US20230340697A1

US20230340697A1 - Libraries of genetic packages comprising novel hc cdr1, cdr2, and cdr3 and novel lc cdr1, cdr2, and cdr3 designs

Info

Publication number: US20230340697A1
Application number: US18/160,407
Authority: US
Inventors: Robert Charles Ladner
Original assignee: Takeda Pharmaceutical Co Ltd
Current assignee: Takeda Pharmaceutical Co Ltd
Priority date: 2008-04-24
Filing date: 2023-01-27
Publication date: 2023-10-26
Also published as: ES2528963T3; EP2281078A4; JP2011518565A; WO2009132287A3; CA3049612C; EP2281078B1; US9388510B2; US20110172125A1; US20200347117A1; CA2722409C; PT2281078E; CA3049612A1; AU2009240481A1; CA2968164C; EP2281078A2; CY1116306T1; CA2968164A1; JP5780951B2; US20160355571A1; AU2009240481B2

Abstract

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

Description

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 16/838,910, filed Apr. 2, 2020, which is a divisional of U.S. application Ser. No. 15/177,199, filed Jun. 8, 2016, which is a continuation application of U.S. patent application Ser. No. 12/989,307, filed Mar. 10, 2011, which is a national phase application under 35 U.S.C. § 371 of International Application No. PCT/US2009/041688 filed Apr. 24, 2009, which claims priority to U.S. Application Ser. No. 61/047,529, filed on Apr. 24, 2008. The disclosure of the prior application is considered part of (and is incorporated by reference in) the disclosure of this application.

REFERENCE TO AN ELECTRONIC SEQUENCE LISTING

The contents of the electronic sequence listing (D061770049US04-SUBSEQ-KVC.xml; Size: 1,107,696 bytes; and Date of Creation: Jul. 13, 2023) is herein incorporated by reference in its entirety.

BACKGROUND

It is now common practice in the art to prepare libraries of genetic packages that individually display, display and express, or comprise a member of a diverse family of peptides, polypeptides or proteins and collectively display, display and express, or comprise at least a portion of the amino acid diversity of the family. In many common libraries, the peptides, polypeptides or proteins are related to antibodies (e.g., single chain Fv (scFv), Fv, Fab, whole antibodies or minibodies (i.e., dimers that consist of V_Hlinked to V_L)). Often, they comprise one or more of the CDRs and framework regions of the heavy and light chains of human antibodies.
Peptide, polypeptide or protein libraries have been produced in several ways. See, e.g., Knappik et al., J. Mol. Biol., 296, pp. 57-86 (2000), which is incorporated herein by reference. One method is to capture the diversity of native donors, either naive or immunized. Another way is to generate libraries having synthetic diversity. A third method is a combination of the first two. Typically, the diversity produced by these methods is limited to sequence diversity, i.e., each member of the library has the same length but differs from the other members of the family by having different amino acids or variegation at a given position in the peptide, polypeptide or protein chain. Naturally diverse peptides, polypeptides or proteins, however, are not limited to diversity only in their amino acid sequences. For example, human antibodies are not limited to sequence diversity in their amino acids, they are also diverse in the lengths of their amino acid chains.

SUMMARY

For antibodies, heavy chain diversity in length occurs, for example, during variable region rearrangements. See e.g., Corbett et al., J. Mol. Biol., 270, pp. 587-97 (1997). The joining of V genes to J genes, for example, results in the inclusion of a recognizable D segment in CDR3 in about half of the heavy chain antibody sequences, thus creating regions encoding varying lengths of amino acids. D segments are more common in antibodies having long HC CDR3s. The following also may occur during joining of antibody gene segments: (i) the end of the V gene may have zero to several bases deleted or changed; (ii) the end of the D segment may have zero to many bases removed or changed; (iii) a number of approximately random bases may be inserted between V and D or between D and J; and (iv) the 5′ end of J may be edited to remove or to change several bases. These rearrangements result in antibodies that are diverse both in amino acid sequence and in length. HC CDR3s of different lengths may fold into different shapes, giving the antibodies novel shapes with which to bind antigens. The conformations depend on both the length and the sequence of the CDR3. It should be remembered that a HC CDR3 of length 8, for example, and of any sequence cannot adequately mimic the behavior of a CDR3 of length 22, for example.
Libraries that contain only amino acid sequence diversity are, thus, disadvantaged in that they do not reflect the natural diversity of the peptide, polypeptide or protein that the library is intended to mimic. Further, diversity in length may be important to the ultimate functioning of the protein, peptide or polypeptide. For example, with regard to a library comprising antibody regions, many of the peptides, polypeptides, proteins displayed, displayed and expressed, or comprised by the genetic packages of the library may not fold properly or their binding to an antigen may be disadvantaged, if diversity both in sequence and length are not represented in the library.
An additional disadvantage of such libraries of genetic packages that display, display and express, or comprise peptides, polypeptides and proteins is that they are not focused on those members that are based on natural occurring diversity and thus on members that are most likely to be functional and least likely to be immunogenic. Rather, the libraries, typically, attempt to include as much diversity or variegation as possible at every CDR position. This makes library construction time-consuming and less efficient than necessary. The large number of members that are produced by trying to capture complete diversity also makes screening more cumbersome than it needs to be. This is particularly true given that many members of the library will not be functional or will be non-specifically sticky.
In addition to the labor of constructing synthetic libraries is the question of immunogenicity. For example, there are libraries in which all CDR residues are either Tyr (Y) or Ser (S). Although antibodies (Abs) selected from these libraries show high affinity and specificity, their very unusual composition may make them immunogenic. The present invention is directed toward making Abs that could well have come from the human immune system and so are less likely to be immunogenic. The libraries of the present invention retain as many residues from V-D-J or V-J fusions as possible. To reduce the risk of immunogenicity, it may be prudent to change each non-germline amino acid in both framework and CDRs back to germline to determine whether the change from germline is needed to retain binding affinity. Thus, a library that is biased at each varied position toward germline will reduce the likelihood of isolating Abs that have unneeded non-germline amino acids.
Abs are large proteins and are subject to various forms of degradation. One form of degradation is the deamidation of Asn and Gln residues (especially in Asn-Gly or Gln-Gly) and the isomerization of Asp residues. Another form of degration is the oxidation of methionines, tryptophan, and cysteine. Another form of degradation is the cleavage of Asp-Pro dipeptides. Another form of degradation is the formation of pyroglutamate from N-terminal Glu or Gln. It is advantageous to provide a library in which the occurrence of problematic sequences is minimized.
Provided are libraries of vectors or packages that encode members of a diverse family of human antibodies comprising heavy chain (HC) CDR3s that are between about 3 amino acids in length to about 35 amino acids in length. The HC CDR3s may also, in certain embodiments, may be rich in Tyr (Y) and Ser (S) and/or comprise diversified D regions and/or comprise extended JH regions. For example, the HC CDR3s may contain greater than about 40% (e.g., between about 43% and about 80%; e.g., greater than about 40% but less than about 100%) Y and/or S residues, e.g., as provided in the examples herein. Also provided are focused libraries comprising such HC CDR3s. Also provided are designs for HC CDR1, HC CDR2, and a library of VKIII A27 with diversity in the CDRs. A library of vectors or packages that encode members of a diverse family of human antibodies comprising HC CDR3s described herein can further have diversity at one or more (e.g., at one, two or three) of HC CDR1, HC CDR2, LC CDR1, LC CDR2, and LC CDR3. For example, the library can have diversity at one or more (e.g., at one, two or three) of HC CDR1, HC CDR2, LC CDR1, LC CDR2, and LC CDR3 as described herein.
A diversified D region is a D region into which one or more amino acid changes have been introduced (e.g., as compared to the sequence of a naturally occurring D region; for example, a stop codon can be changed to a Tyr residue).
An extended JH region is a JH region that has one or more amino acid residues present at the amino terminus of the framework sequence of the JH region (e.g., amino terminal to FR4 sequences, e.g., which commence with WGQ . . . ). For example, JH1 is an extended JH region. As other examples, JH2, JH3, JH4, JH5, and JH6 are extended JH regions.
Provided also are methods of making and screening the above libraries and the HC CDR3s and antibodies obtained in such screening. Compositions and kits for the practice of these methods are also described herein.
In some aspects, the disclosure features a focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins (e.g., a diverse family of antibodies) and collectively display, display and express, or comprise at least a portion of the diversity of the family, wherein the vectors or genetic packages comprise variegated DNA sequences that encode a heavy chain (HC) CDR3 selected from the group consisting of:

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

wherein the HC CDR3 comprises amino acids from a D region (e.g., a diversified D region) (or fragment thereof (e.g., 3 or more amino acids of the D region, e.g., diversified D region)) or a JH region (e.g., an extended JH region).
In some embodiments, the HC CDR3 is enriched in Tyr (Y) and Ser (S) (e.g., greater than 40% of the residues of the HC CDR3 are Y and/or S).
In some embodiments, the library (e.g., the vectors or genetic packages thereof) comprises a D region or a fragment of a D region (e.g., wherein the D region is adjacent to a JH region).
In some embodiments, the library comprises a JH region, e.g., an extended JH region.
In some embodiments, the HC CDR3 comprises amino acids from a D region or a fragment of a D region (e.g., wherein the D region is adjacent to a JH region).
In some embodiments, the D region is selected from the group consisting of D2-2 (RF 2), D2-8(RF 2), D2-15(RF 2), D2-21(RF 2), D3-16(RF 2), D3-22 (RF 2), D3-3 (RF-2), D3-9 (RF 2), D3-10 (RF 2), D1-26 (RF 3), D4-11 (RF 2), D4-4 (RF 2), D5-5 (RF 3), D5-12 (RF 3), D5-18 (RF 3), D6-6 (RF1), D6-13 (RF 1), and D6-19 (RF 1).
In some embodiments, the HC CDR3 comprises amino acids from a JH region. The JH region may be an extended JH region. In some embodiments, the extended JH region is selected from the group consisting of JH1, JH2, JH3, JH4, JH5, and JH6. In some embodiments, the JH region may be enriched in Y and/or S residues, for example, it may contain greater than about 40% (e.g., between about 43% and about 80%; e.g., greater than about 40% but less than about 100%) Y and/or S residues.
In some embodiments, the D region comprises one or more cysteine (Cys) residues and in some embodiments, the one or more Cys residues are held constant (e.g., are not varied).
In some embodiments, the HC CDR3 (e.g., the DNA encoding the HC CDR3) comprises one or more filling codons between FR3 and the D region and each filling codon is individually NNK, TMY, TMT, or TMC (TMY, TMT, or TMC encode S or Y).
In some embodiments, the HC CDR3 (e.g., the DNA encoding the HC CDR3) comprises one or more filling codons between the D region and JH and each filling codon is individually NNK, TMY, TMT, or TMC.
In some embodiments, the library (e.g., the vectors or genetic packages of the library) further comprises a HC CDR1, HC CDR2, and/or a light chain and also comprises diversity in the HC CDR1, HC CDR2, or light chain comprises diversity in HC CDR1 and/or HC CDR2, and/or a light chain (e.g., kappa or lambda light chain) (respectively). For example, HC CDR3 diversity can be constructed in the background of diversity in HC CDR1, HC CDR2, and/or light chains. For example, the light-chain diversity may be encoded in the same DNA molecule as the HC diversity or the LC and HC diversities may be encoded in separate DNA molecules.
In some aspects, the disclosure features a library comprising a HC CDR3 that is 3, 4, or 5 amino acids in length, wherein the CDR3 comprises amino acids from a JH region (e.g., extended JH region) or from a D region (e.g., a diversified D region) (or fragment thereof (e.g., 3 or more amino acids of the D region, e.g., diversified D region)) joined to the FR4 portion of a JH region.
In some embodiments, the HC CDR3 is from a D region joined to the FR4 portion of a JH region and comprises a trimer, a tetramer, or a pentamer, wherein the trimer, tetramer, or pentamer does not comprise a cysteine residue.
In some embodiments, the HC CDR3 is from a D region joined to the FR4 portion of a JH region and comprises a trimer, a tetramer, or a pentamer, wherein the trimer, tetramer, or pentamer does not comprise a stop codon.
In some embodiments, the D region (e.g., the DNA encoding the D region) comprises a TAG codon and the TAG codon is replaced by a codon selected from the group consisting of TCG, TTG, TGG, CAG, AAG, TAT, and GAG.
In some embodiments, the D region (e.g., the DNA encoding the D region) comprises a TAA codon and the TAA codon is replaced by a codon selected from the group consisting of TCA, TTA, CAA, AAA, TAT, and GAA.
In some embodiments, the D region (e.g., the DNA encoding the D region) comprises a TGA codon and the TGA codon is replaced by a codon selected from the group consisting of TGG, TCA, TTA, AGA, and GGA.
In some embodiments, the library further comprises diversity in HC CDR1 and/or HC CDR2, and/or a light chain (e.g., kappa or lambda light chain). For example, HC CDR3 diversity can be constructed in the background of diversity in HC CDR1, HC CDR2, and/or light chains. For example, the light-chain diversity may be encoded in the same DNA molecule as the HC diversity or the LC and HC diversities may be encoded in separate DNA molecules.
In some aspects, the disclosure provides a method of diversifying a library, the method comprising mutagenizing a library described herein.
In some embodiments, the mutagenizing comprises error-prone PCR.
In some embodiments, the mutagenizing comprises wobbling.
In some embodiments, the mutagenizing comprises dobbling.
In some embodiments, the mutagenizing introduces on average about 1 to about 10 mutations (e.g., about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10 mutations; e.g., base changes) per HC CDR3.
“Wobbling” is a method of making variegated DNA so that an original sequence is favored. If the original sequence had, for example, an Ala that could be encoded with GCT the mixture (0.7 G, 0.1 A, 0.1 T, 0.1 C) can be used for the first position, (0.7 C, 0.1 A, 0.1 T, 0.1 G) at the second position, and (0.7 T, 0.1 A, 0.1 G, 0.1 C) at the third. Other ratios of “doping” can be used. This allows Ala to appear about 50% of the time while V, D, G, T, P, and S occur about 7% of the time. Other AA types occur at lower frequency.
In some aspects, the present disclosure is drawn, e.g., to keeping a (purified) HC CDR1-2 repertoire, and building synthetic HC CDR3 and LC diversity.
In some embodiments, the disclosure provides a cassette for displaying a wobbled heavy chain (HC) CDR3, for example, wherein the cassette comprises the cassette shown in Table 400.
In some aspects, the present disclosure features a library in which Tyr levels are controlled in the HC CDR3. In some embodiments, the HC CDR3 regions contain about 15% or greater (e.g., about 16%, about 18%, about 20%, or greater) Tyr residues. In some embodiments, high levels (e.g., more than about 20%) of Tyr are inserted into the HC CDR3 of library members, e.g., at D regions and J stumps (or synthetic sequences corresponding thereto) that contain Tyr. In some embodiments, at leadin or DJ filler positions (or synthetic sequences corresponding thereto), Tyr is allowed, but at no more than 20%. In some embodiments, the HC CDR3 regions contain less than about 15% (e.g., about 14%, about 12%, about 10%, about 8%, about 6% or less) Tyr residues. In some embodiments, the HC leadin or DJ filler positions (or synthetic sequences corresponding thereto) contain less than about 15% (e.g., about 14%, about 12%, about 10%, about 8%, about 6% or less) Tyr residues.
In some aspects, the disclosure features a library of genetic packages that encode a human antibody heavy chain in which a parent amino-acid sequence comprises a VH sequence followed by zero to ten amino acids selected from the group consisting of (Y, S, D, L, R), followed by a human D-region or fragment of a D-region, followed by zero to ten amino acids selected from the group consisting of (Y,S,R,D,L), followed by a JH segment that comprises at least W103 onward wherein the variable DNA encoding this sequence is synthesized in a way that the parental amino-acid sequence is the most likely one (e.g., by wobbling).
In some aspects, the disclosure features a library of light chains having germline framework regions and wherein the CDRs are varied such that residues remote from the combining site or having buried side groups are held constant. In some embodiments, a method of variable DNA synthesis is used so that germline sequence is the most likely one (e.g., by wobbling).
In some aspects, the disclosure features a library of diverse members encoding antigen binding variable regions as disclosed herein.
In some aspects, the disclosure features a library of diverse members encoding HC CDR3 regions as disclosed herein. In some embodiments, the library is a library of Table 1097.
In some aspects, the disclosure features a library of diverse members, each member encoding comprising a HC CDR 3, wherein

- at least 1, 2, 3, 4, 5, 6, 7, or 8 positions in the HDCR3, respectively, is occupied by G, S, R, D, L, and Y in the library in the following proportions [1.0G, 0.57S, 0.46R, 0.42D, 0.36L, 0.35Y] and optionally,
- the last 4 positions of HC CDR3 are represented as follows:
- the parental amino acid is present at 3, 4, 5, 6, 7, 8, 10 times as likely as other amino-acid types, wherein the other amino-acid types comprise Y, S, D, R, G.

In some aspects, the disclosure features a library of diverse members, each member encoding comprising a HC CDR 3, wherein

- at least one and preferably all of the first 1, 2, 3, 4, 5, 6, 7, or 8 positions in the HC CDR3, is occupied by G, S, R, D, L, and Y, in the library in the following proportions [1.0G, 0.57S, 0.46R, 0.42D, 0.36L, 0.35Y] and optionally
- the last 4 positions of HCDR3 are represented as follows:
- the parental amino acid is present at 3, 4, 5, 6, 7, 8, 10 times as likely as other amino-acid types, wherein the other amino-acid types comprise Y, S, D, R, G.

In some aspects, the disclosure features a library of diverse members, each member encoding a HC CDR 3, wherein

- the length of HC CDR3 is 10, 11, or 12 positions;
- each of the first 6, 7, or 8 positions in the HC CDR3, respectively, is occupied by G, S, R, D, L, and Y in the library in the following proportions [1.0G, 0.57S, 0.46R, 0.42D, 0.36L, 0.35Y];
- the last 4 positions of HCDR3 are represented as follows:
- the parental amino acid is present at 3, 4, 5, 6, 7, 8, 10 times as likely as other amino-acid types, wherein the other amino-acid types comprise Y, S, D, R, G.

In some embodiments, each of the last 4 HC CDR3 positions is represented in the library as 7/12 parental, plus 1/12 each of Y, S, D, R, and G.
In some embodiments, each of the last 4 HC CDR3 positions is represented in the library as A6=7/12 A, plus 1/12 each of Y, S, D, R, and G; F7=7/12 F plus 1/12 each of Y, S, D, R, and G; D8=7/11 D plus 1/11 of Y, S, R, and G; I9=7/12 I plus 1/12 Y, S, R, D, G.
In some embodiments, the members further encode HC CDR1, HC CDR2.
In some embodiments, the members further encode Framework (FR) regions 1-4.
In some embodiments, the members encode HC CDR1, HC CDR2 and FR regions 1-4.
In some embodiments, the members comprise a 3-23 HC framework.
In some embodiments, the library further comprises a LC variable region.
In some embodiments, the library comprises members encoding diverse LC variable regions.
In some embodiments, the members comprising a LC variable region comprise an A27 LC framework.
In some embodiments, the library is a display library, e.g., a phage display library.
In some embodiments, the library has at least 10⁴, 10⁵10⁶, 10⁷, 10⁸, 10⁹10¹⁰, 10¹¹diverse members.
In some aspects, the disclosure features a method of selecting a library member, comprising, contacting a library described herein with a target, allowing a member to bind to said target, and recovering the member which binds the target.
These embodiments of the present invention, other embodiments, and their features and characteristics will be apparent from the description, drawings, and claims that follow.

