.
• FR framework regions
• CDR complementary determining regions
• the database is used to define subgroups of antibody sequences which show a high degree of similarity in both the sequence and the canonical fold of CDR loops (as determined by analysis of antibody structures). For each of the subgroups a consensus sequence is deduced which represents the members of this subgroup; the complete collection of consensus sequences represent therefore the complete structural repertoire of human antibodies.
• genes are then constructed e.g. by total gene synthesis or by the use of synthetic genetic subunits.
• These genetic subunits correspond to structural sub-elements on the (poly)peptide level.
• On the DNA level these genetic subunits are defined by cleavage sites at the start and the end of each of the sub-elements, which are unique in the vector system. All genes which are members of the collection of consensus sequences are constructed such that they contain a similar pattern of corresponding genetic sub-sequences.
• said (poly)peptides are or are derived from the HuCAL consensus genes: V ⁇ 1 , V ⁇ 2, V ⁇ 3, V ⁇ 4, V ⁇ 1 , V ⁇ 2, V ⁇ 3, VH1A, VH1 B, VH2, VH3, VH4, VH5, VH6, C ⁇ , C ⁇ , CH1 or any combination of said HuCAL consensus genes.
• the invention provides a method for identifying one or more genes encoding one or more antibody fragments which binds to a target, comprising the steps of expressing the antibody fragments, and then screening them to isolate one or more antibody fragments which bind to a given target molecule.
• an scFv fragment library comprising the combination of HuCAL VH3 and HuCAL V ⁇ 2 consensus genes and at least a random sub-sequence encoding the heavy chain CDR3 sub-element is screened for binding antibodies.
• the modular design of the genes can then be used to excise from the genes encoding the antibody fragments one or more genetic subsequences encoding structural sub-elements, and replacing them by one or more second sub-sequences encoding structural sub-elements.
• the expression and screening steps can then be repeated until an antibody having the desired affinity is generated.
• Particularly preferred is a method in which one or more of the genetic subunits (e.g. the CDRs) are replaced by a random collection of sequences (the library) using the said cleavage sites. Since these cleavage sites are (i) unique in the vector system and (ii) common to all consensus genes, the same (pre-built) library can be inserted into all artificial antibody genes. The resulting library is then screened against any chosen antigen. Binding antibodies are selected, collected and used as starting material for the next library. Here, one or more of the remaining genetic subunits are randomized as described above.
• a further embodiment of the present invention relates to fusion proteins by providing for a DNA sequence which encodes both the (poly)peptide, as described above, as well as an additional moiety.
• Particularly preferred are moieties which have a useful therapeutic function.
• the additional moiety may be a toxin molecule which is able to kill cells (Vitetta et al., 1993).
• toxins well known to the one skilled in the art, such as the bacterial toxins Pseudomonas exotoxin A, and diphtheria toxin, as well as the plant toxins ricin, abrin, modeccin, saporin, and gelonin.
• the toxin can be targeted to, for example, diseased cells, and thereby have a beneficial therapeutic effect.
• the additional moiety may be a cytokine, such as IL-2 (Rosenberg & Lotze, 1986), which has a particular effect (in this case a T-cell proliferative effect) on a family of cells.
• the additional moiety may confer on its (poly)peptide partner a means of detection and/or purification.
• the fusion protein could comprise the modified antibody fragment and an enzyme commonly used for detection purposes, such as alkaline phosphatase (Blake et al., 1 984) .
• moieties which can be used as detection or purification tags, which are well known to the practitioner skilled in the art. Particularly preferred are peptides comprising at least five histidine residues (Hochuli et al., 1 988), which are able to bind to metal ions, and can therefore be used for the purification cf the protein to which they are fused (Lindner et al., 1992). Also provided for by the invention are additional moieties such as the commonly used C-myc and FLAG tags (Hopp et al., 1988; Knappik & Pluckthun, 1994).
• mini-antibodies are dimers comprising two antibody fragments, each fused to a self-associating dimerization domain.
• Dimerization domains which are particularly preferred include those derived from a leucine zipper (Pack & Pluckthun, 1 992) or helix-turn-helix motif (Pack et al., 1 993).
• the random collection of sub-sequences (the library) is inserted into a singular nucleic acid sequence encoding one (poly)peptide, thus creating a (poly)peptide library based on one universal framework.
• a random collection of CDR sub-sequences is inserted into a universal antibody framework, for example into the HuCAL H3 ⁇ 2 single-chain Fv fragment described above.
• the invention provides for nucleic acid sequence(s), vector(s) containing the nucleic acid sequence(s), host cell(s) containing the vector(s), and (poly)peptides, obtainable according to the methods described above.
• the invention provides for modular vector systems being compatible with the modular nucleic acid sequences encoding the (poly)peptides.
• the modules of the vectors are flanked by restriction sites unique within the vector system and essentially unique with respect to the restriction sites incorporated into the nucleic acid sequences encoding the (poly)peptides, except for example the restriction sites necessary for cloning the nucleic acid sequences into the vector.
• the list of vector modules comprises origins of single-stranded replication, origins of double-stranded replication for high- and low copy number plasmids, promotor/operator, repressor or terminator elements, resistance genes, potential recombination sites, gene III for display on filamentous phages, signal sequences, purification and detection tags, and sequences of additional moieties.
• the vectors are preferably, but not exclusively, expression vectors or vectors suitable for expression and screening of libraries.
• the invention provides for a kit, comprising one or more of the list of nucleic acid sequence(s), recombinant vector(s), (poly)peptide(s), and vector(s) according to the methods described above, and suitable host cell(s) for producing the (poly)peptide(s).
• the invention provides for the creation of libraries of human antibodies.
• a database of published antibody sequences of human origin is established.
• the database is used to define subgroups of antibody sequences which show a high degree of similarity in both the sequence and the canonical fold (as determined by analysis of antibody structures).
• a consensus sequence is deduced which represents the members of this subgroup; the complete collection of consensus sequences represent therefore the complete structural repertoire of human antibodies.
• genes are then constructed by the use of synthetic genetic subunits.
• These genetic subunits correspond to structural sub-elements on the protein level. On the DNA level, these genetic subunits are defined by cleavage sites at the start and the end of each of the subelements, which are unique in the vector system. All genes which are members of the collection of consensus sequences are constructed such that they contain a similar pattern of said genetic subunits.