DETAILED DESCRIPTION

Antibodies (“Ab”) concentrate their diversity into those regions that are involved in determining affinity and specificity of the Ab for particular targets. These regions may be diverse in sequence or in length. Generally, they are diverse in both ways. However, within families of human antibodies the diversities, both in sequence and in length, are not truly random. Rather, some amino acid residues are preferred at certain positions of the CDRs and some CDR lengths are preferred. These preferred diversities account for the natural diversity of the antibody family.
According to this invention, and as more fully described below, libraries of vectors and genetic packages that encode members of a diverse family of human antibodies comprising heavy chain (HC) CDR3s that are between about 3 to about 35 amino acids in length may be prepared and used. The HC CDR3s may also, in certain embodiments, may be rich in Y and S and/or comprise diversified D regions. Also provided are focused libraries comprising such HC CDR3s.
When an immune cell constructs an antibody heavy chain, it connects a V segment to a D segment and that to a J segment. The D segment is optional and about 50% of human Abs have recognizable Ds. The cell may perform considerable editing at the junction sites (V-to-D, D-to-J, or V-to-J) both removing and adding bases, but not exactly randomly. The initially rearranged antibody is presented on the surface of the cell and if it binds an antigen (Ag), the cell is stimulated to perform somatic mutations to improve the affinity. There are hot spots encoded in the immunoglobulin germline genes so that certain places in the Ab gene are very likely to go through a particular set of mutations in search of a better binder to a persistent Ag. In nature, some of the mutations are in framework positions but most are in the complementarity determining regions (CDRs). Of particular interest is the CDR3 of the heavy chain (HC) because it shows not only a high degree of sequence diversity but also length diversity. Antibody (Ab) libraries have been built in which the CDRs are replaced with random DNA, and useful Abs have been obtained. However, some therapeutic Abs show a significant degree of antigenicity. It is possible that Abs that are closer to human germline would be less antigenic.

Definitions

For convenience, before further description of the present invention, certain terms employed in the specification, examples and appended claims are defined here.
The singular forms “a”, “an”, and “the” include plural references unless the context clearly dictates otherwise.
The term “affinity” or “binding affinity” refers to the apparent association constant or K_a. The K_ais the reciprocal of the dissociation constant (K_d). A binding protein may, for example, have a binding affinity of at least 10⁵, 10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰and 10¹¹M⁻¹for a particular target molecule. Higher affinity binding of a binding protein to a first target relative to a second target can be indicated by a higher K_A(or a smaller numerical value K_D) for binding the first target than the K_A(or numerical value K_D) for binding the second target. In such cases, the binding protein has specificity for the first target (e.g., a protein in a first conformation or mimic thereof) relative to the second target (e.g., the same protein in a second conformation or mimic thereof; or a second protein). Differences in binding affinity (e.g., for specificity or other comparisons) can be at least 1.5, 2, 3, 4, 5, 10, 15, 20, 37.5, 50, 70, 80, 91, 100, 500, 1000, or 10⁵fold.
Binding affinity can be determined by a variety of methods including equilibrium dialysis, equilibrium binding, gel filtration, ELISA, surface plasmon resonance, or spectroscopy (e.g., using a fluorescence assay). Exemplary conditions for evaluating binding affinity are in TRIS-buffer (50 mM TRIS, 150 mM NaCl, 5 mM CaCl₂) at pH7.5). These techniques can be used to measure the concentration of bound and free binding protein as a function of binding protein (or target) concentration. The concentration of bound binding protein ([Bound]) is related to the concentration of free binding protein ([Free]) and the concentration of binding sites for the binding protein on the target where (N) is the number of binding sites per target molecule by the following equation:
[Bound]=N·[Free]/((1/K _A)+[Free]).
It is not always necessary to make an exact determination of K_A, though, since sometimes it is sufficient to obtain a quantitative measurement of affinity, e.g., determined using a method such as ELISA or FACS analysis, is proportional to K_A, and thus can be used for comparisons, such as determining whether a higher affinity is, e.g., 2-fold higher, to obtain a qualitative measurement of affinity, or to obtain an inference of affinity, e.g., by activity in a functional assay, e.g., an in vitro or in vivo assay.
The term “antibody” refers to a protein that includes at least one immunoglobulin variable domain or immunoglobulin variable domain sequence. For example, an antibody can include a heavy (H) chain variable region (abbreviated herein as VH), and a light (L) chain variable region (abbreviated herein as VL). In another example, an antibody includes two heavy (H) chain variable regions and two light (L) chain variable regions. Heavy chain and light chain may also be abbreviated as HC and LC, respectively. The term “antibody” encompasses antigen-binding fragments of antibodies (e.g., single chain antibodies, Fab and sFab fragments, F(ab′)₂, Fd fragments, Fv fragments, scFv, and domain antibodies (dAb) fragments (de Wildt et al., Eur J Immunol. 1996; 26(3):629-39.)) as well as complete antibodies. An antibody can have the structural features of IgA, IgG, IgE, IgD, IgM (as well as subtypes thereof). Antibodies may be from any source, but primate (human and non-human primate) and primatized are preferred.
The VH and VL regions can be further subdivided into regions of hypervariability, termed “complementarity determining regions” (“CDR”), interspersed with regions that are more conserved, termed “framework regions” (“FR”). The extent of the framework region and CDRs has been precisely defined (see, Kabat, E. A., et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242, and Chothia, C. et al. (1987) J. Mol. Biol. 196:901-917, see also www.hgmp.mrc.ac.uk). Kabat definitions are used herein. Each VH and VL is typically composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4.
The VH or VL chain of the antibody can further include all or part of a heavy or light chain constant region, to thereby form a heavy or light immunoglobulin chain, respectively. In one embodiment, the antibody is a tetramer of two heavy immunoglobulin chains and two light immunoglobulin chains, wherein the heavy and light immunoglobulin chains are inter-connected by, e.g., disulfide bonds. In IgGs, the heavy chain constant region includes three immunoglobulin domains, CH1, CH2 and CH3. The light chain constant region includes a CL domain. The variable region of the heavy and light chains contains a binding domain that interacts with an antigen. The constant regions of the antibodies typically mediate the binding of the antibody to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (Clq) of the classical complement system. The light chains of the immunoglobulin may be of types, kappa or lambda. In one embodiment, the antibody is glycosylated. An antibody can be functional for antibody-dependent cytotoxicity and/or complement-mediated cytotoxicity.
One or more regions of an antibody can be human or effectively human. For example, one or more of the variable regions can be human or effectively human. For example, one or more of the CDRs can be human, e.g., HC CDR1, HC CDR2, HC CDR3, LC CDR1, LC CDR2, and LC CDR3. Each of the light chain CDRs can be human. HC CDR3 can be human. One or more of the framework regions can be human, e.g., FR1, FR2, FR3, and FR4 of the HC or LC. For example, the Fc region can be human. In one embodiment, all the framework regions are human, e.g., derived from a human somatic cell, e.g., a hematopoietic cell that produces immunoglobulins or a non-hematopoietic cell. In one embodiment, the human sequences are germline sequences, e.g., encoded by a germline nucleic acid. In one embodiment, the framework (FR) residues of a selected Fab can be converted to the amino-acid type of the corresponding residue in the most similar primate germline gene, especially the human germline gene. One or more of the constant regions can be human or effectively human. For example, at least 70, 75, 80, 85, 90, 92, 95, 98, or 100% of an immunoglobulin variable domain, the constant region, the constant domains (CH1, CH2, CH3, CL), or the entire antibody can be human or effectively human.
All or part of an antibody can be encoded by an immunoglobulin gene or a segment thereof. Exemplary human immunoglobulin genes include the kappa, lambda, alpha (IgA1 and IgA2), gamma (IgG1, IgG2, IgG3, IgG4), delta, epsilon and mu constant region genes, as well as the many immunoglobulin variable region genes. Full-length immunoglobulin “light chains” (about 25 KDa or about 214 amino acids) are encoded by a variable region gene at the NH2-terminus (about 110 amino acids) and a kappa or lambda constant region gene at the COOH-terminus. Full-length immunoglobulin “heavy chains” (about 50 KDa or about 446 amino acids), are similarly encoded by a variable region gene (about 116 amino acids) and one of the other aforementioned constant region genes, e.g., gamma (encoding about 330 amino acids). The length of human HC varies considerably because HC CDR3 varies from about 3 amino-acid residues to over 35 amino-acid residues.
Herein, the terms “D segment” and “D region” are used interchangeably and are identical. It is to be understood that these items have both DNA and amino-acid representations and that which is meant is clear from the context.
A “library” or “display library” refers to a collection of nucleotide, e.g., DNA, sequences within clones; or a genetically diverse collection of polypeptides displayed on replicable display packages capable of selection or screening to provide an individual polypeptide or a mixed population of polypeptides.
The term “package” as used herein refers to a replicable genetic display package in which the particle is displaying a polypeptide at its surface. The package may be a bacteriophage which displays an antigen binding domain at its surface. This type of package has been called a phage antibody (pAb).
A “pre-determined target” refers to a target molecule whose identity is known prior to using it in any of the disclosed methods.
The term “replicable display package” as used herein refers to a biological particle which has genetic information providing the particle with the ability to replicate. The particle can display on its surface at least part of a polypeptide. The polypeptide can be encoded by genetic information native to the particle and/or artificially placed into the particle or an ancestor of it. The displayed polypeptide may be any member of a specific binding pair e.g., heavy or light chain domains based on an immunoglobulin molecule, an enzyme or a receptor etc. The particle may be, for example, a virus e.g., a bacteriophage such as fd or M13.
The term “vector” refers to a DNA molecule, capable of replication in a host organism, into which a gene is inserted to construct a recombinant DNA molecule. A “phage vector” is a vector derived by modification of a phage genome, containing an origin of replication for a bacteriophage, but not one for a plasmid. A “phagemid vector” is a vector derived by modification of a plasmid genome, containing an origin of replication for a bacteriophage as well as the plasmid origin of replication.
In discussing oligonucleotides, the notation “[RC]” indicates that the Reverse Complement of the oligonucleotide shown is the one to be used.
Human Antibody Heavy Chain CDR3s
The heavy chain (“HC”) Germ-Line Gene (GLG) 3-23 (also known as VP-47) accounts for about 12% of all human Abs and is preferred as the framework in the preferred embodiment of the invention. It should, however, be understood that other well-known frameworks, such as 4-34, 3-30, 3-30.3 and 4-30.1, may also be used without departing from the principles of the focused diversities of this invention.
In addition, JH4 (YFDYW₁₀₃GQGTLVTVSS (SEQ ID NO:1)) occurs more often than JH3 in native antibodies. Hence, it is preferred for the focused libraries of this invention. However, JH3 (AFDIW₁₀₃GQGTMVTVSS (SEQ ID NO:2)), JH6
(SEQ ID NO: 3)

(YYYYYGMDV W ₁₀₃ GQGTTVTVSS),

JH1, JH2, or JH5 could be used as well. JH2 has the advantage of having RG at 105-106 instead of QG in all the other human JHs. JH3 has the disadvantage of M₁₀₈. In a collection of 1419 Abs that were ELISA positive for at least one target, we saw 17 JH1s, 31 JH2s, 452 JH3s, 636 JH4s, 32 JH5s, and 251 JH6s. If present, the double underscored portions of the JHs are considered to be part of CDR3. In Table 3, the FR4 parts of the JHs are underscored.
The frequency at which each amino-acid appeared in the HC CDR3s of these 1419 Abs was tabulated and recorded in Table 75. Note that the most common amino acid is Tyr with Gly, Asp, Ser, and Arg following in that order. Rel. Up is the relative abundance of each type compared to Cys, the least common. Rel. Down is the abundance of each type compared to Tyr, the most common. Hence the preferred amino-acid types to substitute into HC CDR3s are Y, G, D, S, and R.
Naturally, HC CDR3s vary in length. About half of human HCs consist of the components: V::nz::D::ny::JHn where V is a V gene, nz is a series of bases that are essentially random, D is a D segment, often with heavy editing at both ends, ny is a series of bases that are essentially random, and JHn is one of the six JH segments, often with heavy editing at the 5′ end. The D segments appear to provide spacer segments that allow folding of the IgG. The greatest diversity is at the junctions of V with D and of D with JH.
Corbett et al. (Corbett S J, Tomlinson I M, Sonnhammer E L, Buck D, Winter G. J Mol Biol. 1997 V270:587-97.) showed that the human immune system does not insert multiple D segments and recombing D segments. Nevertheless, D segments have been selected to be good components of HC CDR3s and the present invention comprises HC CDR3 that contain more than one D segment.
Human D segments have some very strong biases. The tally of the 522 amino-acids in human D segments is Y 70 (13.4%), L 63 (12.1%), V 52 (10%), G 49 (9.4%), 141 (7.9%), T 40 (7.7%), S 33 (6.3%), W 27 (5.2%), D 21 (4%), A 19 (3.6%), R 16 (3.1%), TAG 15 (2.9%), N 14 2.7%), Q 11 (2.1%), C 9 (1.7%), E 9 (1.7%), F 8 (1.5%), M 8 (1.5%), TGA 8 (1.5%), TAA 7 (1.3%), P 1 (0.2%), H 1 (0.2%), and K 0 (0%). There is one D (2-8 RF 1) that has an unpaired Cys but also a TGA stop codon, so it is little used. Thus, D segments are primarily hydrophobic. The frequencies of amino acids in human HC CDR3s are shown in Table 75. There are both similarities and differences in the frequencies. In HC CDR3s overall, Tyr is the most common and only Gly comes close (96% as common as Tyr). Asp (75% as common as Tyr), Ser (53% as common as Tyr). Leu, Val, and Ile are relatively common in the D segments if all the D segments are counted as equal. The immune system does not use the D segments with equal frequency. Table 77 shows the frequency of utilization of D segments. The D segments that are often used are very rich in Tyr, Gly, Ser, and Asp. Arg is not found in the most often used D segments nor is Arg encoded in any of the CDR portions of JH segments. Arg comes to prominence either by mutation of V, D, and J or in the filler regions between V and D, D and J, or V and J. In this sample, 50% of all the amino acids are Tyr, Gly, Asp, Ser, or Arg. In one embodiment of the present invention, substitutions of “parental” HC CDR3 sequences is limited to the set of amino acids consisting of Tyr, Gly, Ser, Asp, and Arg. In one embodiment of the present invention, Arg is made common in the filler regions between V and D, between D and J, or between V and J.
In the preferred libraries of this invention, both types of HC CDR3s are used. In HC CDR3s that have no identifiable D segment, the structure is V::nz::JHn (n=1,6) where JH is usually edited at the 5′ end. In HC CDR3s that have an identifiable D segment, the structure is V::nz::D::ny::JHn.
Provided herein are HC CDR3s that are between about 3 to a about 35 amino acids in length. The HC CDR3s may also, in certain embodiments, be rich in Y and S and/or comprise diversified D regions, where a D region is present. For example, the HC CDR3s may contain between about 43% and about 80% Y and/or S residues, e.g., about 43%, about 48%, about 69%, about 63%, about 71%, about 62%, about 58%, about 68%, about 80%, about 77%, or greater than about 40%, or about 40% to less than about 100%, of the residues are Y and/or S. For example, not all of the residues in the CDR3 are Y and/or S. The HC CDR3s may, in certain embodiments, comprise an extended JH region. Exemplary HC CDR3 component designs of the preferred libraries of this invention are shown and described in Examples 1, 2, and 3.
In some embodiments, diversity (e.g., in a CDR, e.g., HC CDR3, or framework region (e.g., framework region near or adjacent to a CDR, e.g., CDR3, e.g., HC CDR3) is generated to create on average about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, or about 1 to about 10 mutations (e.g., base change), e.g., per CDR (e.g., HC CDR3) or framework region (e.g., framework region near or adjacent to a CDR, e.g., CDR3, e.g., HC CDR3). In some implementations, the mutagenesis is targeted to regions known or likely to be at the binding interface. Further, mutagenesis can be directed to framework regions near or adjacent to the CDRs. In the case of antibodies, mutagenesis can also be limited to one or a few of the CDRs, e.g., to make precise step-wise improvements. Likewise, if the identified ligands are enzymes, mutagenesis can provide antibodies that are able to bind to the active site and vicinity. The CDR or framework region (e.g., an HC CDR3 described herein) may be, in certain embodiments, subjected to error-prone PCR to generate the diversity. This approach uses a “sloppy” version of PCR, in which the polymerase has a fairly high error rate (up to 2%), to amplify the wild-type sequence, and is generally described in Pritchard, et al. (2005) J. Theor. Biol. 234: 497-509 and Leung et al. (1989) Technique 1:11-15. Other exemplary mutagenesis techniques include DNA shuffling using random cleavage (Stemmer (1994) Nature 389-391; termed “nucleic acid shuffling”), RACHITT™ (Coco et al. (2001) Nature Biotech. 19:354), site-directed mutagenesis (Zoller et al. (1987) Nucl Acids Res 10:6487-6504), cassette mutagenesis (Reidhaar-Olson (1991) Methods Enzymol. 208:564-586) and incorporation of degenerate oligonucleotides (Griffiths et al. (1994) EMBO J. 13:3245).
In some embodiments of the invention, D segments in which a majority of the residues are either Ser or Tyr are picked. In some embodiments, when the DNA encoding the D region is synthesized, each Ser or Tyr residue is encoded by TMT, TMC, or TMY so that the encoded amino acid is either Ser or Tyr.
In some embodiments, the HC CDR3 sequences described herein may be subjected to selection for open reading frames by fusing the sequence encoding the HC CDR3 of interest in frame to an antibiotic resistance gene, such as Kan^Rgene and selecting for kanamycin resistance. Cells in which the potential CDR3 has a stop codon or a frame shift will not have the antibiotic resistance and that sequence will be eliminated.
Methods of Construction of Libraries Comprising Human Antibody Heavy Chain CDR3s and Libraries Comprising Human Antibody Heavy Chain CDR3s
An antibody library is a collection of proteins that include proteins that have at least one immunoglobulin variable domain sequence. For example, camelized variable domains (e.g., VH domains) can be used as a scaffold for a library of proteins that include only one immunoglobulin variable domain sequence. In another example, the proteins include two variable domains sequences, e.g., a VH and VL domain, that are able to pair. An antibody library can be prepared from a nucleic acid library (an antibody-coding library) that includes antibody-coding sequences, e.g., comprising the sequences encoding the HC CDR3s provided herein.
In cases where a display library is used, each member of the antibody-coding library can be associated with the antibody that it encodes. In the case of phage display, the antibody protein is physically associated (directly or indirectly) with a phage coat protein. A typical antibody display library member displays a polypeptide that includes a VH domain and a VL domain. The display library member can display the antibody as a Fab fragment (e.g., using two polypeptide chains) or a single chain Fv (e.g., using a single polypeptide chain). Other formats can also be used.
As in the case of the Fab and other formats, the displayed antibody can include one or more constant regions as part of a light and/or heavy chain. In one embodiment, each chain includes one constant region, e.g., as in the case of a Fab. In other embodiments, additional constant regions are included. It is also possible to add one or more constant regions to a molecule after it is identified as having useful antigen binding site. See, e.g., US 2003-0224408.
Antibody libraries can be constructed by a number of processes (see, e.g., de Haard et al. (1999) J. Biol. Chem 274:18218-30; Hoogenboom et al. (1998) Immunotechnology 4:1-20, Hoogenboom et al. (2000) Immunol Today 21:371-8, and Hoet et al. (2005) Nat Biotechnol. 23(3):344-8.
In certain embodiments for constructing libraries, the heavy chains comprising the CDR3s described herein and the kappa and lambda light chains are best constructed in separate vectors. First, a synthetic gene is designed to embody each of the synthetic variable domains. The light chains may be bounded by restriction sites for ApaLI (positioned at the very end of the signal sequence) and AscI (positioned after the stop codon). The heavy chain may be bounded by SfiI (positioned within the PelB signal sequence) and NotI (positioned in the linker between CH1 and the anchor protein). Signal sequences other than PelB may also be used, e.g., a M13 pIII signal sequence.
The initial genes may be made with “stuffer” sequences in place of the desired CDRs. A “stuffer” is a sequence that is to be cut away and replaced by diverse DNA, but which does not allow expression of a functional antibody gene. For example, the stuffer may contain several stop codons and restriction sites that will not occur in the correct finished library vector. Stuffers are used to avoid have any one CDR sequence highly represented.
In another embodiment of the present invention, the heavy chain and the kappa or lambda light chains are constructed in a single vector or genetic packages (e.g., for display or display and expression) having appropriate restriction sites that allow cloning of these chains. The processes to construct such vectors are well known and widely used in the art. Preferably, a heavy chain and kappa light chain library and a heavy chain and lambda light chain library would be prepared separately.
Most preferably, the display is on the surface of a derivative of M13 phage. The most preferred vector contains all the genes of M13, an antibiotic resistance gene, and the display cassette. The preferred vector is provided with restriction sites that allow introduction and excision of members of the diverse family of genes, as cassettes. The preferred vector is stable against rearrangement under the growth conditions used to amplify phage.
In another embodiment of this invention, the diversity captured by the methods of the present invention may be displayed and/or expressed in a phagemid vector (e.g., pMID21 (DNA sequence shown in Table 35)) that displays and/or expresses the peptide, polypeptide or protein. Such vectors may also be used to store the diversity for subsequent display and/or expression using other vectors or phage.
In still other embodiments, a method termed the Rapid Optimization of LIght Chains or “ROLIC”, described in U.S. Ser. No. 61/028,265 filed Feb. 13, 2008, U.S. Ser. No. 61/043,938 filed Apr. 10, 2008, and U.S. Ser. No. 12/371,000 filed Feb. 13, 2009, a large population of LCs is placed in a phage vector that causes them to be displayed on phage. A small population (e.g., 3, 10, or 25) of HCs are cloned into E. coli so that the HCs are secreted into the periplasm, e.g., those HCs having the CDR3s described herein. The E. coli are then infected with the phage vectors encoding the large population of LCs to produce the HC/LC protein pairings on the phage. The phage particles carry only a LC gene.
In another aspect, in a method termed the Economical Selection of Heavy Chains or “ESCH”, also described in U.S. Ser. No. 61/028,265 filed Feb. 13, 2008, U.S. Ser. No. 61/043,938 filed Apr. 10, 2008, and U.S. Ser. No. 12/371,000 filed Feb. 13, 2009, a small population of LCs may be placed in a vector that causes them to be secreted. A new library of HCs in phage is constructed, such as those provided herein comprising the CDR3s. The LCs and HCs can then be combined by the much more efficient method of infection. Once a small set of effective HC are selected, these can be used as is, fed into ROLIC to obtain an optimal HC/LC pairing, or cloned into a Fab library of LCs for classical selection.
In another embodiment of this invention, the diversity captured by the methods of the present invention may be displayed and/or expressed using a vector suitable for expression in a eukaryotic cell, e.g., a yeast vector, e.g., for expression in a yeast cell.
Other types of protein display include cell-based display (see, e.g., WO 03/029,456); ribosome display (see, e.g., Mattheakis et al. (1994) Proc. Natl. Acad. Sci. USA 91:9022 and Hanes et al. (2000) Nat Biotechnol. 18:1287-92); protein-nucleic acid fusions (see, e.g., U.S. Pat. No. 6,207,446); and immobilization to a non-biological tag (see, e.g., U.S. Pat. No. 5,874,214).
Antibodies isolated from the libraries of the present disclosure may be analyzed to determine the type of the LC and the closest germline gene. In a preferred embodiment, non-germline framework residues are changed back to the germline amino acid so long as binding affinity and specificity are not adversely affected to an unacceptable extent. The substitutions may be done as a group or singly. Human germline sequences are disclosed in Tomlinson, I. A. et al., 1992, J. Mol. Biol. 227:776-798; Cook, G. P. et al., 1995, Immunol. Today 16 (5): 237-242; Chothia, D. et al., 1992, J. Mol. Bio. 227:799-817. The V BASE directory provides a comprehensive directory of human immunoglobulin variable region sequences (compiled by Tomlinson, I. A. et al. MRC Centre for Protein Engineering, Cambridge, UK). Antibodies are “germlined” by reverting one or more non-germline amino acids in framework regions to corresponding germline amino acids of the antibody, so long as binding properties are substantially retained. Similar methods can also be used in the constant region, e.g., in constant immunoglobulin domains.
For example, an antibody can include one, two, three, or more amino acid substitutions, e.g., in a framework, CDR, or constant region, to make it more similar to a reference germline sequence. One exemplary germlining method can include identifying one or more germline sequences that are similar (e.g., most similar in a particular database) to the sequence of the isolated antibody. Mutations (at the amino acid level) are then made in the isolated antibody, either incrementally or in combination with other mutations. For example, a nucleic acid library that includes sequences encoding some or all possible germline mutations is made. The mutated antibodies are then evaluated, e.g., to identify an antibody that has one or more additional germline residues relative to the isolated antibody and that is still useful (e.g., has a functional activity). In one embodiment, as many germline residues are introduced into an isolated antibody as possible.
In one embodiment, mutagenesis is used to substitute or insert one or more germline residues into a framework and/or constant region. For example, a germline framework and/or constant region residue can be from a germline sequence that is similar (e.g., most similar) to the non-variable region being modified. After mutagenesis, activity (e.g., binding or other functional activity) of the antibody can be evaluated to determine if the germline residue or residues are tolerated (i.e., do not abrogate activity). Similar mutagenesis can be performed in the framework regions.
Selecting a germline sequence can be performed in different ways. For example, a germline sequence can be selected if it meets a predetermined criteria for selectivity or similarity, e.g., at least a certain percentage identity, e.g., at least 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 99.5% identity. The selection can be performed using at least 2, 3, 5, or 10 germline sequences. In the case of CDR1 and CDR2, identifying a similar germline sequence can include selecting one such sequence. In the case of CDR3, identifying a similar germline sequence can include selecting one such sequence, but may include using two germline sequences that separately contribute to the amino-terminal portion and the carboxy-terminal portion. In other implementations, more than one or two germline sequences are used, e.g., to form a consensus sequence.
CDR1, CDR2, and Light-Chain Diversity
It is to be understood that the libraries of HC CDR3 are constructed in the background of diversity in HC CDR1, HC CDR2, and light chains. The light-chain diversity may be encoded in the same DNA molecule as the HC diversity or the LC and HC diversities may be encoded in separate DNA molecules. In Table 22 the fusion of a signal sequence:: VH::CH1::His6::Myc::IIIstump (His6 is disclosed as SEQ ID NO: 934). CDR1 comprises residues 31-35; there is diversity at residues 31, 33, and 35. In one embodiment, residues 31, 33, and 35 can be any amino-acid type except cysteine. CDR2 comprises residues 50 through 65. There is diversity at positions 50, 52, 52a, 56, and 58. In one embodiment, residues 50, and 52 can be any of the types Ser, Gly, Val, Trp, Arg, Tyr; residue 52a can be Pro or Ser and residues 56 and 58 can be any amino-acid type except Cys. The diversity of HC CDR3 is cloned into a diversity of HC CDR1 and 2 that is at least 1. E 4, 1. E 5, 1. E 6, 1.E 7, 5. E 7, or 1. E 8.
In one embodiment, residues 31, 33, 35, 50, 52, 56, and 58 can be any amino-acid type except Cys or Met and residue 52a can be Gly, Ser, Pro, or Tyr. The diversity of HC CDR3 is cloned into a diversity of HC CDR1 and 2 that is at least 1. E 4, 1. E 5, 1. E 6, 1. E 7, 5. E 7, or 1. E 8.
In one embodiment, the diversity of the HC is cloned into a vector (phage or phagemid) that contains a diversity of light chains. This diversity is at least 25, 50, 100, 500, 1. E 3, 1. E 4, 1. E 5, 1. E 6, or 1. E7. The diversity of HC CDR3 is at least 221, 272, 500, 1000, 1. E 4, 1. E 5, 1. E 6, 1. E7, 1. E 8, or 1. E 9.
In one embodiment, the diversity of the HC is cloned into a phage vector that displays the HC on a phage protein such as III, VIII, VII, VI, or IX or a fragment of one of these sufficient to cause display and light chains are combined with the HC by infecting a cell collection wherein each cell secrets a light chain. The diversity of the light chains in the cells is at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, or 100. The diversity of HC CDR3 is at least 221, 272, 500, 1000, 1. E 4, 1. E 5, 1. E 6, 1. E7, 1. E 8, or 1. E 9.
Table 30 shows the sequence of the phage vector DY3FHC87 (SEQ ID NO:894) which carries a bla gene, a display cassette for heavy chains under control of a P_lacpromoter. DY3FHC87 contains all the genes of M13 as well. Infecting F+ E. coli cells that harbor a diversity of light chains in a vector such as pLCSK23 (Sequence in Table 40) (SEQ ID NO:896). The vector pLCSK23 carries a Kan^Rgene. Under the control of Plac promoter, there is a gene beginning at base 2215 having a signal sequence (bases 2215-2277), a VL (in this sequence the VL encodes the sequence shown in (SEQ ID NO:897) from base 2278 to base 2598, Ckappa from base 2599 to 2922, a linker that allows an NotI site from 2923 to 2931, and a V5 tag (bases 2932-2973). There are an SfiI site at 2259-2271 and a KpnI site at 2602-2605 to allow easy replacement of Vkappas. (SEQ ID NO:897) is an example of the proteins that are secreted. It is to be understood that CKappa and the V5 tag are constant. All of the proteins shown in Table 19 (VK1O2gl-JK3, VK1O2var1, VK1O2var2, VK1O2var3, VK1O2var4, VK1O2var5, VK3L6gl-JK4, VK3L6var1, VK3L6var2, VK3L6var3, VK3L6var4, VK3L6var5, VK3L6var6, VK3L6var7, VK3L6var8, VK3A27gl-JK3, VK3A27var1, VK3A27var2, VK3A27var3, VK3A27var4, VK3A27var5, VK3A27var6, VK3A27var7, VK3L2gl-JK3, and VK1glL8-JK5) will have these sequences attached at the carboxy end.
Light Chain Diversity
Table 800 shows a kappa LC (light chain) that is known to pair well with 3-23 and with five CDR mutations with one HC based on 3-23, LC K1(012)::JK1 makes a high affinity Ab to a protein target. 012 is a frequently used VKI. The gene has been designed to have useful, distinct restriction sites in the signal sequence (ApaLI), FR1 (XhoI, SgfI), FR2 (KpnI), FR3(XbaI), and Fr4::Ckappa (BsiWI) so that each CDR and be replaced with a varied population.
In human LCs, CDR3 is most important and CDR1 is next most important. CDR2 seldom makes contact with the Ag. Diversity is introduced into the CDRs as shown in Table 900 and Table 1000 (CDR1), Table 1100 and Table 1200 (CDR2), Tables 1300, 1400, and 1500 (CDR3). For Economical Selection of Heavy Chains (ESHC), a small number, for example, 50 LCs with diversity in CDR3 as in Table 1200 are picked for expression in pLCSK24 for secretion into the periplasm. More LCs can be used if several cell lines are maintained so that each cell line contains, for example, 50 or fewer LC.
Table 900 shows diversity for LC CDR1. The library can contain the 012 residue with the added diversity of the AA types shown as “allowed”; reading “allowed” as “additional allowed types” in Tables 900, 1000, 1100, 1200, 1300, 1400. 012 has R₂₄ASQSISSYLN₃₄(SEQ ID NO: 935). Other VK1 loci have Q at 24. Other loci have M at 25. S₂₆and Q₂₇are invariant in VKI. Other VKI loci have D or G at 28. I₂₉and L₃₃are invariant in VKI and the side groups are oriented inward. Other VKI loci allow the diversity shown in Table 900 at positions 30, 31, 32, and 34. In Table 900, only seven of the eleven positions are varied and the total diversity is 576.
Table 1000 shows a higher level of diversity for LC CDR1. Here 8 of 11 positions have been varied. Those that are constant are either far from the combining site or have buried side groups.
Table 1100 shows a low level variegation for CDR2. CDR2 is far from the antigen combining site and diversity here may not be very useful. Indeed, the GL diversity is very limited. Table 1100 includes the GL diversity. Table 1200 contains a higher level of diversity, 1920 sequences allowed.
Table 1300 shows a low level of diversity for LC CDR3, 2160 sequences. Table 1400 shows a higher level which allows 105,840 sequences.
For ROLIC, about 3×10⁷LC are produced having the diversity shown in Tables 900, 1100, and 1300.
Heavy Chain Diversity
Ab HC (heavy chain) have diversity in CDR1, CDR2, and CDR3. The diversity in CDR3 is especially complex because there is both sequence and length diversity. The sequence diversity is not random. Cells making Ab genes join a V segment to a D segment to a JH segment. The D segment is optional; about half of natural human Abs have a recognizable D. There can be extensive editing at the V-D, D-J, or V-J boundaries with none to many bases added or removed. An Ab that has a germline V::D::JH could be viewed as a germline Ab.
Human D segments are shown in Table 21. Each germline (GL) D segment may appear in an Ab gene in any of the three forward reading frames. In some reading frames, some of the D segments encode stop codons. These D segments do occur rarely with the stop codon modified. Table 600 shows the frequency of each D segment as a percent of all observed D segments. Most of the examples herein that contain D segments use Ds that are fairly common (>2% of all observed Ds).
In one aspect, the present invention involves composing Ab HC genes by fusing 3-23 (or another VH, such as 4-34) to one of a) a number of amino acids picked from the set comprising (S, Y, D, R, N), b) a D region, c) a JH region, and d) the FR4 portion of a JH region. These fusions can be a GL 3-23 or a 3-23 that has synthetic diversity in CDR1 and/or CDR2. The lengths of the HC CDR3 and be any number from about 3 to about 24. Preferably, the library would contain member with HC CDR3 of lengths 6, 8, 10, 12, 14, 16, 18, and 20. Alternatively, the lengths could be 5, 8, 11, 14, 17, and 20 or any other combination.
Table 21 shows a number of examples of designs of suitable CDR3s with lengths from 6 to 20. The codons that specify the uppercase letters in column 2 are to be synthesized with wobbling. Column 3 shows the level of doping. Table 100 shows ratios in which the various lengths of HC CDR3 could be combined to form a library that is expected to contain Abs that bind almost all protein targets.

TABLE 100

Length	6	8	10	12	14	16	20
Diversity	1. ×	2. ×	4. × 10⁵	8. × 10⁵	8. × 10⁵	8. × 10⁵	4. × 10⁵
	10⁵	10⁵

For length 6, Table 21 four examples are given. For example, 6a has VH(3-23) joined directly to JH1 with the first six AAs wobbled, 6b has Tyr joined to D4-17 in second reading frame joined to the FR4 AAs of JH1, and 6c has D5-5(3) joined to the FR residues of JH1. Since these give different kinds of diversity, including all is preferred, but a library containing only one of these should give useful Abs.
For length 8, Table 21 shows three examples. 8a has YY fused to all of JH1 while 8b has one Y fused to D6-13(1) fused to the FR region of JH1. Lengths 10, 12, 14, 16, and 20 are also shown in Table 21. The HC CDR3 diversity could be built in a germline 3-23 or 3-23 containing synthetic diversity. Alternatively, a different VH, such as 4-34 could be used.
ROLIC is a method in which a small population of HCs are expressed in F⁺ E. coli as soluble proteins. The population is infected with phage that carry LC::III_stumpfusions. The phage produced obtain a HC from the periplasm of the cell that produces them. These phage can be bound to immobilized target and the binder are separated from the non-binders. The size of the population is important because when the recovered phage are propagated, the recovered phage must find the same type of cell as it came from to continue the association between LC and HC. Thus it is desirable that the number of HC be small in each cell line. Thus it may be desirable to maintain a number of cell lines with up to 10, 20, 30, or 40 different HC in each cell line. Thus we may have 1, 2, 4, 6, 8, 10, 24, 48, or 96 cell lines and we perform the same number of parallel phage productions, selections, and amplifications. After one or two rounds, we test colonies for production of phage that bind the target by an ELISA assay. Each ELISA⁺ colony contains a useful LC and a useful HC, but they are not on the same piece of DNA. Nevertheless, we know the start and end of each LC and each HC and can therefore use PCR on the colony to produce a Fab display or Fab secretion cassette that can be put into a display phage or phagemid or into a Fab-production plasmid.
In Efficient Selection of HCs (ESHC), we reverse the roles of LC and HC in ROLIC and have LCs in a plasmid so that they are produced as soluble proteins in the periplasm of F⁺ E. coli. We produce the HC diversity in a phage vector that has no LC gene. We infect the LC-producing F⁺ E. coli with the HC-carrying phage. We obtain phage that carry an HC gene and both HC and LC proteins. We select these phage for binding to the target. In many Abs, the LC is permissive and does not contribute greatly to binding affinity. Picking the best LC can greatly increase affinity, but it is usually possible to select a Fab with a very limited repertoire of LCs. Thus, we place a small set of LCs, preferable germline in the framework regions in the LC-producing F⁺ E. coli. If there are, for example, 25 LC in the LC cell line, then we obtain a 25-fold reduction in the number of cell transformants that need to be made.
The libraries described have a range of HC CDR3 lengths. To favor proper folding, the HC CDR3 have either a D segment or no D segment joined to most, all, or the framework portion of a JH segment. The sequences are diversified by using wobble DNA synthesis. Although this theoretically allows any amino-acid type at any position, in practice, the actual sequences are strongly biased toward the parental sequences and AA types that are close in the genetic code table.
By using ESHC, we can sample new designs of synthetic HC CDR3 diversity. In the examples given, we use a pool of, for example, 50 LCs. A library of 5×10⁸HC should perform as well as an old-style library of 2.5×10¹⁰but require far less effort.
When wobbling a sequence, picking the initial codons affects the actual mixture of AAs seen in the library. Table 300 shows which amino-acid substitutions require 1, 2, or 3 base changes from each starting parental codon. For example, if we start with get or gcc for Ala, all three stop codons require three base changes and so are rare. If using 76:8:8:8 mixtures, Ala will appear in 57% of the cases (0.76*0.76). V, G, T, P, S will each appear in about 6% and D about 3%. E, I, L, F, Y, H, N, C, and R will be down about 10-fold. M, W, Q, K, Am, Oc, and Op will be even rarer. If we started with gca, then E would replace D in needing only one base change, but opal and ochre stops require only two base changes, which is undesirable. The preferred codons are marked with a star (*). The choice for serine is complicate our desire to have Y substitute for S with high frequency. This brings Op and Oc into the group that differ from the parent by only two bases. This problem can be overcome by cloning the HC CDR3 repertoire before an antibiotic resistance gene such as KanR or AmpR and selecting for resistance, thus eliminating the members that contain stop codons. In addition, the library can be produced in supE E. coli which insert Q instead of stopping.