• the invention provides a method for identifying one or more genes encoding one or more antibody fragments which binds to a target, comprising the steps of expressing the antibody fragments, and then screening them to isolate one or more antibody fragments which bind to a given target molecule.
• the modular design of the genes can then be used to excise from the genes encoding the antibody fragments one or more genetic subsequences encoding structural sub-elements, and replacing them by one or more second sub-sequences encoding structural sub-elements.
• the expression and screening steps can then be repeated until an antibody having the desired affinity is generated.
• Particularly preferred is a method in which one or more of the genetic subunits (e.g. the CDR's) are replaced by a random collection of sequences (the library) using the said cleavage sites. Since these cleavage sites are (i) unique in the vector system and (ii) common to all consensus genes, the same (pre-built) library can be inserted into all artificial antibody genes. The resulting library is then screened against any chosen antigen. Binding antibodies are eluted, collected and used as starting material for the next library. Here, one or more of the remaining genetic subunits are randomised as described above.
• protein comprises monomeric polypeptide chains as well as homo- or heteromultimeric complexes of two or more polypeptide chains connected either by covalent interactions (such as disulphide bonds) or by non-covalent interactions (such as hydrophobic or electrostatic interactions).
• the amino acid sequences of three or more proteins are aligned to each other (allowing for introduction of gaps) in a way which maximizes the correspondence between identical or similar amino acid residues at all positions.
• These aligned sequences are termed homologous if the percentage of the sum of identical and/or similar residues exceeds a defined threshold. This threshold is commonly regarded by those skilled in the art as being exceeded when at least 15% of the amino acids in the aligned genes are identical, and at least 30% are similar.
• families of homologous proteins are: immunoglobulin superfamily, scavenger receptor superfamily, fibronectin superfamilies (e.g. type II and III), complement control protein superfamily, cytokine receptor superfamily, cystine knot proteins, tyrosine kinases, and numerous other examples well known to one of ordinary skill in the art.
• the consensus sequence is that sequence which comprises the amino acids which are most frequently represented at each position. In the event that two or more amino acids are equally represented at a single position, the consensus sequence includes both or all of those amino acids.
• the consensus sequence is per se in most cases artificial and has to be analyzed in order to change amino acid residues which, for example, would prevent the resulting molecule to adapt a functional tertiary structure or which would block the interaction with other (poly)peptide chains in multimeric complexes.
• This can be done either by (i) building a three-dimensional model of the consensus sequence using known related structures as a template, and identifying amino acid residues within the model which may interact unfavorably with each other, or (ii) analyzing the matrix of aligned amino acid sequences in order to detect combinations of amino acid residues within the sequences which frequently occur together in one sequence and are therefore likely to interact with each other. These probable interaction-pairs are then tabulated and the consensus is compared with these "interaction maps". Missing or wrong interactions in the consensus are repaired accordingly by introducing appropriate changes in amino acids which minimize unfavorable interactions.
• Structural sub-elements are stretches of amino acid residues within a protein/(poly)peptide which correspond to a defined structural or functional part of the molecule. These can be loops (e.g. CDR loops of an antibody) or any other secondary or functional structure within the protein/(poly)peptide (domains, ⁇ -helices, ⁇ -sheets, framework regions of antibodies, etc.).
• a structural sub-element can be identified using known structures of similar or homologous (poly)peptides, or by using the above mentioned matrices of aligned amino acid sequences. Here the variability at each position is the basis for determining stretches of amino acid residues which belong to a structural sub-element (e.g. hypervariable regions of an antibody).
• a sub-sequence is defined as a genetic module which is flanked by unique cleavage sites and encodes at least one structural sub-element. It is not necessarily identical to a structural sub-element.
• a short DNA sequence which is used as a specific target for a reagent which cleaves DNA in a sequence-specific manner e.g. restriction endonucleases.
• Cleavage sites are compatible with each other, if they can be efficiently ligated without modification and, preferably, also without adding an adapter molecule.
• a cleavage site is defined as unique if it occurs only once in a vector containing at least one of the genes of interest, or if a vector containing at least one of the genes of interest could be treated in a way that only one of the cleavage sites could be used by the cleaving agent.
• a cleavage site in at least two corresponding sequences, which occurs at the same functional position (i.e. which flanks a defined sub-sequence), which can be hydrolyzed by the same cleavage tool and which yields identical compatible ends is termed a common cleavage site.
• a method which uses the unique cleavage sites and the corresponding cleavage reagents to cleave the target DNA at the specified positions in order to isolate, remove or replace the genetic sub-sequence flanked by these unique cleavage sites.
• the term expression refers to in vivo or in vitro processes, by which the information of a gene is transcribed into mRNA and then translated into a protein/(poly)peptide.
• the term expression refers to a process which occurs inside cells, by which the information of a gene is transcribed into mRNA and then into a protein.
• the term expression also includes all events of post-translational modification and transport, which are necessary for the (poly)peptide to be functional.
• a (poly)peptide sequence is assumed to exhibit an amino acid pattern characteristic for a species if it is deduced from a collection of homologous proteins from just this species.
• the IgSF is a family of proteins comprising domains being characterized by the immunoglobulin fold.
• the IgSF comprises for example T-cell receptors and the immunoglobulins (antibodies).
• Antibody framework
• a framework of an antibody variable domain is defined by Kabat et al. (1 991 ) as the part of the variable domain which serves as a scaffold for the antigen binding loops of this variable domain.
• the CDRs (complementarity determining regions) of an antibody consist of the antigen binding loops, as defined by Kabat et al. (1991 ). Each of the two variable domains of an antibody Fv fragment contain three CDRs.
• Antibody Library based on modular consensus genes according to the invention (see Example 1 ).
• antibody fragments are smaller than whole antibodies. Examples are Fv, disulphide-linked Fv, single-chain Fv (scFv), or Fab fragments. Additionally, antibody fragments are often engineered to include new functions or properties.
• binding A molecule or ligand or any part of a molecukle or ligand which is recognized by an antibody is called the target.
• the corresponding amino acid sequences of two or more genes are aligned to each other in a way which maximizes the correspondence between identical or similar amino acid residues at all positions.