TABLE 300

Amino	Parental
acid	codon	1 base change	2 base changes	3 base changes

A *	gct, gcc	V, D, G, T, P, S	E, I, L, F, Y, H, N, C, R	M, W, Q, K, Am, Oc, Op
A	gca	V, E, G, T, P, S	D, I, L, Oc, Q, K, Op, R	M, W, H, N, C, Am, F, Y
A	gcg	V, E, G, T, P, S	D, M, L, Am, Q, K, R, W	I, F, Y, Oc, Op, H, N, C
C	tgt, tgc	Y, S, F, W, Op,	L, H, N, D, P, T, A, V, I	Am, Oc, Q, K, E, M
		R, G
D	gat, gac	E, G, A, V, N,	F, S, C, L, P, Q, K, R, Oc,	M, W, Op
		H, Y	Am, I, T
E	gaa	D, G, A, V, K,	Am, L, I, S, P, T, R, Op, Y,	M, F, C, W
		Q, Oc	H, N
E *	gag	D, G, A, V, K,	M, L, S, P, T, Y, H, N, Oc,	F, C, I, Op
		Q, Am	R, W
F	ttt, ttc	L, I, V, S, Y, C	M, Am, Op, Oc, W, P, T,	Q, K, E
			A, H, N, D, R, G
G *	ggt, ggc	D, A, V, S, R, C	E, W, F, L, I, T, P, Y, H, N	Am, Oc, Op, M, Q, K
G	gga	E, A, V, R, Oc	D, W, L, I, S, P, T, Op, Q,	Am, Oc, M, F, Y, H, N
			K
G	ggg	E, A, V, R, W	D, Oc, L, M, S, P, T, Am,	Oc, I, F, Y, H, N
			Op, Q, K
H	cat, cac	Q, Y, N, D, L,	F, S, C, I, T, V, A, D, G,	Op, W, M, E
		P, R	Am, Oc
I *	att, atc	M, L, F, V, T,	Y, C, P, H, R, A, D, G	Am, Op, Oc, W, Q, K, E
		N, S
I	ata	M, L, V, T, K, R	Op, Oc, S, P, Q, A, E, G, F,	Am, C, D, H, W, Y
			N
K	aaa	N, Q, Oc, E, P,	H, Y, D, M, L, V, S, T, A,	C, F, W
		I, R	Am, Op, G
K *	aag	N, Q, Am, E, P,	H, Y, D, I, L, V, S, T, A,	C, F, Op
		M, R	Oc, G, W
L	tta	F, S, Oc, Op, I,	Y, C, W, M, P, T, A, Q, K,	D, H, N
		V	E, R, G, Am
L	ttg	F, S, Am, W, M,	Y, C, Oc, Op, P, T, A, Q,	D, H, N
		V	K, E, R, G, I
L *	ctt, ctc	F, I, V, P, H, R	M, S, Y, C, T, N, A, D, G	Am, Oc, Op, W, E, K, Q
L	cta	I, V, P, Q, R	F, M, S, Oc, Op, T, K, A, E,	Am, W, D, N, C, Y
			G, H
L	ctg	M, V, P, Q, R	F, I, S, Am, T, K, A, E, G,	Oc, Op, D, N, C, Y
			H, W
M	atg	L, V, T, K, R, I	F, N, S, P, A, Am, Q, E, W,	Oc, Op, Y, C, H, D
			G
N	aat, aac	K, Y, H, D, I, T,	F, C, L, P, R, V, A, G, M,	Op, W
		S	Q, E, Am, Oc
P *	cct, ccc	S, T, A, L, H, R	F, Y, C, I, N, V, D, G, Q	Am, Oc, Op, W, M, E, K
P	cca	S, T, A, L, Q, R	Oc, Op, I, K, V, E, G, H	Am, W, M, D, N, C, F, Y
P	ccg	S, T, A, L, Q, R	Am, M, K, V, E, G, H	C, D, F, I, N, W, Y, Oc, Op
Q	caa	Oc, K, E, R, P,	Y, Am, N, D, S, T, A, I, V,	F, C, W, M
		L, H	G, Op
Q *	cag	H, Am, K, E, R,	N, D, Y, M, T, V, A, G, W,	C, F, Op, I
		P, L	Oc, S
R *	cgt, cgc	C, S, G, H, P, L	Op, W, Q, F, Y, I, T, N, V,	Am, Oc, M, E, K
			A, D
R	cga	G, Op, Q, P, L	Oc, S, C, W, H, I, V, T, A,	Am, M, C, D, N, F, Y
			E, K
R	cgg	G, W, Q, P, L	Am, Op, S, M, V, T, A, K,	F, Y, I, Oc, D, N
			E, H, C
R	aga	G, Op, S, K, T, I	C, W, N, M, L, V, P, A, Oc,	F, Y, H, D, Am
			Q, E
R	agg	G, W, S, K, T,	C, Op, Am, L, I, V, A, Q,	F, Y, H, D, Oc
		M	P, E, N
S *	tct, tcc	F, Y, C, P, T, A	L, Oc, Op, Am, W, I, V, N,	E, K, M, Q
			D, R, G, H
S	tca	L, Oc, Op, P, T,	F, Y, C, W, Q, R, I, K, V, E,	M, W, D, N, H
		A	G, Am
S	tcg	L, Am, W, P, T,	F, Y, C, Op, Oc, Q, R, M,	I, D, N, H
		A	K, V, E, G
S	agt, agc	C, R, G, N, T, I	F, Y, L, P, H, V, A, D, K,	Am, Oc, M, E, Q
			W, Op
T *	act, acc	S, P, A, I, N	F, Y, C, L, H, R, M, K, V,	Am, Oc, Op, W, E, Q
			D, G
T	aca	S, P, A, I, K, R	L, Oc, Op, Q, M, E, G, V,	F, Y, C, Am, W, D, H
			N
T	acg	S, P, A, M, K, R	I, N, L, Am, W, Q, V, E, G	C, F, Y, Oc, Op, D, H
V *	gtt, gtc	F, L, I, A, D, G	S, P, T, Y, H, N, E, C, R, M	Am, Oc, Op, W, Q, K
V	gta	L, I, A, E, G	F, M, D, S, P, T, Oc, Op, Q,	Am, W, C, Y, H, N
			R, K
V	gtg	L, M, A, E, G	F, I, D, S, P, T, Am, Q, R,	Oc, Op, C, Y, H, N
			K, W
W	tgg	C, R, G, Am, S,	P, Q, F, M, T, K, V, A, E,	D, N, H, I
		L, Op	Oc, Y
Y	tat, tac	C, S, F, N, H,	L, W, Q, K, E, P, I, T, V, A,	M
		D, Oc, Am	G, Op, R

Am is TAG stop,
Op is TGA,
Oc is TAA

Methods of Using the Libraries
Off-Rate Selection. Since a slow dissociation rate can be predictive of high affinity, particularly with respect to interactions between polypeptides and their targets, the methods described herein can be used to isolate ligands with a desired kinetic dissociation rate (i.e., reduced) for a binding interaction to a target.
To select for slow dissociating antibodies from a display library, the library is contacted to an immobilized target. The immobilized target is then washed with a first solution that removes non-specifically or weakly bound antibodies. Then the bound antibodies are eluted with a second solution that includes a saturating amount of free target, i.e., replicates of the target that are not attached to the particle. The free target binds to antibodies that dissociate from the target. Rebinding of the eluted antibodies is effectively prevented by the saturating amount of free target relative to the much lower concentration of immobilized target.
The second solution can have solution conditions that are substantially physiological or that are stringent (e.g., low pH, high pH, or high salt). Typically, the solution conditions of the second solution are identical to the solution conditions of the first solution. Fractions of the second solution are collected in temporal order to distinguish early from late fractions. Later fractions include antibodies that dissociate at a slower rate from the target than biomolecules in the early fractions. Further, it is also possible to recover antibodies that remain bound to the target even after extended incubation. These can either be dissociated using chaotropic conditions or can be amplified while attached to the target. For example, phage bound to the target can be contacted to bacterial cells.
Selecting or Screening for Specificity. The display library screening methods described herein can include a selection or screening process that discards antibodies that bind to a non-target molecule. Examples of non-target molecules include, e.g., a carbohydrate molecule that differs structurally from the target molecule, e.g., a carbohydrate molecule that has a different biological property from the target molecule. In the case of a sulfated carbohydrate, a non-target may be the same carbohydrate without the sulfate or with the sulfate in a different position. In the case of a phosphopeptide, the non-target may be the same peptide without the phosphate or a different phosphopeptide.
In one implementation, a so-called “negative selection” step is used to discriminate between the target and related non-target molecule and a related, but distinct non-target molecules. The display library or a pool thereof is contacted to the non-target molecule. Members that do not bind the non-target are collected and used in subsequent selections for binding to the target molecule or even for subsequent negative selections. The negative selection step can be prior to or after selecting library members that bind to the target molecule.
In another implementation, a screening step is used. After display library members are isolated for binding to the target molecule, each isolated library member is tested for its ability to bind to a non-target molecule (e.g., a non-target listed above). For example, a high-throughput ELISA screen can be used to obtain this data. The ELISA screen can also be used to obtain quantitative data for binding of each library member to the target. The non-target and target binding data are compared (e.g., using a computer and software) to identify library members that specifically bind to the target.
In certain embodiments, the antibodies comprising the CDR3s of the invention may be able to bind carbohydrates. Methods for evaluating antibodies for carbohydrate binding include ELISA, immunohistochemistry, immunoblotting, and fluorescence-activated cell sorting. These methods can be used to identify antibodies which have a K_Dof better than a threshold, e.g., better than 100 nM, 50 nM, 10 nM, 5 nM, 1 nM, 500 pM, 100 pM, or 10 pM.
ELISA. Proteins encoded by a display library can also be screened for a binding property using an ELISA assay. For example, each protein is contacted to a microtitre plate whose bottom surface has been coated with the target, e.g., a limiting amount of the target. The plate is washed with buffer to remove non-specifically bound polypeptides. Then the amount of the protein bound to the plate is determined by probing the plate with an antibody that can recognize the polypeptide, e.g., a tag or constant portion of the polypeptide. The antibody is linked to an enzyme such as alkaline phosphatase, which produces a calorimetric product when appropriate substrates are provided. The protein can be purified from cells or assayed in a display library format, e.g., as a fusion to a filamentous bacteriophage coat. Alternatively, cells (e.g., live or fixed) that express the target molecule, e.g., a target that contains a carbohydrate moiety, can be plated in a microtitre plate and used to test the affinity of the peptides/antibodies present in the display library or obtained by selection from the display library.
In another version of the ELISA assay, each polypeptide of a diversity strand library is used to coat a different well of a microtitre plate. The ELISA then proceeds using a constant target molecule to query each well.
Cell Binding Assays. Antibodies can be evaluated for their ability to interact with one or more cell types, e.g., a hematopoietic cell. Fluorescent activated cell sorting (FACS) is one exemplary method for testing an interaction between a protein and a cell. The antibody is labeled directly or indirectly with a fluorophore, before or after, binding to the cells, and then cells are counted in a FACS sorter.
Other cell types can be prepared for FACS by methods known in the art.
Homogeneous Binding Assays. The binding interaction of candidate polypeptide with a target can be analyzed using a homogenous assay, i.e., after all components of the assay are added, additional fluid manipulations are not required. For example, fluorescence resonance energy transfer (FRET) can be used as a homogenous assay (see, for example, Lakowicz et al., U.S. Pat. No. 5,631,169; Stavrianopoulos, et al., U.S. Pat. No. 4,868,103). A fluorophore label on the first molecule (e.g., the molecule identified in the fraction) is selected such that its emitted fluorescent energy can be absorbed by a fluorescent label on a second molecule (e.g., the target) if the second molecule is in proximity to the first molecule. The fluorescent label on the second molecule fluoresces when it absorbs to the transferred energy. Since the efficiency of energy transfer between the labels is related to the distance separating the molecules, the spatial relationship between the molecules can be assessed. In a situation in which binding occurs between the molecules, the fluorescent emission of the ‘acceptor’ molecule label in the assay should be maximal. A binding event that is configured for monitoring by FRET can be conveniently measured through standard fluorometric detection means well known in the art (e.g., using a fluorimeter). By titrating the amount of the first or second binding molecule, a binding curve can be generated to estimate the equilibrium binding constant.
Another example of a homogenous assay is Alpha Screen (Packard Bioscience, Meriden Conn.). Alpha Screen uses two labeled beads. One bead generates singlet oxygen when excited by a laser. The other bead generates a light signal when singlet oxygen diffuses from the first bead and collides with it. The signal is only generated when the two beads are in proximity. One bead can be attached to the display library member, the other to the target. Signals are measured to determine the extent of binding.
The homogenous assays can be performed while the candidate polypeptide is attached to the display library vehicle, e.g., a bacteriophage.
Surface Plasmon Resonance (SPR). The binding interaction of a molecule isolated from a display library and a target can be analyzed using SPR. SPR or Biomolecular Interaction Analysis (BIA) detects biospecific interactions in real time, without labeling any of the interactants. Changes in the mass at the binding surface (indicative of a binding event) of the BIA chip result in alterations of the refractive index of light near the surface (the optical phenomenon of surface plasmon resonance (SPR)). The changes in the refractivity generate a detectable signal, which are measured as an indication of real-time reactions between biological molecules. Methods for using SPR are described, for example, in U.S. Pat. No. 5,641,640; Raether (1988) Surface Plasmons Springer Verlag; Sjolander and Urbaniczky (1991) Anal. Chem. 63:2338-2345; Szabo et al. (1995) Curr. Opin. Struct. Biol. 5:699-705 and on-line resources provide by BIAcore International AB (Uppsala, Sweden).
Information from SPR can be used to provide an accurate and quantitative measure of the equilibrium dissociation constant (K_D), and kinetic parameters, including k_onand k_off, for the binding of a biomolecule to a target. Such data can be used to compare different biomolecules. For example, proteins encoded by nucleic acid selected from a library of diversity strands can be compared to identify individuals that have high affinity for the target or that have a slow k_off. This information can also be used to develop structure-activity relationships (SAR). For example, the kinetic and equilibrium binding parameters of matured versions of a parent protein can be compared to the parameters of the parent protein. Variant amino acids at given positions can be identified that correlate with particular binding parameters, e.g., high affinity and slow k_off. This information can be combined with structural modeling (e.g., using homology modeling, energy minimization, or structure determination by crystallography or NMR). As a result, an understanding of the physical interaction between the protein and its target can be formulated and used to guide other design processes.
Protein Arrays. Proteins identified from the display library can be immobilized on a solid support, for example, on a bead or an array. For a protein array, each of the polypeptides is immobilized at a unique address on a support. Typically, the address is a two-dimensional address. Methods of producing polypeptide arrays are described, e.g., in De Wildt et al. (2000) Nat. Biotechnol. 18:989-994; Lueking et al. (1999) Anal. Biochem. 270:103-111; Ge (2000) Nucleic Acids Res. 28, e3, I-VII; MacBeath and Schreiber (2000) Science 289:1760-1763; WO 01/40803 and WO 99/51773A1. Polypeptides for the array can be spotted at high speed, e.g., using commercially available robotic apparati, e.g., from Genetic MicroSystems or BioRobotics. The array substrate can be, for example, nitrocellulose, plastic, glass, e.g., surface-modified glass. The array can also include a porous matrix, e.g., acrylamide, agarose, or another polymer.
Kits
Also provided are kits for use in carrying out a method according to any aspect of the invention. The kits may include the necessary vectors. One such vector will typically have an origin of replication for single stranded bacteriophage and either contain the sbp member nucleic acid or have a restriction site for its insertion in the 5′ end region of the mature coding sequence of a phage capsid protein, and with a secretory leader coding sequence upstream of said site which directs a fusion of the capsid protein exogenous polypeptide to the periplasmic space.
Also provided are packages encoding the HC CDR3s as defined above and polypeptides comprising the HC CDR3s and fragments and derivatives thereof, obtainable by use of any of the above defined methods. The derivatives may comprise polypeptides fused to another molecule such as an enzyme or a Fc tail.
The kit may include a phage vector (e.g., DY3F87HC) which has a site for insertion of HC CDR3s for expression of the encoded polypeptide in free form. The kit may also include a plasmid vector for expression of soluble light chains, e.g., pLCSK23. The kit may also include a suitable cell line (e.g., TG1). The diversity of light chains encoded by pLCSK23 may be 10, 15, 20, 25, 30, or 50. The LCs in the diversity may be constructed or picked to have certain desirable properties, such as, being germline in the framework regions and having diversity in CDR3 and/or CDR1. The germlines may be of highly utilized ones, e.g., VK1_2-02, VK3_1-A27, VK3_5-L6, VK3_3-L2 for kappa and VL2_2a2, VL1_1c, VL1_1g, VL3_3r for lambda.
For example, one could clone genes for
VK1O2gl-JK3, VK1O2var1, VK1O2var2, VK1O2var3, VK1O2var4, VK1O2var5, VK3L6gl-JK4, VK3L6var1, VK3L6var2, VK3L6var3, VK3L6var4, VK3L6var5, VK3L6var6, VK3L6var7, VK3L6var8, VK3A27gl-JK3, VK3A27var1, VK3A27var2, VK3A27var3, VK3A27var4, VK3A27var5, VK3A27var6, VK3A27var7, VK3L2gl-JK3, VK1glL8-JK5, and VK1GLO12-JK3 (amino-acid sequences shown in Table 19) into pLCSK23.

TABLE 19

26 VL to be used in pLCSK23.

VK1O2gl-JK3 (SEQ ID NO: 4)

DIQMTQSPSS LSASVGDRVT ITCRASQSIS SYLNWYQQKP GKAPKLLIYA ASSLQSGVPS	60
RFSGSGSGTD FTLTISSLQP EDFATYYCQQ SYSTPFTFGP GTKVDIK	107

VK1O2var1 (SEQ ID NO: 5) S28D

DIQMTQSPSS LSASVGDRVT ITCRASQDIS SYLNWYQQKP GKAPKLLIYA ASSLQSGVPS	60
RFSGSGSGTD FTLTISSLQP EDFATYYCQQ SYSTPFTFGP GTKVDIK	107

VK1O2var2 (SEQ ID NO: 6) S91R

DIQMTQSPSS LSASVGDRVT ITCRASQSIS SYLNWYQQKP GKAPKLLIYA ASSLQSGVPS	60
RFSGSGSGTD FTLTISSLQP EDFATYYCQQ RYSTPFTFGP GTKVDIK	107

VK1O2var3 (SEQ ID NO: 7) S91E

DIQMTQSPSS LSASVGDRVT ITCRASQSIS SYLNWYQQKP GKAPKLLIYA ASSLQSGVPS	60
RFSGSGSGTD FTLTISSLQP EDFATYYCQQ EYSTPFTFGP GTKVDIK	107

VK1O2var4 (SEQ ID NO: 8) S31R

DIQMTQSPSS LSASVGDRVT ITCRASQSIS RYLNWYQQKP GKAPKLLIYA ASSLQSGVPS	60
RFSGSGSGTD FTLTISSLQP EDFATYYCQQ SYSTPFTFGP GTKVDIK	107

VK1O2var5 (SEQ ID NO: 9) S31E, S93R

DIQMTQSPSS LSASVGDRVT ITCRASQSIS EYLNWYQQKP GKAPKLLIYA ASSLQSGVPS	60
RFSGSGSGTD FTLTISSLQP EDFATYYCQQ SYRTPFTFGP GTKVDIK	107

VK3L6gl-JK4 (SEQ ID NO: 10)

EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ASNRATGIPA	60
RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RSNWPLTFGG GTKVEIK	107

VK3L6var1 (SEQ ID NO: 11) S31R

EIVLTQSPAT LSLSPGERAT LSCRASQSVS RYLAWYQQKP GQAPRLLIYD ASNRATGIPA	60
RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RSNWPLTFGG GTKVEIK	107

VK3L6var2 (SEQ ID NO: 12) S92R

EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ASNRATGIPA	60
RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RRNWPLTFGG GTKVEIK	107

VK3L6var3 (SEQ ID NO: 13) S92G

EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ASNRATGIPA	60
RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RGNWPLTFGG GTKVEIK	107

VK3L6var4 (SEQ ID NO: 14) S92Y

EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ASNRATGIPA	60
RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RYNWPLTFGG GTKVEIK	107

VK3L6var5 (SEQ ID NO: 15) S92E

EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ASNRATGIPA	60
RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RENWPLTFGG GTKVEIK	107

VK3L6var6 (SEQ ID NO: 16) Y32F

EIVLTQSPAT LSLSPGERAT LSCRASQSVS SFLAWYQQKP GQAPRLLIYD ASNRATGIPA	60
RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RSNWPLTFGG GTKVEIK	107

VK3L6var7 (SEQ ID NO: 17) Y32D

EIVLTQSPAT LSLSPGERAT LSCRASQSVS SDLAWYQQKP GQAPRLLIYD ASNRATGIPA	60
RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RSNWPLTFGG GTKVEIK	107

VK3L6var8 (SEQ ID NO: 18) N93G

EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ASNRATGIPA	60
RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RSGWPLTFGG GTKVEIK	107

VK3A27gl-JK3 (SEQ ID NO: 19)

EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP	60
DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYGSSPFTFG PGTKVDIK	108

VK3A27var1 (SEQ ID NO: 20) S31R

EIVLTQSPGT LSLSPGERAT LSCRASQSVS RSYLAWYQQK PGQAPRLLIY GASSRATGIP	60
DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYGSSPFTFG PGTKVDIK	108

VK3A27var2 (SEQ ID NO: 21) S32R

EIVLTQSPGT LSLSPGERAT LSCRASQSVS SRYLAWYQQK PGQAPRLLIY GASSRATGIP	60
DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYGSSPFTFG PGTKVDIK	108

VK3A27var3 (SEQ ID NO: 22) S32D

EIVLTQSPGT LSLSPGERAT LSCRASQSVS SDYLAWYQQK PGQAPRLLIY GASSRATGIP	60
DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYGSSPFTFG PGTKVDIK	108

VK3A27var4 (SEQ ID NO: 23) G93E

EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP	60
DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYESSPFTFG PGTKVDIK	108

VK3A27var5 (SEQ ID NO: 24) G93R

EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP	60
DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYRSSPFTFG PGTKVDIK	108

VK3A27var6 (SEQ ID NO: 25) S30D, G93E

EIVLTQSPGT LSLSPGERAT LSCRASQSVD SSYLAWYQQK PGQAPRLLIY GASSRATGIP	60
DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYESSPFTFG PGTKVDIK	108

VK3A27var7 (SEQ ID NO: 26) S94R

EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP	60
DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYGRSPFTFG PGTKVDIK	108

VK3L2gl-JK3 (SEQ ID NO: 27)

EIVMTQSPAT LSVSPGERAT LSCRASQSVS SNLAWYQQKP GQAPRLLIYG ASTRATGIPA	60
RFSGSGSGTE FTLTISSLQS EDFAVYYCQQ YNNWPFTFGP GTKVDIK	107

VK1glL8-JK5 (SEQ ID NO: 28)

DIQLTQSPSF LSASVGDRVT ITCRASQGIS SYLAWYQQKP GKAPKLLIYA ASTLQSGVPS	60
RFSGSGSGTE FTLTISSLQP EDFATYYCQQ LNSYPITFGQ GTRLEIK	107

VK1GLO12-JK3 (SEQ ID NO: 897)

DIQMTQSPSS LSASVGDRV TITCRASQSI SSYLNWYQQK PGKAPKLLIY AASSLQSGVP	60
SRFSGSGSGT DFTLTISSL QPEDFATYYC QQSYSTPFTF GPGTKVDIKR GTVAAPSVFI	120
FPPSDEQLKS GTASVVCLL NNFYPREAKV QWKVDNALQS GNSQESVTEQ DSKDSTYSLS	180
STLTLSKADY EKHKVYACE VTHQGLSSPV TKSFNRGECA AAGKPIPNPL LGLDST	236

The kits may include ancillary components required for carrying out the method, the nature of such components depending of course on the particular method employed. Useful ancillary components may comprise helper phage, PCR primers, buffers, and/or enzymes of various kinds. Buffers and enzymes are typically used to enable preparation of nucleotide sequences encoding Fv, scFv or Fab fragments derived from rearranged or unrearranged immunoglobulin genes according to the strategies described herein.
Methods of Introducing Diversity
There are many ways of generating DNA that is variable. One way is to use mixed-nucleotide synthesis (MNS). One version of MNS uses equimolar mixtures of nucleotides as shown in Table 5. For example, using NNK codons gives all twenty amino acids and one TAG stop codon. The distribution is 3(R/S/L): 2(A/G/V/T/P): 1(C/D/E/F/H/I/K/M/N/Q/W/Y) (e.g., 3 of each of Arg, Ser, and Leu, and so forth). An alternative, herein termed “wobbling”, uses mixed nucleotides but not in equimolar amounts. For example, if a parental codon were TTC (encoding Phe), we could use a mixture of (0.082 T, 0.06 C, 0.06 A, and 0.06 G) in place of T and a mixture of (0.082 C, 0.06 T, 0.06 A, and 0.06 G) in place of C. This would give TTC or TTT (encoding Phe) 59% of the time and Leu 13%, S/V/I/C/Y ˜5%, and other amino-acid types less often.
Van den Brulle et al. (Biotechniques 45:340-3 (2008)) describe a method of synthesis of variable DNA in which type IIs restriction enzymes are used to transfer trinucleotides from an anchored hair-pin oligonucleotide (PHONs) to a so called “splinker”. See also EP patents 1 181 395, EP 1 411 122, EP 1 314 783 and EP applications EP 01127864.5, EP 04001462.3, EP 08006472.8. By using mixtures of anchored PHONs and splinkers, one can build libraries in which desired amino-acid types are allowed in designer-determined ratios. Thus, one can direct that one amino-acid type is present, for example 82% of the time and 18 other amino-acid types (all non-parental amino-acid types except Cys) are present at 2% each. Herein, we will refer to such a synthesis as “dobbling” (digital wobbling). In some aspects, dobbling is preferred to wobbling, but wobbling provides useful embodiments, partly because the structure of the genetic code table causes wobbling to make mostly conservative substitutions. Dobbling does offer the possibility to exclude unwanted amino-acid types. In CDRs, unpaired cysteines are known, even in Abs approved as therapeutics, but in some embodiments, one would like to avoid them. In some embodiments, when diversifying a D region that contains a pair of cysteines, the cysteins are not allowed to vary because the disulfide-closed loop is an important structural element and because one does not want unpaired cysteines.
In addition, one can synthesize a DNA molecule that encodes a parental amino-acid sequence and subject that DNA to error-prone PCR using primers that cover the framework regions so that mutations in the framework regions are avoided.

TABLE 5

Standard codes for mixed nucleotides

N is equimolar	A,	C,	G,	T
B is equimolar	C,	G,	T		(not A)
D is equimolar	A,	G,	T		(not C)
H is equimolar	A,	C,	T		(not G)
V is equimolar	A,	C,	G		(not T)
K is equimolar	G,	T			(Keto)
M is equimolar	A,	C			(aMino)
R is equimolar	A,	G			(puRine)
S is equimolar	C,	G			(Strong)
W is equimolar	A,	T			(weak)
Y is equimolar	C,	T			(pYrimidine)

TABLE 6

Example of mixed nucleotides for wobbling

e = 0.82	A + 0.06	C + 0.06	G + 0.06 T
q = 0.06	A + 0.82	C + 0.06	G + 0.06 T
j = 0.06	A + 0.06	C + 0.82	G + 0.06 T
z = 0.06	A + 0.06	C + 0.06	G + 0.82 T

EXEMPLIFICATION

The present invention is further illustrated by the following examples which should not be construed as limiting in any way. The contents of all references, pending patent applications and published patents, cited throughout this application are hereby expressly incorporated by reference.

Prophetic Example 1: Libraries With Very Short HC CDR3s

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

TABLE 7

Amino-acid sequences of parental CDR3s of lengths 3, 4, 5

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

Length 3

V-3JH1	TAVYYCAK FQH WGQGTLVTVSS	(SEQ ID NO: 31)
V-3JH2	TAVYYCAK FDL WGRGTLVTVSS	(SEQ ID NO: 32)
V-3JH3	TAVYYCAK FDI WGQGTMVTVSS	(SEQ ID NO: 33)
V-3JH4	TAVYYCAK FDY WGQGTLVTVSS	(SEQ ID NO: 34)
V-3JH5	TAVYYCAK FDP WGQGTLVTVSS	(SEQ ID NO: 35)
V-3JH6	TAVYYCAK MDV WGQGTTVTVSS	(SEQ ID NO: 36)
V-3D1-1.1.1-JH1	TAVYYCAK GTT WGQGTLVTVSS	(SEQ ID NO: 37)
V-3D1-1.1.2-JH1	TAVYYCAK TTG WGQGTLVTVSS	(SEQ ID NO: 38)
V-3D3-3.3.3-JH2	TAVYYCAK IFG WGRGTLVTVSS	(SEQ ID NO: 39)

Length 4

V-4JH1	TAVYYCAK YFQH WGQGTLVTVSS	(SEQ ID NO: 40)
V-4JH2	TAVYYCAK YFDL WGRGTLVTVSS	(SEQ ID NO: 41)
V-4JH3	TAVYYCAK AFDI WGQGTMVTVSS	(SEQ ID NO: 42)
V-4JH4	TAVYYCAK YFDY WGQGTLVTVSS	(SEQ ID NO: 43)
V-4JH5	TAVYYCAK WFDP WGQGTLVTVSS	(SEQ ID NO: 44)
V-4JH6	TAVYYCAK GMDV WGQGTTVTVSS	(SEQ ID NO: 45)
V-4D3-10.1a-JH2	TAVYYCAK LLWF WGRGTLVTVSS	(SEQ ID NO: 46)

Length 5

V-5JH1	TAVYYCAK EYFQH WGQGTLVTVSS	(SEQ ID NO: 47)
V-5JH2	TAVYYCAK WYFDL WGRGTLVTVSS	(SEQ ID NO: 48)
V-5JH3	TAVYYCAK yAFDI WGQGTMVTVSS	(SEQ ID NO: 49)
V-5JH4	TAVYYCAK sYFDY WGQGTLVTVSS	(SEQ ID NO: 50)
V-5JH5	TAVYYCAK NWFDP WGQGTLVTVSS	(SEQ ID NO: 51)
V-5JH6	TAVYYCAK YGMDV WGQGTTVTVSS	(SEQ ID NO: 52)
V-5D2-8.2a-JH2	TAVYYCAK DIVLM WGRGTLVTVSS	(SEQ ID NO: 53)

TABLE 8

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

!	CDR3.......
!	A E D T A V Y Y C A K D I V L M
	\|gct\|gag\|gaT\|aCT\|GCA\|GtT\|taT\|taC\|tgc\|gct aag jez ezq jzz qzz ezj
!
!	W G Q G T T V T V S S (SEQ ID NO: 54)
	tgg ggc cag ggt act acG GTC ACC gtc tcc agt-3′ (SEQ ID NO: 55)
!	BstEII...

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

TABLE 1

Designs of very short exemplary HC CDR3s

C3XXX

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

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

! XbaI...

!

! CDR3.......

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

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

!

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

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

! BstEII...

!

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

(SEQ ID NO: 58)

(ON_5) 5′-AcTggAgAcggTgAccgTAgTAcccTggccccA-3′ ! 33 bases (SEQ ID NO: 256)

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

agt-3′ (SEQ ID NO: 59))

! Use ON-1 and ON-3 shown below

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

!

C3X4

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

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

! XbaI...

!

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

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

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

!

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

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

! BstEII...

!

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

ggc cag ggt act ac-3′ (SEQ ID NO: 62)

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

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

C3X5

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

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

! XbaI...

!

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

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

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

!

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

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

! BstEII...

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

ggc cag ggt act ac-3′ (SEQ ID NO: 65)

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

aRg encodes K or R

Alternatively, the current HC diversity can be cloned into DY3F87HC and the CDR3 diversity described above is cloned into that diversity as XbaI-BstEII fragments. A library of, for example, 25 LC are cloned into pLCSK23 and used to create a cell line in TG1 E. coli. These cells are infected with the DY3F87HC phage which harbor the novel HC CDR3 (and CDR1-2) diversity. The phage obtained from this infection are selected for binding to a desired target. After two to four rounds of selection, the selected HCs are transferred to pHCSK22 and used to create a cell line which can be used with ROLIC to combine the selected HC with all the LCs in the ROLIC LC library. In this way, a library of 1. E 9 can be give Abs that normally would require construction of a library of 1. E 16 (assuming a LC diversity of 1. E 7).

Prophetic Example 2: Libraries with Very Long HC CDR3s

Sidhu et al. (J Mol Biol. 2004 338:299-310. and US application 20050119455 Å1) report high-affinity Abs selected from a library in which only Y and S were allowed in the CDRs which were limited in length to 20 amino acids. It may be possible to generate high affinity Abs from a library that has HC CDR3s with one or more of the following forms of diversity: a) several (but not all) sites allowing Y or S, b) including 4-6 NNK codons, c) introducing D segments (with or without diversification in the D), and/or d) using error-prone PCR. We have already sampled the Ab space in which HC CDR3 is in the range ˜8 to ˜22 with a median length of 13. Thus, libraries in which HC CDR3 is either ˜23 AAs or ˜35 AAs are possible and may have advantages with certain types of targets. For example, GPCRs are integral membrane proteins with seven helical segments transversing the lipid bilayer of the call that are thought to have multiple states. An antibody having a very long HC CDR3 could form a protuberance that fits into the channel formed by the seven strands. Finding Abs that bind GPCRs has been difficult and intentionally building libraries in which all the members have very long HC CDR3s may ameliorate this problem. The lengths may be made somewhat variable, say 23, 24, or 25 in one library and 33, 34, or 35 in a second.
Below are a number of representative designs. The CDR3 have been broken up and diversity generated that lets the various parts have differing relationships depending on the value of X. A full-length JH1 has been used, and in some designs diversity allowed diversity in the CDR3 part of JH1. Other JHs could be used. In the designs, the D segments are either rich in Y or have an S-rich disulfide loop. The amino-acid sequences of human D segments are shown in Table 3. The places where the D region has either S or Y or allowed other combinations have in particular been varied. Table 4 shows the amino-acid sequences of human J regions.
Each of the libraries could be built in at least four ways: 1) DNA encoding a particular amino acid sequence is first synthesized and subjected to error-prone PCR, 2) the library can be synthesized by wobbling or with mixtures of nucleotides, 3) the library can be built using dobbling, and 4) routes (2) or (3) could be followed by error-prone PCR. As an example of route (1), in Design 12, DNA encoding SEQ ID NO:908 could be synthesized, as shown in SEQ ID NO:911. This DNA could be subjected to error-prone PCR using the primers shown in SEQ ID NO:909 and SEQ ID NO:910. Because these primers cover the framework regions, the errors will occur only in the CDR3.
A library of HCs with CDR3 with length 23 of, for example, 2×10⁹members and a second library with HC CDR3s of length ˜35 also having 2×10⁹members could be built. Alternatively, the DNA could be mixed to build one library of 4×10⁹.

TABLE 4

Human JH amino-acid sequences

		H3
		------
		CDR3
		--------
		100 110
		\| \|
	JH1	---AEYFQHWGQGTLVTVSS (SEQ ID NO: 66)

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

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

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

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

	JH6	YYYYYGMDVWGQGTTVTVSS (SEQ ID NO: 3)

In each of the following designs, the amino-acid sequence begins with YYCA(K/R) (SEQ ID NO: 936) which is the end of FR3. FR4 starts with WG and is shown bold.

Design 1

SEQ ID NO:898 comprises the end of FR3 joined to two residues (DY) of types often found in the filler sequence that the immune system places between V and D. These are followed by D2-2.2, preferred because it has a disulfide loop and is rich in Ser and Tyr residues. This is followed by YGYSY (SEQ ID NO: 937), which is rich in Tyr and Ser residues, which is followed by full-length JH1.

XX::D2-2.2::XX::JH1
1 1 2 2
FR3 1 5 0 5 0 3FR4
YYCAK DYGYCSSTSCYTYGYSYAEYFQHWGQGTLVTVSS (SEQ ID NO: 898)
YYCAK XX GYCSXXSCYT XXYSYAEYFQHWGQGTLVTVSS (SEQ ID NO: 69)
R GYCSSTSCYT AEYFQHWGQGTLVTVSS (JH1)
(SEQ ID NO: 70) (SEQ ID NO: 66)
1 1 1 1
9 9 0 0 0 1
4 5 0 2abcdefghijklmnp3 0

Amino-acid diversity = 1.28 E 8
DNA diversity = 2.15 E 9
Stop-free = 83%
Gratuitous Cys-free = 83%
Free of stop and Cys = 68%

Design 1(C23D222) has 94 being R or K, then 2 Xs, D2-2 in second reading frame with two Xs in the loop, followed by two Xs, and JH1. D2-2 2^ndreading frame has a disulfide-closed loop into which diversity at two points has been introduced. This CDR3 is 23 long. Using primers that include DNA up to . . . YYCA (SEQ ID NO: 938) and from WGQG (SEQ ID NO: 939) . . . , error-prone PCR on the CDR3 could be performed before amplifying out to XbaI and BstEII for cloning into the library of kappa LC and HC CDR1/2. Thus, the AAs that are shown as fixed will be allowed to vary some. The AAs that are part of the PCR overlap region will be reinforced by the final non-error prone PCR. Error-prone PCR is not a necessary part of the design.

C23D222JH1
! scab DNA S R D N S K N T L Y L Q M N S
5′-ttc\|act\|atc\|TCT\|AGA\|gac\|aac\|tct\|aag\|aat\|act\|ctc\|tac\|ttg\|cag\|atg\|aac\|agC-
! XbaI...
!
! L R A E D T A V Y Y C A K\|R
\|TTA\|AGg\|gct\|gag\|gaT\|aCT\|GCA\|GtT\|taT\|taC\|tgc\|gct aRg -
!
! CDR3----------------------------------------------------------------
! X X D2-2 RF2............................. X X JH1..
! any any G Y C S any any S C Y T any any Y S Y A
nnk nnk ggt tat tgt tcc nnk nnk tct tgc tat act nnk nnk tat tcc tac gct-
!
! CDR3---------------
! E Y F Q H
gaa tat ttc cag cac-
!
! W G Q G T L V T V S S (SEQ ID NO: 71)
tgg ggc cag ggt act ctG GTC ACC gtc tcc agt-3′ (SEQ ID NO: 72)
! BstEII...

(ON_C23D222) 5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg nnk nnk ggt tat tgt tcc nnk-
nnk tct tgc tat act nnk nnk tat tcc tac gct gaa tat ttc cag cac-
tgg ggc cag ggt act ct-3′ ! 107 bases (SEQ ID NO: 73)
(ON_1) 5′-GCA\|GtT\|taT\|taC\|tgc\|gct-3′ (SEQ ID NO: 74)
(ON_2) 5′-AgAgTAcccTggccccAgAcgTccATAccgTAATAgT-3′ ! 37 bases (SEQ ID NO:
75)
(ON_2 is reverse complement of 5′-ac tat tac ggt atg gac gtc tgg
ggc cag ggt act ct-3′) (SEQ ID NO: 76)
(ON_3) 5′-ttc\|act\|atc\|TCT\|AGA\|gac\|aac\|tct\|aag\|aat\|act\|ctc\|tac\|ttg\|cag\|atg-
aac\|agC\|TTA\|AGg\|gct\|gag\|gaT\|aCT\|GCA\|GtT\|taT\|taC\|tgc\|gct-3′ (SEQ ID
NO: 77)
(ON_4) 5′-AcTggAgAcggTgAccAgAgTAcccTggccccA-3′ ! 33 bases (SEQ ID NO: 78)
(5′-tgg ggc cag ggt act ctG GTC ACC gtc tcc agt-3′ [RC] (SEQ ID NO: 79))

Design 2

1 1 2 2
1 5 0 5 0 3
YYCAK GSYYYGSGSYYNVDSYYAEYFQHWGQGTLVTVSS (SEQ ID NO: 899)
YYCAK XXYYYGXGSXYNXXSYYAEYFQHWGQGTLVTVSS (SEQ ID NO: 80)
R YYYGSGSYYN AEYFQHWGQGTLVTVSS (JH1)
(SEQ ID NO: 81) (SEQ ID NO: 66)

Amino-acid diversity = 1.28 E 8
DNA diversity = 2.15 E 9
Stop-free = 83%
Gratuitous Cys-free = 83%
Free of stop and Cys = 68%

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

C23D310JH1
! scab DNA S R D N S K N T L Y L Q M N S
5′-ttc\|act\|atc\|TCT\|AGA\|gac\|aac\|tct\|aag\|aat\|act\|ctc\|tac\|ttg\|cag\|atg\|aac\|agC-
! XbaI...
!
! L R A E D T A V Y Y C A K\|R
\|TTA\|AGg\|gct\|gag\|gaT\|aCT\|GCA\|GtT\|taT\|taC\|tgc\|gct aRg -
!
! CDR3-------------------------------------------------------------------
!
! any any Y Y Y G any G S any Y N any any S Y Y
nnk nnk tac tac tat ggt nnk ggc tct nnk tac aat nnk nnk tct tat tac
!
! A E Y F Q H
gct gag tac ttt caa cat
!
! JH1......................................
! W G Q G T L V T V S S (SEQ ID NO: 82)
tgg ggc cag ggt act ctG GTC ACC gtc tcc agt-3′ (SEQ ID NO: 83)
! BstEII...