• These aligned sequences are termed homologous if the percentage of the sum of identical and/or similar residues exceeds a defined threshold. This threshold is commonly regarded by those skilled in the art as being exceeded when at least 15 per cent of the amino acids in the aligned genes are identical, and at least 30 per cent are similar.
• Fig. 1 Flow chart outlining the process of construction of a synthetic human antibody library based on consensus sequences.
• Fig. 2 Alignment of consensus sequences designed for each subgroup (amino acid residues are shown with their standard one-letter abbreviation).
• A kappa sequences
• B lambda sequences
• C heavy chain sequences. The positions are numbered according to Kabat (1991 ). In order to maximize homology in the alignment, gaps (—) have been introduced in the sequence at certain positions.
• Fig. 3 Gene sequences of the synthetic V kappa consensus genes. The corresponding amino acid sequences (see Fig. 2) as well as the unique cleavage sites are also shown.
• Fig. 4 Gene sequences of the synthetic V lambda consensus genes. The corresponding amino acid sequences (see Fig. 2) as well as the unique cleavage sites are also shown.
• Fig. 5 Gene sequences of the synthetic V heavy chain consensus genes. The corresponding amino acid sequences (see Fig. 2) as well as the unique cleavage sites are also shown.
• Fig. 6 Oligonucleotides used for construction of the consensus genes.
• the oligos are named according to the corresponding consensus gene, e.g. the gene V ⁇ 1 was constructed using the six oligonucleotides 01 K1 to
• G1 K6 The oligonucleotides used for synthesizing the genes encoding the constant domains C ⁇ (OCLK1 to 8) and CH1 (OCH1 to 8) are also shown.
• Fig. 7 A/B Sequences of the synthetic genes encoding the constant domains C ⁇
• Fig. 7D Oligonucleotides used for synthesis of module M24.
• Fig. 8 Sequence and restriction map of the synthetic gene encoding the consensus single-chain fragment VH3-V ⁇ 2.
• the signal sequence (amino acids 1 to 21 ) was derived from the E. coli phoA gene (Skerra & Pluckthun, 1988). Between the phoA signal sequence and the VH3 domain, a short sequence stretch encoding 4 amino acid residues (amino acid 22 to 25) has been inserted in order to allow detection of the single- chain fragment in Western blot or ELISA using the monoclonal antibody M1 (Knappik & Pluckthun, 1994). The last 6 basepairs of the sequence were introduced for cloning purposes (EcoRI site).
• Fig. 9 Plasmid map of the vector plG10.3 used for phage display of the H3 ⁇ 2 scFv fragment.
• the vector is derived from plG10 and contains the gene for the lac operon repressor, lacl, the artificial operon encoding the H3 ⁇ 2- gene3ss fusion under control of the lac promoter, the Ipp terminator of transcription, the single-strand replication origin of the E. coli phage f1 (F1_ORI), a gene encoding ⁇ -lactamase (bla) and the ColEI derived origin of replication.
• Fig. 1 0 Sequencing results of independent clones from the initial library, translated into the corresponding amino acid sequences.
• A Amino acid sequence of the VH3 consensus heavy chain CDR3 (position 93 to 102, Kabat numbering).
• B Amino acid sequences of 12 clones of the 10-mer library.
• C Amino acid sequences of 1 1 clones of the 15-mer library, * : single base deletion.
• Fig. 1 1 Expression test of individual library members.
• A Expression of 9 independent clones of the 10-mer library.
• B Expression of 9 independent clones of the 15-mer library.
• the lane designated with M contains the size marker. Both the gp3-scFv fusion and the scFv monomer are indicated.
• Fig. 1 2 Enrichment of specific phage antibodies during the panning against FITC- BSA.
• the initial as well as the subsequent fluorescein-specific sub- libraries were panned against the blocking buffer and the ratio of the phage eluted from the FITC-BSA coated well vs. that from the powder milk coated well from each panning round is presented as the ..specificity factor".
• Fig. 1 3 Phage ELISA of 24 independent clones after the third round of panning tested for binding on FITC-BSA.
• Fig. 1 4 Competition ELISA of selected FITC-BSA binding clones.
• the ELISA signals (OD 405nm ) of scFv binding without inhibition are taken as 100%.
• Fig. 1 5 Sequencing results of the heavy chain CDR3s of independent clones after 3 rounds of panning against FITC-BSA, translated into the corresponding amino acid sequences (position 93 to 102. Kabat numbering).
• Fig. 1 6 Coomassie-Blue stained SDS-PAGE of the purified anti-fluorescein scFv fragments: M: molecular weight marker, A: total soluble cell extract after induction, B: fraction of the flow-through, C, D and E: purified scFv fragments 1 HA-3E4, 1 HA-3E5 and 1 HA-3E10, respectively.
• Fig. 1 7 Enrichment of specific phage antibodies during the panning against ⁇ - estradiol-BSA, testosterone-BSA, BSA, ESL-1 , interleukin-2, lymphotoxin- ⁇ , and LeY-BSA after three rounds of panning.
• Fig. 1 8 ELISA of selected ESL-1 and ⁇ -estradiol binding clones
• Fig. 1 9 Selectivity and cross-reactivity of HuCAL antibodies: in the diagonal specific binding of HuCAL antibodies can be seen, off-diagonal signals show non-specific cross-reactivity.
• Fig. 20 Sequencing results of the heavy chain CDR3s of independent clones after 3 rounds of panning against ⁇ -estradiol-BSA, translated into the corresponding amino acid sequences (position 93 to 102, Kabat numbering). One clone is derived from the 10mer library.
• Fig. 21 Sequencing results of the heavy chain CDR3s of independent clones after 3 rounds of panning against testosterone-BSA, translated into the corresponding amino acid sequences (position 93 to 102, Kabat numbering).
• Fig. 22 Sequencing results of the heavy chain CDR3s of independent clones after 3 rounds of panning against lymphotoxin- ⁇ , translated into the corresponding amino acid sequences (position 93 to 102, Kabat numbering).
• One clone comprises a 14mer CDR, presumably introduced by incomplete coupling of the trinucleotide mixture during oligonucleotide synthesis.