(C23D310) 5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg nnk nnk tac tac tat ggt nnk ggc-
tct nnk tac aat nnk nnk tct tat tac gct gag tac ttt caa cat tgg ggc cag-
ggt act ct-3′ (SEQ ID NO: 84)
ON_1, ON_2, ON_3, and ON_4 as above.

Design 3

1 1 2 2
1 5 0 5 0 3
YYCAK DYYYYGSGSYYNSDSYSAEYFQHWGQGTLVTVSS (SEQ ID NO: 900)
YYCAK XZ YZZGZGZXYN ZXZYZ AXZFQHWGQGTLVTVSS (SEQ ID NO: 940)
R YYYGSGSYYN AEYFQHWGQGTLVTVSS (JH1)
(SEQ ID NO: 81) (SEQ ID NO: 66)

Amino-acid diversity = 1.64 E 8
DNA diversity = 1.07 E 9
Stop-free = 88%
Gratuitous Cys-free = 88%
Free of stop and Cys = 77%

Design 3 (C23D310B) has 94 as R or K, XZ, D3-10 (RF2) with 2^nd, 3^rd, 5^thand 7^thas Z(Y|S) and 8^thresidue changed to X, ZXZYZ (SEQ ID NO:992), and JH1 (with the E changed to X). Z is either Y or S. The CDR3 is 23 AA long and could be further diversified by use of error-prone PCR.

A V Y Y C A R\|K any Y\|S Y Y\|S Y\|S G Y\|S G
(C23D310b) 5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg nnk tmc tac tmc tmt ggt tmc ggc-

Y\|S any Y N Y\|S any Y\|S Y Y\|S A any Y\|S F Q H W G Q
tmt nnk tac aat tmt nnk tmc tat tmc gct nnk tmc ttt caa cat tgg ggc cag-

G T L (SEQ ID NO: 85)
ggt act ct-3′ (SEQ ID NO: 86)
ON_1, ON_2, ON_3, and ON_4 as above.

Design 4

1 1 2 2 2 3 3
1 5 0 5 0 3 5 0 5
YYCAK YYSFSYYPYYYDSSGYYYGYYSDYSYSYYAEYFQHWGQGTLVTVSS (SEQ ID NO: 901)
YYCAK YYSXSYYX YZYDSZGYZY XYYSXYZYZZZ AZZFQHWGQGTLVTVSS (SEQ ID NO: 87)
R YYYDSSGYYY AEYFQHWGQGTLVTVSS (JH1)
(SEQ ID NO: 88) (SEQ ID NO: 66)
1 1 1 1
9 9 0 0 0 1
4 5 0 2abcdefghijklmnopqrstuvwxyab3 0
′′
Amino-acid diversity = 1.64 E 8
DNA diversity = 1.07 E 9
Stop-free = 88%
Gratuitous Cys-free = 88%
Free of stop and Cys = 77%

Design 4 has CDR3 of length 35. Residue 94 can be K or R, then YYS::X::SYY::X::D3-22(2^ndRF with one S as X and 3 Zs)::X::YYS::X::YZZZ (SEQ ID NO:993)::JH1 (with 2 Zs). Error-prone PCR could be used to add more diversity.

C35D322JH1
! scab DNA S R D N S K N T L Y L Q M N S
5′-ttc\|act\|atc\|TCT\|AGA\|gac\|aac\|tct\|aag\|aat\|act\|ctc\|tac\|ttg\|cag\|atg\|aac\|agC-
! XbaI...
!
! L R A E D T A V Y Y C A K\|R
\|TTA\|AGg\|gct\|gag\|gaT\|aCT\|GCA\|GtT\|taT\|taC\|tgc\|gct aRg -
!
! CDR3-------------------------------------------------------------------
!
! Y Y S any S Y Y any Y Y\|S Y D S Y\|S G Y Y\|S Y
tac tat tcc nnk tct tac tat nnk tat tmt tac gat agt tmt ggt tac tmc tat
!
any Y Y S any Y Y\|S Y Y\|S Y\|S Y\|S A Y\|S Y\|S F Q H
nnk tac tat agc nnk tat tmc tac tmc tmt tmc gct tmt tmc ttc caa cac
!
! W G Q G T L V T V S S (SEQ ID NO: 89)
tgg ggc cag ggt act ct G GTC ACC gtc tcc agt-3′ (SEQ ID NO: 90)
! BstEII...

(c35d322B) 5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg tac tat tcc nnk tct tac tat nnk-
tat tmt tac gat agt tmt ggt tac tmc tat nnk tac tat agc nnk tat tmc tac-
tmc tmt tmc gct tmt tmc ttc caa cac tgg ggc cag ggt act ct-3′ (SEQ ID NO: 91)
ON_1, ON_2, ON_3, and ON_4 as above.

1 1 2 2
1 5 0 5 0 3
YYCAK SSGYCSSTSCYTGVYYYAEYFQHWGQGTLVTVSS (SEQ ID NO: 902)
YYCAK ZZ GZCZZXZCZT XXYZYX ZYFQHWGQGTLVTVSS (SEQ ID NO: 92)
R GYCSSTSCYT AEYFQHWGQGTLVTVSS (JH1)
(SEQ ID NO: 70) (SEQ ID NO: 66)

Amino-acid diversity = 1.64 E 8
DNA diversity = 1.07 E 9
Stop-free = 88%
Gratuitous Cys-free = 88%
Free of stop and Cys = 77%

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

C23D222JH1b
! scab DNA S R D N S K N T L Y L Q M N S
5′-ttc\|act\|atc\|TCT\|AGA\|gac\|aac\|tct\|aag\|aat\|act\|ctc\|tac\|ttg\|cag\|atg\|aac\|agC-
! XbaI...
!
! L R A E D T A V Y Y C A K\|R
\|TTA\|AGg\|gct\|gag\|gaT\|aCT\|GCA\|GtT\|taT\|taC\|tgc\|gct aRg -
!
! CDR3-------------------------------------------------------------------
! Y\|S Y\|S G Y\|S C Y\|S Y\|S any Y\|S C Y\|S T any any Y Y\|S Y any
tmc tmt ggt tmt tgc tmc tmt nnk tmt tgt tmc acc nnk nnk tat tmt tac nnk
!
! Y\|S Y F Q H
tmt tat ttc cag cac
!
! W G Q G T L V T V S S (SEQ ID NO: 93)
tgg ggc cag ggt act ctG GTC ACC gtc tcc agt-3′ (SEQ ID NO: 94)
! BstEII...

(C23D222JH1b) 5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg tmc tmt ggt tmt tgc tmc tmt-
nnk tmt tgt tmc acc nnk nnk tat tmt tac nnk tmt tat ttc cag cac tgg ggc-
cag ggt act ct-3′ (SEQ ID NO: 95)

Design 6

1 1 2 2 2 3 3
1 5 0 5 0 3 5 0 5
YYCAK SYDYYGYCSSTSCYTYYSYVSYSSYYSYYAEYFQHWGQGTLVTVSS (SEQ ID NO: 903)
YYCAK ZYXZYGZCZZXSCZTYZSZXZYSZYZSZYAEZFQHWGQGTLVTVSS (SEQ ID NO: 96)
R GYCSSTSCYT D2-2.2 AEYFQHWGQGTLVTVSS (JH1)
(SEQ ID NO: 70) (SEQ ID NO: 66)

Amino-acid diversity = 2.00 E 8
DNA diversity = 5.37 E 8
Stop-free = 91%
Gratuitous Cys-free = 91%
Free of stop and Cys = 83%

C35D222JH1
!
! scab DNA S R D N S K N T L Y L Q M N S
5′-ttc\|act\|atc\|TCT\|AGA\|gac\|aac\|tct\|aag\|aat\|act\|ctc\|tac\|ttg\|cag\|atg\|aac\|agC-
! XbaI...
!
! L R A E D T A V Y Y C A K\|R
\|TTA\|AGg\|gct\|gag\|gaT\|aCT\|GCA\|GtT\|taT\|taC\|tgc\|gct aRg -
!
! CDR3-------------------------------------------------------------------
! Y\|S Y any Y\|S Y G Y\|S C Y\|S Y\|S any S C Y\|S T Y Y\|S S
tmt tac nnk tmc tac ggc tMt tgc tmt tmc nnk tCt tgt tmc acc tat tmt tcc
!
! Y\|S any Y\|S Y S any Y Y\|S S Y\|S Y A E Y F Q H
tmt nnk tmc tat tct nnk tac tmc agt tmt tat gct gag tat ttc cag cac
!
! W G Q G T L V T V S S (SEQ ID NO: 97)
tgg ggc cag ggt act ctG GTC ACC gtc tcc agt-3′ (SEQ ID NO: 98)
! BstEII...

(C35D222JH1)5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg tmt tac nnk tmc tac ggc tat- tgc tmt tmc
nnk tmt tgt tmc acc tat tmt tcc tmt nnk tmc tat tct nnk tac-
tmc agt tmt tat gct gag tat ttc cag cac tgg ggc cag ggt act ct-3′ (SEQ ID NO: 99)

Design 7

1 1 2 2 2 3 3
1 5 0 5 0 3 5 0 5
YYCAK YYSYYGYCSSTSCYTYSSSVSYSYYSSYYAEYFQHWGQGTLVTVSS (SEQ ID NO: 904)
YYCAK ZYZZYGZCZZXZCZTYZSZXZYSZYZSZYAψZJQBWGQGTLVTVSS (SEQ ID NO: 100)
R GYCSSTSCYT D2-2.2 AEYFQHWGQGTLVTVSS (JH1)
(SEQ ID NO: 70) (SEQ ID NO: 66)
(J = FSY, B = YHND, ψ = EKQ)

Amino-acid diversity = 9.44 E 8
DNA diversity = 2.42 E 9
Stop-free = 93%
Gratuitous Cys-free = 93%
Free of stop and Cys = 88%

C35D222JH1B
!
! scab DNA S R D N S K N T L Y L Q M N S
5′-ttc\|act\|atc\|TCT\|AGA\|gac\|aac\|tct\|aag\|aat\|act\|ctc\|tac\|ttg\|cag\|atg\|aac\|agC-
! XbaI...
!
! L R A E D T A V Y Y C A K\|R
\|TTA\|AGg\|gct\|gag\|gaT\|aCT\|GCA\|GtT\|taT\|taC\|tgc\|gct aRg -
!
! CDR3----------------------------------------------------------------
! Y\|S Y Y\|S Y\|S Y G Y\|S C Y\|S Y\|S any Y\|S C Y\|S T Y Y\|S S
tmt tac tmc tmc tac ggc tMt tgc tmt tmc nnk tmt tgt tmc acc tat tmt tcc
!
! Q Y N\|D
! Y\|S any Y\|S Y S Y\|S Y Y\|S S Y\|S Y A E\|K Y\|S F\|S Q H\|Y
tmt nnk tmc tat tct tmt tac tmc agt tmt tat gct Vag tmt tHc cag Nac
!
! W G Q G T L V T V S S (SEQ ID NO: 101)
tgg ggc cag ggt act ctG GTC ACC gtc tcc agt-3′ (SEQ ID NO: 102)
! BstEII...

Design 8

1 1 2 2 2 3 3
1 5 0 5 0 3 5 0 5
YYCAK SRSYYDYVWGSYRYTSSYSYYSYSYSSYAEYFQHWGQGTLVTVSS (SEQ ID NO: 905)
YYCAK ZXZ YZBZVWGZZRZT ZSZXZYZZZYZSZ AψZFQHWGQGTLVTVSS (SEQ ID NO: 103)
R YYDYVWGSYRYT D3-16.2 AEYFQHWGQGTLVTVSS (JH1)
(SEQ ID NO: 104) (SEQ ID NO: 66)
(J = FSY, B = YHND, ψ = EKQ)

Amino-acid diversity = 9.44 E 8
DNA diversity = 1.61 E 9
Stop-free = 93%
Gratuitous Cys-free = 93%
Free of stop and Cys = 88%

C34D316JH1A
!
! scab DNA S R D N S K N T L Y L Q M N S
5′-ttc\|act\|atc\|TCT\|AGA\|gac\|aac\|tct\|aag\|aat\|act\|ctc\|tac\|ttg\|cag\|atg\|aac\|agC-
! XbaI...
!
! L R A E D T A V Y Y C A K\|R
\|TTA\|AGg\|gct\|gag\|gaT\|aCT\|GCA\|GtT\|taT\|taC\|tgc\|gct aRg -
!
! CDR3----------------------------------------------------------------
! N\|D
! Y\|S any Y\|S Y Y\|S Y\|H Y\|S V W G Y\|S Y\|S R Y\|S T Y\|S
tmt nnk tmc tac tmt Nat tmt gtt tgg ggt tmt tmc cgt tmt act tmt
!
! S Y\|S any Y\|S Y Y\|S Y\|S Y\|S Y Y\|S S Y\|S
agt tmc nnk tmt tac tmc tmt tmc tat tmc agt tmt
!
! Q
! A E\|K Y\|S F Q H
GCT vag tmc ttc cag cat
!
! W G Q G T L V T V S S (SEQ ID NO: 105)
tgg ggc cag ggt act ct G GTC ACC gtc tcc agt-3′ (SEQ ID NO: 106)
! BstEII...

(C34D316JH1A) 5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg tmt nnk tmc tac tmt Nat tmt-
gtt tgg ggt tmt tmc cgt tmt act tmt agt tmc nnk tmt tac tmc tmt tmc tat-
tmc agt tmt GCT vag tmc ttc cag cat tgg ggc cag ggt act ct -3′ (SEQ ID NO: 107)

Design 9

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

1 1 2 2 2 3 3
1 5 0 5 0 3 5 0 5
YYCAK YGYSSDSYYSSYYDYVWGSYRYTYSSYYAEYFQHWGQGTLVTVSS (SEQ ID NO: 906)
YYCAK ZXZZZXZYZZZYZBZVWGZZRZTYZSZYAψZFQHWGQGTLVTVSS (SEQ ID NO: 108)
R D3-16.2 YYDYVWGSYRYT AEYFQHWGQGTLVTVSS (JH1)
(SEQ ID NO: 104) (SEQ ID NO: 66)
(J = FSY, B = YHND, ψ = EKQ)

Amino-acid diversity = 1.31 E 8
DNA diversity = 5.37 E 8
Stop-free = 91%
Gratuitous Cys-free = 91%
Free of stop and Cys = 83%

C34D316JH1B
!
! scab DNA S R D N S K N T L Y L Q M N S
5′-ttc\|act\|atc\|TCT\|AGA\|gac\|aac\|tct\|aag\|aat\|act\|ctc\|tac\|ttg\|cag\|atg\|aac\|agC-
! XbaI...
!
! L R A E D T A V Y Y C A K\|R
\|TTA\|AGg\|gct\|gag\|gaT\|aCT\|GCA\|GtT\|taT\|taC\|tgc\|gct aRg -
!
! CDR3-------------------------------------------------------------------
Y\|S any Y\|S Y\|S Y\|S any Y\|S Y Y\|S Y\|S Y\|S
tmt nnk tmc tmt tmc nnk tmt tac tmc tmt tmc
!
! N\|D
! Y Y\|S Y\|H Y\|S V W G Y\|S Y\|S R Y\|S T
tac tmt Nat tmt gtt tgg ggt tmt tmc cgt tmt act
!
! Y Y\|S S Y\|S Y
tat tmc agt tmt tac
!
! Q
! A E\|K Y\|S F Q H
GCT vag tmc ttc cag cat
!
! W G Q G T L V T V S S (SEQ ID NO: 109)
tgg ggc cag ggt act ct G GTC ACC gtc tcc agt-3′ (SEQ ID NO: 110)
! BstEII...

(C35D316JH1B)
5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg tmt nnk tmc tmt tmc nnk tmt tac tmc tmt tmc
tac tmt Nat tmt gtt tgg ggt tmt tmc cgt tmt act tat tmc agt tmt tac GCT vag
tmc ttc cag cat tgg ggc cag ggt act ct-3′ (SEQ ID NO: 111)

Design 10

1 1 2 2
1 5 0 5 0 4
YYCAK GSSYYYGSGSYYNSDYYSAEYFQHWGQGTLVTVSS (SEQ ID NO: 907)
YYCAK XZZ YZZGZGZXYN ZXZYZ AXZFQHWGQGTLVTVSS (SEQ ID NO: 112)
R YYYGSGSYYN AEYFQHWGQGTLVTVSS (JH1)
(SEQ ID NO: 81) (SEQ ID NO: 66)

Design 10 (C24D310B) is like Design 3, but the CDR3 is of length 24. Design 10 has 94 as R or K, XZZ, D3-10 (RF2) with 2^nd, 3^rd, 5^th, and 7^thas Z(Y|S) and 8^thresidue changed to X, ZXZYZ (SEQ ID NO: 994), and JH1 (with the E changed to X). Z is either Y or S. The CDR3 is 24 AA long and could be further diversified by use of error-prone PCR.

(C24D310b)

(SEQ ID NO: 113)

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

tmt ggt tmc ggc tmt nnk tac aat tmt nnk tmc tat

tmc gct nnk tmc ttt caa cat tgg ggc cag ggt act

ct-3′

ON_1, ON_2, ON_3, and ON_4 as above.

Design 11

1 1 2 2
1 5 0 5 0 5
YYCAR SSRSGYCTNGVCYRSGSYWYFDLWGRGTLVTVSS (SEQ ID NO: 991)
YYCAR ZZXZGZC32GVCZ3ZXZZ4Z12LWGRGTLVTVSS (SEQ ID NO: 114)
K GYCTNGVCYT YWYFDLWGRGTLVTVSS D2-8.2 JH2
(SEQ ID NO: 115) (SEQ ID NO: 67)
(1 = FYS(THT), 2 = YHND(NAT), 3 = ITKR(ANA), 4 = LSW(TBG))

(C24D282) 5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg tmc tmt nnk tmt ggt tmc tgt ana-
nat ggt gtc tgc tmt ana tmc nnk tmt tmt tbg tmt tht nat ctg tgg ggc-
cag ggt act ct-3′ (SEQ ID NO: 116)

(C24D282.1) 5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg tmc tmt nnk tmc ggt tmc tgc ana-
nat ggc gtc tgc tmt ana tmc nnk tmt tmt tbg tmt tht nat ctg tgg ggc-
cag ggt act ct-3′ (SEQ ID NO: 117)

(C24D282.1) 5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg tmc tmt nnk tm c ggt tmc tgc ana-
nat ggc gtc tgc t -3′ (SEQ ID NO: 118) (needs R, M, N, K)

(C24D282.2) 5′-Ag AgT Acc cTg gcc ccA cAg ATN ADA AKA cVA AKA AKA MNN gKA TNT AKA gcA
gAc gcc ATN TNT gcA gKA Acc g-3′ (SEQ ID NO: 119) ! 75 bases

(5′- c ggt tmc tgc ana-
nat ggc gtc tgc t mt ana tmc nnk tmt tmt tbg tmt tht n at ctg tgg ggc-
cag ggt act ct-3′ [RC] (SEQ ID NO: 120) (needs N, M, K, B, H))

Design 12

1 1 2 2 3 3
1 5 0 5 0 5 0 5
YYCAR SSYYSYGYCTNGVCYTYSYSYYSYSYSYWYFDLWGRGTLVTVSS (SEQ ID NO: 908)
YYCAR ZZZZZZGZC32GVCZ3ZZZZYZZYZYZZ4Z12LWGRGTLVTVSS (SEQ ID NO: 121)
K GYCTNGVCYT YWYFDLWGRGTLVTVSS D2-8.2 JH2
(SEQ ID NO: 115) (SEQ ID NO: 67)
(1 = FYS, 2 = YHND, 3 = ITKR, 4 = LSW, Z = YS)

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

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

(C33D282) 5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg tmt tmc tmc tmt tmc tmc ggt-
tmt tgt ana nat ggc gtg tgc tmt ana tmc tmc tmc tmt tat tmt tmc tat tmt-
tac tmt tmc tbg tmc tht nat ctg tgg ggc cag ggt act ct-3′(SEQ ID NO: 122)

(C33D282F) 5′-GCA\|GtT\|taT\|taC\|tgc\|gct agg tct tcc tac tat tcc tac ggt-
tat tgt aca aat ggc gtg tgc tat aca tac tcc tac tct tat tat tcc tat tct-
tac tct tac tgg tac ttt gat ctg tgg ggc cag ggt act ct-3′(SEQ ID NO: 911)

Design 13

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

1 1 2 2 3 3
1 5 0 5 0 5 0 5
YYCAR SSSYYSYYSSGYCTNGVCYTYSSYYSSYYWYFDLWGRGTLVTVSS (SEQ ID NO: 912)
YYCAR ZZZZZZZZZZGYCTNGVCYTZZZZZZZZZWZF2LWGRGTLVTVSS (SEQ ID NO: 123)
K GYCTNGVCYT YWYFDLWGRGTLVTVSS D2-8.2 JH2
(SEQ ID NO: 115) (SEQ ID NO: 67)
(2 = YHND)

(C34D282.2A) 5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg tmt tmc tmc tmt tmt tmc tmc tmt-
tmc tmc ggt tat tgt act aac ggc gtt tgc tat act-3′ (SEQ ID NO: 124)

(C34D282.2B) 5′-Ag AgT Acc cTg gcc ccA cAg gTN gAA AKA ccA AKA AKA AKA gKA-
gKA gKA gKA AKA AKA AgT ATA gcA AAc gcc gTT AgT AcA ATA-3′ (SEQ ID NO: 125)! 86
bases

(5′- tat tgt act aac ggc gtt tgc tat act tmt tmt tmc tmc tmc tmc-
tmt tmt tmt tgg tmt ttc Nac ctg tgg ggc cag ggt act ct-3′ (SEQ ID
NO: 126) [RC])

Design 14

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

1 1 2 2 2 3 3
1 5 0 5 0 3 5 0 5
YYCAK YSYYSGSYYYSDYVWGSYRYTSYDSYYYAEYFQHWGQGTLVTVSS (SEQ ID NO: 913)
YYCAK ZZZZZZZZZZZDYVWGSYRZTZZZZZZZ AEZFQHWGQGTLVTVSS (SEQ ID NO: 127)
R D3-16.2 YYDYVWGSYRYT AEYFQHWGQGTLVTVSS (JH1)
(SEQ ID NO: 104) (SEQ ID NO: 66)

(C34D316.2A) 5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg tmt tmc tmc tmt tmt tmc tmc tmt-
tmc tmc tmc gat tat gtc tgg ggt act tat cgt-3′ (SEQ ID
NO: 128)

(C34D316.2B) 5′-Ag AgT Acc cTg gcc ccA ATg cTg gAA AKA cTc Agc gKA gKA gKA-
gKA gKA gKA AKA AgT gKA Acg ATA AgT Acc ccA gAc ATA ATc-3′ (SEQ ID
NO: 129) ! 86 bases

(5′-gat tat gtc tgg ggt act tat cgt tmc act tmt tmc tmc tmc tmc-
tmc tmc gct gag tmt ttc cag cat tgg ggc cag ggt act ct-3′
(SEQ ID NO: 130) [RC])

Design 15

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

1 1 2 2 2 3 3
1 5 0 5 0 3 5 0 5
YYCAK SYDYSSYSYYYDYVWGSYRYTSYSGDSYYAEYFQHWGQGTLVTVSS (SEQ ID NO: 914)
YYCAK ZZZZZZZZZZZDZVWGZZRZTZZZZZZZZ AEZFQHWGQGTLVTVSS (SEQ ID NO: 131)
YYDYVWGSYRYT AEYFQH WGQGTLVTVSS
(SEQ ID NO: 104) (SEQ ID NO: 66)

(C35D316.2A) 5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg tmt tmc tmc tmt tmt tmc tmc tmt-
tmc tmc tmc gac tmt gtc tgg ggt tmc tmc cgt tmc acc t-3′

	(SEQ ID NO: 132)

(C35D316.2B) 5′-Ag AgT Acc cTg gcc ccA ATg cTg gAA AKA cTc Agc gKA gKA-
gKA gKA gKA gKA gKA AKA ggT gKA Acg gKA gKA Acc ccA gAc AKA gTc gKA g-3′
(SEQ ID NO: 133)

(5′-c tmc gac tmt gtc tgg ggt tmc tmc cgt tmc acc tmt tmc tmc-
tmc tmc tmc tmc tmc gct gag tmt ttc cag cat tgg ggc cag ggt act ct-3′
(SEQ ID NO:134) [RC])

Design 16

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

1 1 2 2 2 3 3
1 5 0 5 0 3 5 0 5
YYCAK SSSYYSYSYSGYCSGGSCYSSYYYSSYYSAEYFQGWGQGTLVTVSS (SEQ ID NO: 915)
YYCAK ZZZZZZZZZZGZ CZGGZC ZSZZZZZZZZZ AEZFQHWGQGTLVTVSS (SEQ ID NO: 135)
R GYCSGGSCYS 2-25.2 AEYFQH WGQGTLVTVSS JH1
(SEQ ID NO: 136) (SEQ ID NO: 66)

(C35D225.2A) 5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg tmt tmt tmt tmt tmt tmt tmt tmt-
tmc tmc ggc tmc tgt tmc ggt ggc tmc tgc tmc tcc t-3′ (SEQ ID NO: 137)

(C350225.2B) 5′-Ag AgT Acc cTg gcc ccA ATg TTg gAA AKA TTc Agc gKA KA-
gKA gKA gKA gKA gKA gKA gKA gKA ggA gcA gKA gcc Acc gKA AcA gKA gcc gKA g-3′
(SEQ ID NO: 138)! 96 bases

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

(C340225.2A) 5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg tmt tmt tmt tmt tmt tmt tmt-
tmc tmc ggc tmc tgt tmc ggt ggc tmc tgc tmc tcc t-3′ (SEQ ID NO: 139)

(C340225.2B) 5′-Ag AgT Acc cTg gcc ccA ATg TTg gAA AKA TTc Agc gKA gKA-
gKA gKA gKA gKA gKA gKA gKA ggA gcA gKA gcc Acc gKA AcA gKA gcc gKA g-3′
(SEQ ID NO: 140)! 93 bases

Design 17

1 1 2 2 2 3 3
1 5 0 5 0 3 5 0 5
YYCAK YSSYSYYDYVWGSYRYTSSSYSYYSYYYAEYFQGWGQGTLVTVSS (SEQ ID NO: 916)
YYCAK ZZZZZZ ZDZVWGZZRZTZ ZZZZZZZZZZ AEZFQHWGQGTLVTVSS (SEQ ID NO: 141)
R YYDYVWGSYRYT D3-16.2 AEYFQHWGQGTLVTVSS (JH1)
(SEQ ID NO: 104) (SEQ ID NO: 66)

(C3503162A) 5′- GCA GtT taT taC tgc gct aRg tmt tmt tmt tmt tmt tmt tmc gac-
tmc gtc tgg ggt tmt tmc cgt tmt acc t-3′ (SEQ ID NO: 142)

(C3503162B) 5′-Ag AgT Acc cTg gcc ccA gTg cTg gAA gKA cTc Agc gKA gKA gKA-
gKA gKA gKA gKA gKA gKA gKA gKA gKA gKA ggT AKA Acg gKA AKA Acc ccA gAc-
gKA gTc g-3′ (SEQ ID NO: 143)

Design 18

1 1 2 2 2 3 3
1 5 0 5 0 3 5 0 5
YYCAK SSYYYSSSYYDYVWGSYRYTSSYYSYSYAEYFQGWGQGTLVTVSS (SEQ ID NO: 917)
YYCAK ZZZZZZZZZ ZDZVWGZZRZTZ ZZZZZZZ AEZFQHWGQGTLVTVSS (SEQ ID NO: 144)
R YYDYVWGSYRYT D3-16.2AEYFQHWGQGTLVTVSS (JH1)
(SEQ ID NO: 104) (SEQ ID NO: 66)

(C35D3162C) 5′- GCA\|GtT\|taT\|taC\|tgc\|gct aRg tmt tmt tmt tmt tmt tmt tmc-
tmc tmc tmc gac tmc gtc tgg ggt tmc tmc cgt tmc acc t-3′ (SEQ ID NO: 145)

82 bases
(C35D3162B) 5′-Ag AgT Acc cTg gcc ccA gTg cTg gAA gKA cTc Agc gKA gKA-
gKA gKA gKA gKA gKA gKA gKA gKA ggT gKA Acg gKA gKA Acc ccA gAc gKA-
gTc g-3′ (SEQ ID NO: 146)

Design 19

1 1 2 2 2 3 3
1 5 0 5 0 3 5 0 5
YYCAK YSGDSYSYYYYDSSGYYYSYYSSSYYSYYAEYFQGWGQGTLVTVSS (SEQ ID NO: 918)
YYCAK ZZZZZZZZZ ZZDSSGZZZ ZZZZZZZZZZZ AEZFQHWGQGTLVTVSS (SEQ ID NO: 147)
R YYYDSSGYYY AEYFQHWGQGTLVTVSS (JH1)
(SEQ ID NO: 88) (SEQ ID NO: 66)

1 1 1 1
9 9 0 0 0 1
4 5 0 2abcdefghijklmnopqrstuvwxyab3 0
′′
Amino-acid diversity = 6.7 E 7
DNA diversity = 6.7 E 7
Stop-free = 100
Gratuitous Cys-free = 100
Free of stop and Cys = 100%

Design 19 has CDR3 of length 35. Residue 94 can be K or R. The ZZZZZZZZZ::D3-22(2^ndRF with six Ys as Z)::ZZZZZZZZZZZ::JH1 (with 1 Z)(SEQ ID NO:995). Error-prone PCR could be used to add more diversity.

C35D322AJH1
! scab DNA S R D N S K N T L Y L Q M N S
5′-ttc\|act\|atc\|TCT\|AGA\|gac\|aac\|tct\|aag\|aat\|act\|ctc\|tac\|ttg\|cag\|atg\|aac\|agC-
! XbaI...
!
! L R A E D T A V Y Y C A K\|R
\|TTA\|AGg\|gct\|gag\|gaT\|aCT\|GCA\|GtT\|taT\|taC\|tgc\|gct aRg -
!
! CDR3------
!
! Y\|S Y\|S Y\|S Y\|S Y\|S Y\|S Y\|S Y\|S Y\|S Y\|S Y\|S D S S G Y\|S Y\|S Y\|S
tmc tmt tmc tmc tmt tmc tmt tmc tmc tmc tmc gac agc tcc ggc tmc tmc tmt
!
Y\|S Y\|S Y\|S Y\|S Y\|S Y\|S Y\|S Y\|S Y\|S Y\|S Y\|S A E Y\|S F Q H
tmc tmt tmc tmc tmt tmc tmt tmc tmc tmc tmc gct gaa tmc ttc caa cac
!
! W G Q G T L V T V S S (SEQ ID NO: 148)
tgg ggc cag ggt act ct G GTC ACC gtc tcc agt-3′ (SEQ ID NO: 149)
! BstEII...

(C35D322AJH1_T)5′-GCA\|GtT\|taT\|taC\|tgc\|gct aRg tmc tmt tmc tmc tmt-
tmc tmt tmc tmc tmc tmc gac agc tcc ggc tmc tmc t-3′ (SEQ ID NO: 150)

(C35D322AJH1_B) 5′-cAg AgT Acc cTg gcc ccA gTg TTg gAA gKA TTc Agc gKA-
gKA gKA gKA AKA gKA AKA gKA gKA AKA gKA AKA gKA gKA gcc ggA gcT gTc-
gKA gKA g-3′ (SEQ ID NO: 151)
ON_1, ON_2, ON_3, and ON_4 as above.

Design 20

1 1 2 2 2 3 3
1 5 0 5 0 3 5 0 5
YYCAK YSSYSS YYYYDSSGYYYSSYSSYS YYYAEYFQGWGQGTLVTVSS (SEQ ID NO: 919)
YYCAK ZZZZZZ(Z)ZZ ZZDSSGZZZZZZZZZ Z(Z)ZZZ AEZFQHWGQGTLVTVSS (SEQ ID NO: 152)
R YYYDSSGYYY AEYFQHWGQGTLVTVSS (JH1)
(SEQ ID NO: 88) (SEQ ID NO: 66)

1 1 1 1
9 9 0 0 0 1
4 5 0 3abcdefghijklmnop q rstuvwxya4 0
′
Amino-acid diversity = 6.7 E 7
DNA diversity = 6.7 E 7
Stop-free = 100
Gratuitous Cys-free = 100
Free of stop and Cy = 100%

Design 20 has CDR3s of length 33, 34, or 35. Residue 94 can be K or R. The ZZZZZZ(Z)ZZ::D3-22(2^ndRF with six Ys as Z)::ZZZZZZZ(Z)ZZZ::JH1 (with 1 Z)(SEQ ID NO:995). PCR combining (C35D322AJH1_T), (C34D322AJH1_T), (C35D322AJH1_B), and (C34D322AJH1_B) allows length as well as sequence diversity.

(C35D322AJH1)T)

(SEQ ID NO: 153)

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

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

tmc t-3′

(C34D322AJH1)T)

(SEQ ID NO: 154)

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

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

t-3′

(C350322AJH1_B)

(SEQ ID NO: 920)

5′-cAg AgT Acc cTg gcc ccA gTg TTg gAA gKA TTc

Agc gKA gKA gKA gKA AKA gKA AKA gKA gKA AKA gKA

AKA gKA gKA gcc ggA gcT gTc-gKA gKA g-3′

(C34D322AJH1_B)

(SEQ ID NO: 155)

5'-cAg AgT Acc cTg gcc ccA gTg TTg gAA gKA TTc Agc

gKA gKA gKA gKA AKA gKA AKA gKA gKA AKA AKA gKA

gKA gcc ggA gcT gTc gKA gKA g-3'

Selection Against Stop Codons:

Because some of these libraries have NNK codons, they will have some TAG stop codons. We could remove the clones with TAG by cloning the amplified DNA into an XbaI-BstEII site between the signal sequence for a bla gene and the actual bla protein and express in Sup⁰cells. Bla^Rcolonies do not contain TAG stops. Alternatively, we could clone the XbaI-BstEII fragments ahead of a kanamycin-resistance gene and select for Kan^R. We would then move the XbaI-BstEII cassette into the phage library.
Also, because wobbling allows some stop codons, we can improve the library by removing the clones with stops by cloning the amplified DNA into an XbaI-BstEII site between the signal sequence for a bla gene and the actual bla protein and express in Sup⁰cells. Bla^Rcolonies do not contain stops. Alternatively, we can clone the XbaI-BstEII fragments ahead of a kanamycin-resistance gene and select for Kan^R. We can then move the XbaI-BstEII cassette into the phage library.

TABLE 20

Human D regions

		RF 1	RF 2	RF 3	Used in designs

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

	1-7	(SEQ ID NO: 159)	(SEQ ID NO: 160)	(SEQ ID NO: 161)
		GITGT	V*LEL	YNWNY

	1-20	(SEQ ID NO: 159)	(SEQ ID NO: 162)	(SEQ ID NO: 163)
		GITGT	V*LER	YNWND

	1-26	(SEQ ID NO: 164)	(SEQ ID NO: 165)	(SEQ ID NO: 166)
		GIVGAT	V*WELL	YSGSYY

D2	2-2	(SEQ ID NOS 171 & 167)	(SEQ ID NO: 70)	(SEQ ID NO: 168)	1, 5, 6, 7,
		RIL**YQLLY	GYCSSTSCYT	DIVVVPAAI

	2-8	(SEQ ID NOS 169 & 392)	(SEQ ID NO: 115)	(SEQ ID NO: 170)	20, 21, 22,
		RILY@WCMLY	GYCTNGVCYT	DIVLMVYAI

	2-15	(SEQ ID NO: 171)	(SEQ ID NO: 136)	(SEQ ID NO: 172)	25,
		RILWWLLL	GYCSGGSCYS	DIVVVVAAT

	2-21	(SEQ ID NO: 173)	(SEQ ID NO: 174)	(SEQ ID NO: 175)
		SILWW$LLF	AYCGGDCYS	HIVVVTAI

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

	3-9	(SEQ ID NO: 179)	(SEQ ID NO: 180)	(SEQ ID NOS 181 & 579)
		VLRYFDWLL@	YYDILTGYYN	ITIF*LVII

	3-10	(SEQ ID NO: 182)	(SEQ ID NO: 81)	(SEQ ID NO: 183)
		VLLWFGELL@	YYYGSGSYYN	ITMVRGVII

	3-16	(SEQ ID NO: 184)	(SEQ ID NO: 104)	(SEQ ID NO: 185)	8, 9, 14, 15,
		VL$LRLGELSLY	YYDYVWGSYRYT	IMITFGGVIVI	17, 18

	3-22	(SEQ ID NO: 186)	(SEQ ID NO: 187)	(SEQ ID NO: 188)	4, 19, 20
		VLL***WLLL	YYYDSSGYYY	ITMIVVVIT

D4	4-4	(SEQ ID NO: 189)	(SEQ ID NO: 192)	(SEQ ID NO: 190)
		$LQ@L	DYSNY	TTVT

	4-11	(SEQ ID NO: 191)	(SEQ ID NO: 192)	(SEQ ID NO: 193)
		$LQ@L	DYSNY	TTVT

	4-17	(SEQ ID NO: 194)	(SEQ ID NO: 195)	(SEQ ID NO: 196)
		$LR@L	DYGDY	TTVT

	4-23	(SEQ ID NO: 197)	(SEQ ID NO: 198)	(SEQ ID NO: 199)
		$LRW@L	DYGGNS	TTVVT

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

	5-12	(SEQ ID NO: 203)	(SEQ ID NO: 204)	(SEQ ID NO: 205)
		VDIVATI	WI*WLRL	GYSGYDY

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

	5-24	(SEQ ID NO: 209)	(SEQ ID NO: 210)	(SEQ ID NO: 211)
		VEMATI	*RWLQL	RDGYNY

D6	6-6	(SEQ ID NO: 212)	(SEQ ID NO: 213)	(SEQ ID NO: 214)
		EYSSSS	SIAAR	V*QLV

	6-13	(SEQ ID NO: 215)	(SEQ ID NO: 216)	(SEQ ID NO: 217)
		GYSSSWY	GIAAAG	V*QQLV

	6-19	(SEQ ID NO: 218)	(SEQ ID NO: 219)	(SEQ ID NO: 220)
		GYSSGWY	GIAVAG	V*QWLV

D7	7-27	(SEQ ID NO: 221)	(SEQ ID NO: 222)	(SEQ ID NO: 223)
		LTG	@LG	NWG

!* for TAG; @ for TAA; $ for TGA
D - Amino acid sequence alignment (RF: reading frame)

TABLE 3

Human JH segments

H3

------

CDR3

--------

100 110

| FR4-------- Used in designs

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

JH2 ---YWYFDL WGRGTLVTVSS (SEQ ID NO: 67)

JH3 -----AFDI WGQGTMVTVSS (SEQ ID NO: 2)

JH4 -----YFDY WGQGTLVTVSS (SEQ ID NO: 1)

JH5 ----NWFDP WGQGTLVTVSS (SEQ ID NO: 68)

JH6 YYYYYGMDV WGQGTTVTVSS (SEQ ID NO: 3)

123456789

JH - Amino acid sequence alignment

TABLE 10

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

! CDR3.......

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

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

!

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

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

! BstEII...