• Fig. 23 Sequencing results of the heavy chain CDR3s of independent clones after 3 rounds of panning against ESL-1 , translated into the corresponding amino acid sequences (position 93 to 102, Kabat numbering). Two clones are derived from the 10mer library. One clone comprises a 16mer CDR, presumably introduced by chain elongation during oligonucleotide synthesis using trinucleotides.
• Fig. 24 Sequencing results of the heavy chain CDR3s of independent clones after 3 rounds of panning against BSA, translated into the corresponding amino acid sequences (position 93 to 102, Kabat numbering).
• Fig. 25 Schematic representation of the modular pCAL vector system.
• Fig. 25a List of restriction sites already used in or suitable for the modular HuCAL genes and pCAL vector system.
• Fig. 26 List of the modular vector elements for the pCAL vector series: shown are only those restriction sites which are part of the modular system.
• Fig. 27 Functional map and sequence of the multi-cloning site module (MCS)
• Fig. 30 Functional map and sequence of the pCAL module M7-III (see Fig. 26).
• Fig. 32 Functional map and sequence of the pCAL module M1 1 -II (see Fig. 26).
• Fig. 34 Functional map and sequence of the pCAL module M17 (see Fig. 26).
• Fig. 35 Functional map and sequence of the modular vector pCAL4.
• Fig. 35a Functional maps and sequences of additional pCAL modules (M2, M3,
• Fig. 35b List of oligonucleotides and primers used for synthesis of pCAL vector modules.
• Fig. 36 Functional map and sequence of the ⁇ -lactamase cassette for replacement of CDRs for CDR library cloning.
• Fig. 37 Oligo and primer design for V ⁇ CDR3 libraries
• Fig. 38 Oligo and primer design for V ⁇ CDR3 libraries
• Fig. 39 Functional map of the pBS13 expression vector series.
• Fig. 40 Expression of all 49 HuCAL scFvs obtained by combining each of the 7
• VH genes with each of the 7 VL genes (pBS13, 30°C): Values are given for the percentage of soluble vs. insoluble material, the total and the soluble amount compared to the combination H3 ⁇ 2, which was set to 100%. In addition, the corresponding values for the McPC603 scFv are given.
• the following example describes the design of a fully synthetic human combinatorial antibody library (HuCAL), based on consensus sequences of the human immunoglobulin repertoire, and the synthesis of the consensus genes.
• the general procedure is outlined in Fig. 1 .
• VH V heavy chain
• V ⁇ V kappa
• V ⁇ V lambda
• the gene sequence was then translated into the corresponding amino acid sequence.
• all amino acid sequences were aligned according to Kabat et al. (1991 ).
• the numbering system of Chuchana et al. (1990) was used.
• the first sub base contained all sequences derived from rearranged V genes, where more than 70 positions of the sequence were known.
• the second sub base contained all germline gene segments (without the D- and J- minigenes; pseudogenes with internal stop codons were also removed). In all cases, where germline sequences with identical amino acid sequence but different names were found, only one sequence was used (see Table 1 ).
• the final databases of rearranged sequences contained 386, 149 and 674 entries for V ⁇ , V ⁇ and VH, respectively.
• the final databases of germline sequences contained 48, 26 and 141 entries for V ⁇ , V ⁇ and VH, respectively.
• the nearest germline counterpart i.e. the germline sequence with the smallest number of amino acid differences was then calculated.
• the number of somatic mutations which occurred in the rearranged gene and which led to amino acid exchanges could be tabulated.
• the germline counterpart could not be calculated exactly, because more than one germline gene was found with an identical number of amino acid exchanges.
• These rearranged sequences were removed from the database.
• the number of amino acid exchanges was found to be unusually large (>20 for VL and >25 for VH), indicating either heavily mutated rearranged genes or derivation from germline genes not present in the database.
• every rearranged gene could be arranged in one of the families established for the germline genes.
• the usage of each germline gene i.e. the number of rearranged genes which originate from each germline gene, could be calculated (see Table 2). It was found that the usage was strongly biased towards a subset of germline genes, whereas most of the germline genes were not present as rearranged genes in the database and therefore apparently not used in the immune system (Table 3). This observation had already been reported in the case of V ⁇ (Cox, et al., 1994). All germline gene families, where no or only very few rearranged counterparts could be assigned, were removed from the database, leaving 4 V ⁇ , 3 V ⁇ , and 6 VH families.
• the conformation of the antigen binding loops of antibody molecules, the CDRs, is strongly dependent on both the length of the CDRs and the amino acid residues located at the so-called canonical positions (Chothia & Lesk, 1987). It has been found that only a few canonical structures exist, which determine the structural repertoire of the immunoglobulin variable domains (Chothia et al., 1939). The canonical amino acid positions can be found in CDR as well as framework regions. The 13 used germline families defined above (7 VL and 6 VH) were now analyzed for their canonical structures in order to define the structural repertoire encoded in these families.
• V ⁇ 1 , 2 and 4 In 3 of the 4 V ⁇ families (V ⁇ 1 , 2 and 4), one different type of CDR1 conformation could be defined for every family.
• the family V ⁇ 3 showed two types of CDR1 conformation: one type which was identical to V ⁇ 1 and one type only found in V ⁇ 3. All V ⁇ CDR2s used the same type of canonical structure.
• the CDR3 conformation is not encoded in the germline gene segments. Therefore, the 4 V ⁇ families defined by sequence homology and usage corresponded also to 4 types of canonical structures found in V ⁇ germline genes.
• the 3 V ⁇ families defined above showed 3 types of CDR1 conformation, each family with one unique type.
• the V ⁇ 1 family contained 2 different CDR1 lengths (13 and 14 amino acids), but identical canonical residues, and it is thought that both lengths adopt the same canonical conformation (Chothia & Lesk, 1987).
• CDR2 of the used V ⁇ germlines only one canonical conformation exists, and the CDR3 conformation is not encoded in the germline gene segments. Therefore, the 3 V ⁇ families defined by sequence homology and usage corresponded also to 3 types of canonical structures.
• VH1 family All the members of the VH1 family defined above contained the CDR1 conformation H1 -1 , but differed in their CDR2 conformation: the H2-2 conformation was found in 6 germline genes, whereas the conformation H2-3 was found in 8 germline genes. Since the two types of CDR2 conformations are defined by different types of amino acid at the framework position 72, the VH1 family was divided into two subfamilies: VH1 A with CDR2 conformation H2-2 and VH1 B with the conformation H2-3. The members of the VH2 family all had the conformations H1 -3 and H2-1 in CDR1 and CDR2, respectively.
• the CDR1 conformation of the VH3 members was found in all cases to be H1 -1 , but 4 different types were found in CDR2 (H2-1 , H2-3, H2-4 and H2-x).
• the canonical framework residue 71 is always defined by an arginine. Therefore, it was not necessary to divide the VH3 family into subfamilies, since the 4 types of CDR2 conformations were defined solely by the CDR2 itself. The same was true for the VH4 family.
• all 3 types of CDR1 conformations were found, but since the CDR1 conformation was defined by the CDR itself (the canonical framework residue 26 was found to be glycine in all cases), no subdivisions were necessary.
• the CDR2 conformation of the VH4 members was found to be H2-1 in all cases. All members of the VH5 family were found to have the conformation H1 -1 and H2-2, respectively.
• the single germline gene of the VH6 family had the conformations H1 -3 and H2-5 in CDR1 and CDR2, respectively.
• the 14 databases of rearranged sequences (4 V ⁇ , 3 V ⁇ and 7 VH) were used to compute the HuCAL consensus sequences of each subgroup (4 HuCAL- V ⁇ , 3 HuCAL- V ⁇ , 7 HuCAL- VH, see Table 4, 5 and 6). This was done by counting the number of amino acid residues used at each position (position variability) and subsequently identifying the amino acid residue most frequently used at each position.
• the consensus was weighted according to the frequency of usage. Additionally, frequently mutated and highly conserved positions could be identified.
• the process described above provided the complete consensus sequences derived solely from the databases of rearranged sequences. It was rationalized that the CDR1 and CDR2 regions should be taken from the databases of used germline sequences, since the CDRs of rearranged and mutated sequences are biased towards their particular antigens. Moreover, the germline CDR sequences are known to allow binding to a variety of antigens in the primary immune response, where only CDR3 is varied. Therefore, the consensus CDRs obtained from the calculations described above were replaced by germline CDRs in the case of VH and V ⁇ . In the case of V ⁇ , a few amino acid exchanges were introduced in some of the chosen germline CDRs in order to avoid possible protease cleavage sites as well as possible structural constraints.
• any sequence could be chosen since these CDRs were planned to be the first to be replaced by oligonucleotide libraries.
• the dummy sequences QQHYTTPP and ARWGGDGFYAMDY were selected for the VL chains (kappa and lambda) and for the VH chains, respectively. These sequences are known to be compatible with antibody folding in E. coli (Carter et al., 1992).
• the final outcome of the process described above was a collection of 14 HuCAL amino acid sequences, which represent the frequently used structural antibody repertoire of the human immune system (see Figure 2). These sequences were back-translated into DNA sequences. In a first step, the back-translation was done using only codons which are known to be frequently used in E. coli. These gene sequences were then used for creating a database of all possible restriction endonuclease sites, which could be introduced without changing the corresponding amino acid sequences. Using this database, cleavage sites were selected which were located at the flanking regions of all sub-elements of the genes (CDRs and framework regions) and which could be introduced in all HuCAL VH, V ⁇ or V ⁇ genes simultaneously at the same position.
• restriction endonuclease sites were identified, which were not located at the flanking regions of the sub-elements but which could be introduced in every gene of a given group without changing the amino acid sequence. These cleavage sites were also introduced in order to make the system more flexible for further improvements. Finally, all but one remaining restriction endonuclease sites were removed in every gene sequence. The single cleavage site, which was not removed was different in all genes of a subgroup and could be therefore used as a "fingerprint" site to ease the identification of the different genes by restriction digest.
• the designed genes, together with the corresponding amino acid sequences and the group-specific restriction endonuclease sites are shown in Figure 3, 4 and 5, respectively.
• the consensus genes were synthesized using the method described by Prodromou & Pearl, 1992, using the oligonucleotides shown in Fig. 6. Gene segments encoding the human constant domains C ⁇ , C ⁇ and CH1 were also synthesized, based on sequence information given by Kabat et al., 1991 (see Fig. 6 and Fig. 7). Since for both the CDR3 and the framework. 4 gene segments identical sequences were chosen in all HuCAL V ⁇ , V ⁇ and VH genes, respectively, this part was constructed only once, together with the corresponding gene segments encoding the constant domains. The PCR products were cloned into pCR-Script KS(+) (Stratagene, Inc.) or pZErO-1 (Invitrogen, Inc.) and verified by sequencing.
• a combination of two of the synthetic consensus genes was chosen after construction to test whether binding antibody fragments can be isolated from a library based on these two consensus frameworks.
• the two genes were cloned as a single-chain Fv (scFv) fragment, and a VH-CDR3 library was inserted.
• scFv single-chain Fv
• VH-CDR3 library was inserted.
• FIT C-BSA small hapten fluorescem bound to BSA
• one randomly chosen combination of synthetic light and heavy gene (HuCAL-V ⁇ 2 and HuCAL-VH3) was used for the construction of a single-chain antibody (scFv) fragment.
• the gene segments encoding the VH3 consensus gene and the CH1 gene segment including the CDR3 - framework 4 region, as well as the V ⁇ 2 consensus gene and the C ⁇ gene segment including the CDR3 - framework 4 region were assembled yielding the gene for the VH3-CH 1 Fd fragment and the gene encoding the V ⁇ 2-C ⁇ light chain, respectively.
• the CH1 gene segment was then replaced by an oligonucleotide cassette encoding a 20-mer peptide linker with the sequence AGGGSGGGGSGGGGSGGGGS.
• the two oligonucleotides encoding this linker were 5'- TCAGCGGGTGGCGGTTCTGGCGGCGGTGGGAGCGGTGGCGGTGGTTC-TGGCGGTGGTGGTTCCGATATCGGTCCACGTACGG-3' and 5'-AATTCCGTACG-TGGACCGATATCGGAACCACCACCGCCAGAACCACCGCCACCGCTCCCACCGC CGCCAGAACCGCCACCCGC-3', respectively.
• the HuCAL-V ⁇ 2 gene was inserted via EcoRV and BsiWI into the plasmid encoding the HuCAL-VH3-iinker fusion, leading to the final gene HuCAL-VH3-V ⁇ 2, which encoded the two consensus sequences in the single-chain format VH-linker-VL.
• the complete coding sequence is shown in Fig. 8.
• Phagemid plG10.3 (Fig. 9) was constructed in order to create a phage-display system (Winter et al., 1994) for the H3 ⁇ 2 scFv gene. Briefly, the EcoRI/HindIII restriction fragment in the phagemid vector plG10 (Ge et al., 1995) was replaced by the c-myc followed by an amber codon (which encodes an glutamate in the amber-suppresser strain XL1 Blue and a stop codon in the non-suppresser strain JM83) and a truncated version of the gene III (fusion junction at codon 249, see Lowman et al., 1991 ) through PCR mutagenesis.
• Heavy chain CDR3 libraries of two lengths (10 and 15 amino acids) were constructed using trinucleotide codon containing oligonucleotides (Virnekas et al., 1994) as templates and the oligonucleotides complementing the flanking regions as primers.
• both phenylalanine and methionine were introduced at position 100 since these two residues were found to occur quite often in human CDR3s of this length (not shown).
• valine and tyrosine were introduced at position 102. All other randomized positions contained codons for all amino acids except cystein, which was not used in the trinucleotide mixture.
• the CDR3 libraries of lengths 10 and 15 were generated from the PCR fragments using oligonucleotide templates O3HCDR103T (5'- GATACGGCCGTGTATTA-TTGCGCGCGT (TRI) 6 GATTATTGGGGCCAAGGCACCCTG-3') and O3HCDR153T (5'-GATACGGCCGT GTATTATTGCGCGCGT(TRI) 10 (TTT/ATG)GAT(GTT/TAT)TGGG-GCCAAGGCACCCTG-3'), and primers O3HCDR35 (5'-GATACGGCCGTGTATTA-TTGC-3") and O3HCDR33 (5'-CAGGGTGCCTTGGCCCC-3'), where TRI are trinucleotide mixtures representing all amino acids without cystein, (TTT/ATG) and (GTT/TAT) are trinucleotide mixtures encoding the amino acids phenylalanine/methionine and valine/tyrosine, respectively.
• the potential diversity of these libraries was 4.7 ⁇ 10 7 and 3.4 ⁇ 10 10 for 10-mer and 15-mer library, respectively.
• the library cassettes were first synthesized from PCR amplification of the oligo templates in the presence of both primers: 25 pmol of the oligo template O3HCDR103T or O3HCDR153T, 50 pmol each of the primers 03HCDR35 and O3HCDR33, 20 nmol of dNTP, 10x buffer and 2.5 units of Pfu DNA polymerase (Stratagene) in a total volume of 100 ⁇ l for 30 cycles (1 minute at 92°C, 1 minute at 62°C and 1 minute at 72°C). A hot-start procedure was used.
• the resulting mixtures were phenol-extracted, ethanol-precipitated and digested overnight with Eagl and Styl.
• the vector plG10.3-scH3 ⁇ 2cat where the Eagl-Styl fragment in the vector plG10.3-scH3 ⁇ 2 encoding the H-CDR3 was replaced by the chloramphenicol acetyltransferase gene (cat) flanked with these two sites, was similarly digested.
• the digested vector 35 ⁇ g was gel-purified and ligated with 100 ⁇ g of the library cassette overnight at 16°C.
• the ligation mixtures were isopropanol precipitated, air-dried and the pellets were redissolved in 100 ⁇ l of ddH20.
• the ligation was mixed with 1 ml of freshly prepared electrocompetent XL1 Blue on ice. 20 rounds of electroporation were performed and the transformants were diluted in SOC medium, shaken at 37°C for 30 minutes and plated out on large LB plates (Amp/Tet/Glucose) at 37°C for 6-9 hrs.
• the number of transformant ⁇ (library size) was 3.2 ⁇ 10 7 and 2.3 ⁇ 10 7 for the 10-mer and the 15-mer library, respectively.
• the colonies were suspended in 2xYT medium (Amp/Tet/Glucose) and stored as glycerol culture.
• phagemids from 24 independent colonies (12 from the 10-mer and 12 from the 15-mer library, respectively) were isolated and analyzed by restriction digestion and sequencing.
• the restriction analysis of the 24 phagemids indicated the presence of intact vector in all cases.
• Sequence analysis of these clones indicated that 22 out of 24 contained a functional sequence in their heavy chain CDR3 regions.
• 1 out of 12 clones of the 10-mer library had a CDR3 of length 9 instead of 10
• 2 out of 12 clones of the 15-mer library had no open reading frame, thereby leading to a non-functional scFv; one of these two clones contained two consecutive inserts, but out of frame (data not shown). All codons introduced were presented in an even distribution.
• Phages displaying the antibody libraries were prepared using standard protocols. Phages derived from the 10-mer library were mixed with phages from the 1 5-mer library in a ratio of 20:1 (1 ⁇ 10 10 cfu/well of the 10-mer and 5x10 8 cfu/well of the 15-mer phages, respectively). Subsequently, the phage solution was used for panning in ELISA plates (Maxisorp, Nunc) coated with FITC-BSA (Sigma) at concentration of 100 ⁇ g/ml in PBS at 4°C overnight. The antigen-coated wells were blocked with 3% powder milk in PBS and the phage solutions in 1 % powder milk were added to each well and the plate was shaken at RT for 1 hr.
• the wells were then washed with PBST and PBS (4 times each with shaking at RT for 5 minutes).
• the bound phages were eluted with 0.1 M triethylamine (TEA) at RT for 10 minutes.
• TAA triethylamine
• the eluted phage solutions were immediately neutralized with 1/2 the volume of 1 M Tris-CI, pH 7.6.
• Eluted phage solutions (ca. 450 ⁇ l) were used to infect 5 m l of XL1 Blue cells at 37°C for 30 min.
• the infected cultures were then plated out on large LB plates (Amp/Tet/Glucose) and allowed to grow at 37°C until the colonies were visible.
• the colonies were suspended in 2xYT medium and the glycerol cultures were made as above described. This panning round was repeated twice, and in the third round elution was carried out with addition of fluorescein in a concentration of 100 ⁇ g/ml in PBS. The enrichment of specific phage antibodies was monitored by panning the initial as well as the subsequent fluorescein-specific sub-libraries against the blocking buffer (Fig. 1 2). Antibodies with specificity against fluorescein were isolated after 3 rounds of panning.
• One of the criteria for the successful biopanning is the isolation of individual phage clones that bind to the targeted antigen or hapten.
• 24 phagemid containing clones were used to inoculate 100 ⁇ l of 2xYT medium (Amp/Tet/Glucose) in an ELISA plate (Nunc), which was subsequently shaken at 37°C for 5 hrs. 100 ⁇ l of 2xYT medium (Amp/Tet/1 mM IPTG) were added and shaking was continued for 30 minutes.
• the heavy chain CDR3 region of 20 clones were sequenced in order to estimate the sequence diversity of fluorescein binding antibodies in the library (Fig. 1 5). In total, 16 of 20 sequences (80%) were different, showing that the constructed library contained a highly diverse repertoire of fluorescein binders.
• the CDR3s showed no particular sequence homology, but contained on average 4 arginine residues. This bias towards arginine in fluorescein binding antibodies had already been described by Barbas et al., 1992.
• BioLogic system Bio-Rad
• the ion-exchange column was one of the POROS ® HS, CM or HQ or PI 20 (PerSeptive Biosystems, Inc.) depended on the theoretical pi of the scFv being purified. The pH of all the buffers was adjusted to one unit lower or higher than the pi of the scFv being purified throughout.
• the sample was loaded onto the first IMAC column, washed with 7 column volumes of 20 mM sodium phosphate, 1 M NaCl and 10 mM imidazole. This washing was followed by 7 column volumes of 20 mM sodium phosphate and 10 mM imidazole.
• the concentration of the fragments was determined from the absorbance at 280 nm using the theoretically determined extinction coefficient (Gill & von Hippel, 1989).
• the scFv fragments could be purified to homogeneity (see Fig. 16).
• the yield of purified fragments ranged from 5 to 10 mg/L/OD.
• Example 2 In order to test the library used in Example 2 further, a new selection procedure was carried out using a variety of antigens comprising ⁇ -estradiol, testosterone, Lewis-Y epitope (LeY), interleukin-2 (IL-2), lymphotoxin- ⁇ (LT- ⁇ ), E-selectin ligand-1 (ESL-1 ), and BSA.
• Antigens comprising ⁇ -estradiol, testosterone, Lewis-Y epitope (LeY), interleukin-2 (IL-2), lymphotoxin- ⁇ (LT- ⁇ ), E-selectin ligand-1 (ESL-1 ), and BSA.
• the library and all procedures were identical to those described in Example 2.
• the ELISA plates were coated with ⁇ -estradiol-BSA (100 ⁇ g/ml), testosterone-BSA (100 ⁇ g/ml), LeY-BSA (20 ⁇ g/ml) IL-2 (20 ⁇ g/ml), ESL-1 (20 ⁇ g/ml) and BSA (100 ⁇ g/ml), LT- ⁇ (denatured protein, 20 ⁇ g/ml).
• bound phages were eluted with 0.1 M triethylamine (TEA) at RT for 10 minutes.
• TAA triethylamine
• Fig. 18 shows the specific binding of the antibodies to the antigen it was selected for, and the low cross-reactivity with the other four antigens.
• FIG. 25 shows a schematic representation of the pCAL vector system and the arrangement of vector modules and restriction sites therein.
• Figure 25a shows a list of all restriction sites which are already incorporated into the consensus genes or the vector elements as part of the modular system or which are not yet present in the whole system. The latter could be used in a later stage for the introduction of or within new modules.
• a series of vector modules was constructed where the restriction sites flanking the gene sub-elements of the HuCAL genes were removed, the vector modules themselves being flanked by unique restriction sites. These modules were constructed either by gene synthesis or by mutagenesis of templates. Mutagenesis was done by add-on PCR, by site-directed mutagenesis (Kunkel et al., 1 991 ) or multisite oligonucleotide-mediated mutagenesis (Sutherland et al., 1995; Perlak, 1990) using a PCR-based assembly method. Figure 26 contains a list of the modules constructed. Instead of the terminator module M9 (HindIII-Ipp-PacI), a larger cassette M9II was prepared to introduce FseI as additional restriction site. M9II can be cloned via HindIII/BsrGI.
• module M1 1 -II All vector modules were characterized by restriction analysis and sequencing.
• sequencing of the module revealed a two-base difference in positions 164/65 compared to the sequence database of the template. These two different bases (CA ⁇ GC) created an additional BanII site. Since the same two-base difference occurs in the f1 origin of other bacteriophages, it can be assumed that the two-base difference was present in the template and not created by mutagenesis during cloning. This BanII site was removed by site-directed mutagenesis, leading to module M1 1 -III.
• FIGS 29 to 34 are showing the functional maps and sequences of the modules used for assembly of the modular vector pCAL4 (see below).
• the functional maps and sequences of additional modules can be found in Figure 35a.
• Figure 35b contains a list of oligonucleotides and primers used for the synthesis of the modules.
• a cloning vector pMCS containing a specific multi-cloning site was constructed.
• an MCS cassette (Fig. 27) was made by gene synthesis. This cassette contains all those restriction sites in the order necessary for the sequential introduction of all vector modules and can be cloned via the 5'-HindIII site and a four base overhang at the 3'-end compatible with an AatII site.
• the vector pMCS ( Figure 28) was constructed by digesting pUC19 with AatII and HindIII, isolating the 2174 base pair fragment containing the bla gene and the ColE1 origin, and ligating the MCS cassette.
• Figure 35a is showing the functional maps and sequences of the vectors pCALO1 to pCALO3.
• a universal ⁇ -lactamase cloning cassette was constructed having a multi-cloning site at the 5'-end as well as at the 3'-end.
• the 5'-multi-cloning site comprises all restriction sites adjacent to the 5'-end of the HuCAL VH and VL CDRs
• the 3'-multi-cloning site comprises all restriction sites adjacent to the 3' end of the HuCAL VH and VL CDRs.
• Both 5'- and 3'-multi-cloning site were prepared as cassettes via add-on PCR using synthetic oligonucleotides as 5'- and 3'-primers using wild type ⁇ -lactamase gene as template.
• Figure 36 shows the functional map and the sequence of the cassette bla-MCS.
• VL-CDR3 libraries comprising 7 random positions were generated from the PCR fragments using oligonucleotide templates V ⁇ 1 &V ⁇ 3, V ⁇ 2 and V ⁇ 4 and primers O_K3L_5 and O_K3L_3 (Fig. 37) for the V ⁇ genes, and V ⁇ and primers O_L3L_5 (5'-GCAGAAGGCGAACGTCC-3') and O_L3LA_3 (Fig. 38) for the V ⁇ genes. Construction of the cassettes was performed as described in Example 2.3. 5.4 Cloning of HuCAL scFv genes with VL-CDR3 libraries
• Each of the 49 single-chains was subcloned into pCAL4 via XbaI/EcoRI and the VL-CDR3 replaced by the ⁇ -lactamase cloning cassette via Bbsl/MscI, which was then replaced by the corresponding VL-CDR3 library cassette synthesized as described above.
• This CDR replacement is described in detail in Example 2.3 where the cat gene was used.
• VH-CDR3 libraries were designed and synthesized as described in Example 2.3.
• Each of the 49 single-chain VL-CDR3 libraries was digested with BssHII/Styl to replace VH-CDR3.
• the "dummy" cassette digested with BssHII/Styl was inserted, and was then replaced by a corresponding VH-CDR3 library cassette synthesized as described above.
• E. coli JM83 was transformed 49 times with each of the vectors and stored as glycerol stock. Between 4 and 6 clones were tested simultaneously, always including the clone H3 ⁇ 2, which was used as internal control throughout. As additional control, the McPC603 scFv fragment (Knappik & Pluckthun, 1995) in pBS1 3 was expressed under identical conditions. Two days before the expression test was performed, the clones were cultivated on LB plates containing 30 ⁇ g/ml chloramphenicol and 60 mM glucose. Using this plates an 3 ml culture (LB medium containing 90 ⁇ g chloramphenicol and 60 mM glucose) was inoculated overnight at 37 °C.
• the overnight culture was used to inoculate 30 ml LB medium containing chloramphenicol (30 ⁇ g/ml).
• the starting OD 600nm was adjusted to 0.2 and a growth temperature of 30 °C was used.
• the physiology of the cells was monitored by measuring every 30 minutes for 8 to 9 hours the optical density at 600 n m .
• antibody expression was induced by adding IPTG to a final concentration of 1 mM.
• a 5 ml aliquot of the culture was removed after 2 h of induction in order to analyze the antibody expression.
• the cells were lysed and the soluble and insoluble fractions of the crude extract were separated as described in Knappik & Pluckthun, 1995.
• the fractions were assayed by reducing SDS-PAGE with the samples normalized to identical optical densities.
• the lanes were scanned and the intensities of the bands of the expected size (appr. 30 kDa) were quantified densitometrically and tabulated relative to the control antibody (see Fig. 40).
• a L-CDR3 library cassette was prepared from the oligonucleotide template CDR3L (5'-TGGAAGCTGAAGACGTGGGCGTGTATTATTGCCAGCAG(TR5)(TRI) 4 CCG(TRI)-TTTGGCCAGGGTACGAAAGTT-3') and primer 5'-AACTTTCGTACCCTGGCC-3' for synthesis of the complementary strand, where (TRI) was a trinucleotide mixture representing all amino acids except Cys, (TR5) comprised a trinucleotide mixture representing the 5 codons for Ala, Arg, His, Ser, and Tyr.
• a H-CDR2 library cassette was prepared from the oligonucleotide template CDRsH (5'-AGGGTCTCGAGTGGGTGAGC(TRI)ATT(TRI) 2-3 (6) 2 (TRI)ACC(TRI)TATGCGGATA-GCGTGAAAGGCCGTTTTACCATTTCACGTGATAATTCGAAAAACACCA-3'), and primer 5'-TGGTGTTTTTCGAATTATCA-3' for synthesis of the complementary strand, where (TRI) was a trinucleotide mixture representing all amino acids except Cys, (6) comprised the incorporation of (A/G) (A/C/G) T, resulting in the formation of 6 codons for Ala, Asn, Asp, Gly, Ser, and Thr, and the length distribution being obtained by performing one substoichiometric coupling of the (TRI) mixture during synthesis, omitting the capping step normally used in DNA synthesis.
• DNA was prepared from the collection of FITC binding clones obtained in Example 2 (approx. 10 4 to clones).
• the collection of scFv fragments was isolated via Xbal/EcoRI digest.
• the vector pCAL4 (100 fmole, 10 ⁇ g) described in Example 4.3 was similarly digested with Xbal/EcoRI, gel-purified and ligated with 300 fmole of the scFv fragment collection over night at 16°C.
• the ligation mixture was isopropanol precipitated, air-dried, and the pellets were redissolved in 100 ⁇ l of dd H 2 O.
• the ligation mixture was mixed with 1 ml of freshly prepared electrocompetent SCS 101 cells (for optimization of L-CDR3), or XL1 Blue cells (for optimization of H-CDR2) on ice.
• One round of electroporation was performed and the transformants were eluted in SOC medium, shaken at 37°C for 30 minutes, and an aliquot plated out on LB plates (Amp/Tet/Glucose) at 37°C for 6-9 hrs.
• the number of transformants was 5 x 10 4 .
• Vector DNA 100 ⁇ g was isolated and digested (sequence and restriction map of scH3 ⁇ 2 see Figure 8) with Bbsl/MscI for optimization of L-CDR3, or Xhol/NspV for optimization of H-CDR2.
• 10 ⁇ g of purified vector fragments (5 pmole) were ligated with 15 pmole of the L-CDR3 or H-CDR2 library cassettes over night at 16°C.
• the ligation mixtures were isopropanol precipitated, air-dried, and the pellets were redissolved in 100 ⁇ l of dd H 2 O.
• the ligation mixtures were mixed with 1 ml of freshly prepared electrocompetent XL1 Blue cells on ice.
• Electroporation was performed and the transformants were eluted in SOC medium and shaken at 37°C for 30 minutes. An aliquot was plated out on LB plates (Amp/Tet/Glucose) at 37°C for 6-9 hrs. The number of transformants (library size) was greater than 10 8 tor both libraries. The libraries were stored as glycerol cultures.

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