TABLE 11

Trimers that can be extracted from human
D segments

	GTT D1-1.1.1	1
	VQL D1-1.2.1	2
	YNW D1-1.3.1	3
	TTG D1-1.1.2	4
	QLE D1-1.2.2	5
	NWN D1-1.3.2	6
	TGT D1-1.1.3	7
	LER D1-1.2.3	8 (SEQ ID NO: 162)
	WND D1-1.3.3	9
	GIT D1-7.1.1	10
	VyL D1-7.1.2	11 *
	ITG D1-7.1.2	12
	yLE D1-7.2.2	13
	LEL D1-7.2.3	14 (SEQ ID NO: 160)
	WNY D1-7.3.3	15
	GIV D1-26.1.1	16
	VyW D1-26.2.1	17 *
	YSG D1-26.3.1	18
	IVG D1-26.1.2	19
	yWE D1-26.2.2	20 *
	SGS D1-26.3.2	21
	VGA D1-26.1.3	22
	WEL D1-26.2.3	23
	GSY D1-26.3.3	24
	GAT D1-26.1.4	25
	ELL D1-26.2.4	26
	SYY D1-26.3.4	27
	RIL D2-2.1.1	28 (SEQ ID NO: 171)
	GYC D2-2.2.1	29 #
	DIV D2-2.3.1	30
	ILy D2-2.1.2	31 *
	YCS D2-2.2.2	32 #
	IVV D2-2.3.2	33
	Lyy D2-2.1.3	34 *
	CSS D2-2.2.3	35 #
	VVV D2-2.3.3	36
	yyY D2-2.1.4	37 *
	SST D2-2.2.4	38
	VVP D2-2.3.4	39
	yYQ D2-2.2.5	40 *
	STS D2-2.2.5	41
	VPA D2-2.3.5	42
	YQL D2-2.1.6	43
	TSC D2-2.2.6	44 #
	PAA D2-2.3.6	45
	QLL D2-2.1.7	46
	SCY D2-2.2.7	47 #
	AAI D2-2.3.7	48
	LLY D2-2.1.8	49
	CYT D2-2.2.8	50 #
	ILY D2-8.1.2	51
	YCT D2-8.2.2	52 #
	IVL D2-8.3.2	53
	LYy D2-8.1.3	54 *
	CTN D2-8.2.3	55 #
	VLM D2-8.3.3	56
	YyW D2-8.1.4	57 *
	TNG D2-8.2.4	58
	LMV D2-8.3.4	59
	yWC D2-8.1.5	60 *#
	NGV D2-8.2.5	61
	MVY D2-8.3.5	62
	WCM D2-8.1.6	63 #
	GVC D2-8.2.6	64 #
	VYA D2-8.3.6	65
	CML D2-8.1.7	66 #
	VCY D2-8.2.7	67 #
	YAI D2-8.3.7	68
	MLY D2-8.1.8	69
	LyW D2-15.1.3	70 *
	CSG D2-15.2.3	71 #
	yWW D2-15.1.4	72 *
	SGG D2-15.2.4	73
	WWy D2-15.1.5	74
	GGS D2-15.2.5	75
	VVA D2-15.3.5	76
	WyL D2-15.1.6	77 *
	GSC D2-15.2.6	78 #
	VAA D2-15.3.6	79
	yLL D2-15.1.7	80 *
	AAT D2-15.3.7	81
	LLL D2-15.1.8	82
	CYS D2-15.2.8	83 #
	SIL D2-21.1.1	84
	AYC D2-21.2.1	85 #
	HIV D2-21.3.1	86
	ILW D2-21.1.2	87
	YCG D2-21.2.2	88 #
	LWW D2-21.1.3	89
	CGG D2-21.2.3	90 #
	WWw D2-21.1.4	91 *
	GGD D2-21.2.4	92
	VVT D2-21.3.4	93
	WwL D2-21.1.5	94 *
	GDC D2-21.2.5	95 #
	VTA D2-21.3.5	96
	wLL D2-21.1.6	97 *
	DCY D2-21.2.6	98 #
	TAI D2-21.3.6	99
	LLF D2-21.1.7	100
	VLR D3-3.1.1	101
	YYD D3-3.2.1	102
	ITI D3-3.3.1	103
	LRF D3-3.1.2	104
	YDF D3-3.2.2	105
	TIF D3-3.3.2	106
	RFL D3-3.1.3	107
	DFW D3-3.2.3	108
	IFG D3-3.3.3	109
	FLE D3-3.1.4	110
	FWS D3-3.2.4	111
	FGV D3-3.3.4	112
	LEW D3-3.1.5	113
	WSG D3-3.2.5	114
	GVV D3-3.3.5	115
	EWL D3-3.1.6	116
	SGY D3-3.2.6	117
	VVI D3-3.3.6	118
	WLL D3-3.1.7	119
	GYY D3-3.2.7	120
	VII D3-3.3.7	121
	YYT D3-3.2.8	122
	LRY D3-9.1.2	123
	YDI D3-9.2.2	124
	RYF D3-9.1.3	125
	DIL D3-9.2.3	126
	IFy D3-9.3.3	127 *
	YFD D3-9.1.4	128
	ILT D3-9.2.4	129
	FyL D3-9.3.4	130 *
	FDW D3-9.1.5	131
	LTG D3-9.2.5	132 (SEQ ID NO: 221)
	yLV D3-9.3.5	133 *
	DWL D3-9.1.6	134
	TGY D3-9.2.6	135
	LVI D3-9.3.6	136
	LLy D3-9.1.8	137 *
	YYN D3-9.2.8	138
	VLL D3-10.1.1	139
	YYY D3-10.2.1	140
	ITM D3-10.3.1	141
	LLW D3-10.1.2	142
	YYG D3-10.2.2	143
	TMV D3-10.3.2	144
	LWF D3-10.1.3	145
	YGS D3-10.2.3	146
	MVR D3-10.3.3	147
	WFG D3-10.1.4	148
	GSG D3-10.2.4	149
	VRG D3-10.3.4	150
	FGE D3-10.1.5	151
	RGV D3-10.3.5	152
	GEL D3-10.1.6	153
	GVI D3-10.3.6	154
	VLw D3-16.1.1	155 *
	IMI D3-16.3.1	156
	LwL D3-16.1.2	157 *
	YDY D3-16.2.2	158
	MIT D3-16.3.2	159
	wLR D3-16.1.3	160 *
	DYV D3-16.2.3	161
	ITF D3-16.3.3	162
	LRL D3-16.1.4	163
	YVW D3-16.2.4	164
	TFG D3-16.3.4	165
	RLG D3-16.1.5	166
	VWG D3-16.2.5	167
	FGG D3-16.3.5	168
	LGE D3-16.1.6	169
	WGS D3-16.2.6	170
	GGV D3-16.3.6	171
	ELS D3-16.1.8	172
	SYR D3-16.2.8	173
	VIV D3-16.3.8	174
	LSL D3-16.1.9	175
	YRY D3-16.2.9	176
	IVI D3-16.3.9	177
	SLY D3-16.1.10	178
	RYT D3-16.2.10	179
	LLw D3-22.1.2	180 *
	TMI D3-22.3.2	181
	Lwy D3-22.1.3	182 *
	YDS D3-22.2.3	183
	MIV D3-22.3.3	184
	wyy D3-22.1.4	185 *
	DSS D3-22.2.4	186
	yyW D3-22.1.5	187 *
	SSG D3-22.2.5	188
	yWL D3-22.1.6	189 *
	VIT D3-22.3.7	190
	wLQ D4-4.1.1	191 *
	DYS D4-4.2.1	192
	TTV D4-4.3.1	193
	LQy D4-4.1.2	194 *
	YSN D4-4.2.2	195
	TVT D4-4.3.2	196
	QyL D4-4.1.3	197 *
	SNY D4-4.2.3	198
	DYG D4-17.2.1	199
	LRw D4-17.1.2	200 * (SEQ ID NO: 197)
	YGD D4-17.2.2	201
	RwL D4-17.1.3	202 *
	GDY D4-17.2.3	203
	LRW D4-23.1.2	204 (SEQ ID NO: 197)
	YGG D4-23.2.2	205
	TVV D4-23.3.2	206
	RWy D4-23.1.3	207 *
	GGN D4-23.2.3	208
	GNS D4-23.2.4	209
	VDT D5-5.1.1	210
	WIQ D5-5.2.1	211
	GYS D5-5.3.1	212
	DTA D5-5.1.2	213
	IQL D5-5.2.2	214
	YSY D5-5.3.2	215
	TAM D5-5.1.3	216
	QLW D5-5.2.3	217
	SYG D5-5.3.3	218
	AMV D5-5.1.4	219
	LWL D5-5.2.4	220
	YGY D5-5.3.4	221
	VDI D5-12.1.1	222
	WIy D5-12.2.1	223 *
	IyW D5-12.2.2	224 *
	IVA D5-12.1.3	225
	VAT D5-12.1.4	226
	WLR D5-12.2.4	227
	GYD D5-12.3.4	228
	ATI D5-12.1.5	229
	VEM D5-24.1.1	230
	yRW D5-24.2.1	231 *
	RDG D5-24.3.1	232
	EMA D5-24.1.2	233
	RWL D5-24.2.2	234
	DGY D5-24.3.2	235
	MAT D5-24.1.3	236
	WLQ D5-24.2.3	237
	GYN D5-24.3.3	238
	LQL D5-24.2.4	239
	YNY D5-24.3.4	240
	EYS D6-6.1.1	241
	SIA D6-6.2.1	242
	VyQ D6-6.3.1	243 *
	YSS D6-6.1.2	244
	IAA D6-6.2.2	245
	yQL D6-6.3.2	246 *
	SSS D6-6.1.3	247
	AAR D6-6.2.3	248
	QLV D6-6.3.3	249 (SEQ ID NO: 214)
	GIA D6-13.2.1	250
	yQQ D6-13.3.2	251 *
	AAA D6-13.2.3	252
	QQL D6-13.3.3	253
	SSW D6-13.1.4	254
	AAG D6-13.2.4	255
	SWY D6-13.1.5	256
	IAV D6-19.2.2	257
	yQW D6-19.3.2	258 *
	AVA D6-19.2.3	259
	QWL D6-19.3.3	260
	SGW D6-19.1.4	261
	VAG D6-19.2.4	262
	WLV D6-19.3.4	263
	GWY D6-19.1.5	264
	yLG D7-27.2.1	265 *
	NWG D7-27.3.1	266 (SEQ ID NO: 223)

In Tables 11-14, the use of a lower case letter in an amino acid sequence indicates that a stop codon was changed to the residue listed as the lower case letter. For example, in the amino acid sequence “yLE”, a Tyr residue was introduced in place of a stop codon.

TABLE 12

Distinct tetramers that can be extracted from
human D segments

GTTG D1-1.1.1	(SEQ ID NO: 257)	1
VQLE D1-1.2.1	(SEQ ID NO: 258)	2
YNWN D1-1.3.1	(SEQ ID NO: 259)	3
TTGT D1-1.1.2	(SEQ ID NO: 263)	4
QLER D1-1.2.2	(SEQ ID NO: 264)	5
NWND D1-1.3.2	(SEQ ID NO: 265)	6
GITG D1-7.1.1	(SEQ ID NO: 266)	7
VyLE D1-7.2.1	(SEQ ID NO: 267)	8
ITGT D1-7.1.2	(SEQ ID NO: 271)	9
yLEL D1-7.2.2	(SEQ ID NO: 272)	10
NWNY D1-7.3.2	(SEQ ID NO: 273)	11
yLER D1-20.2.2	(SEQ ID NO: 275)	12
GIVG D1-26.1.1	(SEQ ID NO: 276)	13
VyWE D1-26.2.1	(SEQ ID NO: 277)	14
YSGS D1-26.3.1	(SEQ ID NO: 278)	15
IVGA D1-26.1.2	(SEQ ID NO: 285)	16
yWEL D1-26.2.2	(SEQ ID NO: 286)	17
SGSY D1-26.3.2	(SEQ ID NO: 287)	18
VGAT D1-26.1.3	(SEQ ID NO: 291)	19
WELL D1-26.2.3	(SEQ ID NO: 292)	20
GSYY D1-26.3.3	(SEQ ID NO: 293)	21
RILy D2-2.1.1	(SEQ ID NO: 294)	22
GYCS D2-2.2.1	(SEQ ID NO: 295)	23
DIVV D2-2.3.1	(SEQ ID NO: 296)	24
ILyy D2-2.1.2	(SEQ ID NO: 303)	25
YCSS D2-2.2.2	(SEQ ID NO: 304)	26
IVVV D2-2.3.2	(SEQ ID NO: 305)	27
LyyY D2-2.1.3	(SEQ ID NO: 312)	28
CSST D2-2.2.3	(SEQ ID NO: 313)	29
VVVP D2-2.3.3	(SEQ ID NO: 314)	30
yyYQ D2-2.1.4	(SEQ ID NO: 321)	31
SSTS D2-2.2.4	(SEQ ID NO: 322)	32
VVPA D2-2.3.4	(SEQ ID NO: 323)	33
yYQL D2-2.1.5	(SEQ ID NO: 330)	34
STSC D2-2.2.5	(SEQ ID NO: 331)	35
VPAA D2-2.3.5	(SEQ ID NO: 332)	36
YQLL D2-2.1.6	(SEQ ID NO: 338)	37
TSCY D2-2.2.6	(SEQ ID NO: 339)	38
PAAI D2-2.3.6	(SEQ ID NO: 340)	39
QLLY D2-2.1.7	(SEQ ID NO: 343)	40
SCYT D2-2.2.7	(SEQ ID NO: 344)	41
RILY D2-8.1.1	(SEQ ID NO: 345)	42
GYCT D2-8.2.1	(SEQ ID NO: 346)	43
DIVL D2-8.3.1	(SEQ ID NO: 347)	44
ILYy D2-8.1.2	(SEQ ID NO: 354)	45
YCTN D2-8.2.2	(SEQ ID NO: 355)	46
IVLM D2-8.3.2	(SEQ ID NO: 356)	47
LYyW D2-8.1.3	(SEQ ID NO: 363)	48
CTNG D2-8.2.3	(SEQ ID NO: 364)	49
VLMV D2-8.3.3	(SEQ ID NO: 365)	50
YyWC D2-8.1.4	(SEQ ID NO: 372)	51
TNGV D2-8.2.4	(SEQ ID NO: 373)	52
LMVY D2-8.3.4	(SEQ ID NO: 374)	53
yWCM D2-8.1.5	(SEQ ID NO: 381)	54
NGVC D2-8.2.5	(SEQ ID NO: 382)	55
MVYA D2-8.3.5	(SEQ ID NO: 383)	56
WCML D2-8.1.6	(SEQ ID NO: 389)	57
GVCY D2-8.2.6	(SEQ ID NO: 390)	58
VYAI D2-8.3.6	(SEQ ID NO: 391)	59
CMLY D2-8.1.7	(SEQ ID NO: 394)	60
VCYT D2-8.2.7	(SEQ ID NO: 395)	61
ILyW D2-15.1.2	(SEQ ID NO: 401)	62
YCSG D2-15.2.2	(SEQ ID NO: 402)	63
LyWW D2-15.1.3	(SEQ ID NO: 409)	64
CSGG D2-15.2.3	(SEQ ID NO: 410)	65
VVVV D2-15.3.3	(SEQ ID NO: 411)	66
yWWy D2-15.1.4	(SEQ ID NO: 418)	67
SGGS D2-15.2.4	(SEQ ID NO: 419)	68
VVVA D2-15.3.4	(SEQ ID NO: 420)	69
WWyL D2-15.1.5	(SEQ ID NO: 427)	70
GGSC D2-15.2.5	(SEQ ID NO: 428)	71
VVAA D2-15.3.5	(SEQ ID NO: 429)	72
WyLL D2-15.1.6	(SEQ ID NO: 435)	73
GSCY D2-15.2.6	(SEQ ID NO: 436)	74
VAAT D2-15.3.6	(SEQ ID NO: 437)	75
yLLL D2-15.1.7	(SEQ ID NO: 440)	76
SCYS D2-15.2.7	(SEQ ID NO: 441)	77
SILW D2-21.1.1	(SEQ ID NO: 442)	78
AYCG D2-21.2.1	(SEQ ID NO: 443)	79
HIVV D2-21.3.1	(SEQ ID NO: 444)	80
ILWW D2-21.1.2	(SEQ ID NO: 451)	81
YCGG D2-21.2.2	(SEQ ID NO: 452)	82
LWWw D2-21.1.3	(SEQ ID NO: 459)	83
CGGD D2-21.2.3	(SEQ ID NO: 460)	84
VVVT D2-21.3.3	(SEQ ID NO: 461)	85
WWwL D2-21.1.4	(SEQ ID NO: 468)	86
GGDC D2-21.2.4	(SEQ ID NO: 469)	87
VVTA D2-21.3.4	(SEQ ID NO: 470)	88
WwLL D2-21.1.5	(SEQ ID NO: 476)	89
GDCY D2-21.2.5	(SEQ ID NO: 477)	90
VTAI D2-21.3.5	(SEQ ID NO: 478)	91
wLLF D2-21.1.6	(SEQ ID NO: 481)	92
DCYS D2-21.2.6	(SEQ ID NO: 482)	93
VLRF D3-3.1.1	(SEQ ID NO: 483)	94
YYDF D3-3.2.1	(SEQ ID NO: 484)	95
ITIF D3-3.3.1	(SEQ ID NO: 485)	96
LRFL D3-3.1.2	(SEQ ID NO: 492)	97
YDFW D3-3.2.2	(SEQ ID NO: 493)	98
TIFG D3-3.3.2	(SEQ ID NO: 494)	99
RFLE D3-3.1.3	(SEQ ID NO: 501)	100
DFWS D3-3.2.3	(SEQ ID NO: 502)	101
IFGV D3-3.3.3	(SEQ ID NO: 503)	102
FLEW D3-3.1.4	(SEQ ID NO: 510)	103
FWSG D3-3.2.4	(SEQ ID NO: 511)	104
FGVV D3-3.3.4	(SEQ ID NO: 512)	105
LEWL D3-3.1.5	(SEQ ID NO: 519)	106
WSGY D3-3.2.5	(SEQ ID NO: 520)	107
GVVI D3-3.3.5	(SEQ ID NO: 521)	108
EWLL D3-3.1.6	(SEQ ID NO: 527)	109
SGYY D3-3.2.6	(SEQ ID NO: 528)	110
VVII D3-3.3.6	(SEQ ID NO: 529)	111
WLLY D3-3.1.7	(SEQ ID NO: 532)	112
GYYT D3-3.2.7	(SEQ ID NO: 533)	113
VLRY D3-9.1.1	(SEQ ID NO: 534)	114
YYDI D3-9.2.1	(SEQ ID NO: 535)	115
LRYF D3-9.1.2	(SEQ ID NO: 542)	116
YDIL D3-9.2.2	(SEQ ID NO: 543)	117
TIFy D3-9.3.2	(SEQ ID NO: 544)	118
RYFD D3-9.1.3	(SEQ ID NO: 551)	119
DILT D3-9.2.3	(SEQ ID NO: 552)	120
IFyL D3-9.3.3	(SEQ ID NO: 553)	121
YFDW D3-9.1.4	(SEQ ID NO: 560)	122
ILTG D3-9.2.4	(SEQ ID NO: 561)	123
FyLV D3-9.3.4	(SEQ ID NO: 562)	124
FDWL D3-9.1.5	(SEQ ID NO: 569)	125
LTGY D3-9.2.5	(SEQ ID NO: 570)	126
yLVI D3-9.3.5	(SEQ ID NO: 571)	127
DWLL D3-9.1.6	(SEQ ID NO: 577)	128
TGYY D3-9.2.6	(SEQ ID NO: 578)	129
LVII D3-9.3.6	(SEQ ID NO: 579)	130
WLLy D3-9.1.7	(SEQ ID NO: 582)	131
GYYN D3-9.2.7	(SEQ ID NO: 583)	132
VLLW D3-10.1.1	(SEQ ID NO: 584)	133
YYYG D3-10.2.1	(SEQ ID NO: 585)	134
ITMV D3-10.3.1	(SEQ ID NO: 586)	135
LLWF D3-10.1.2	(SEQ ID NO: 593)	136
YYGS D3-10.2.2	(SEQ ID NO: 594)	137
TMVR D3-10.3.2	(SEQ ID NO: 595)	138
LWFG D3-10.1.3	(SEQ ID NO: 602)	139
YGSG D3-10.2.3	(SEQ ID NO: 603)	140
MVRG D3-10.3.3	(SEQ ID NO: 604)	141
WFGE D3-10.1.4	(SEQ ID NO: 611)	142
GSGS D3-10.2.4	(SEQ ID NO: 612)	143
VRGV D3-10.3.4	(SEQ ID NO: 613)	144
FGEL D3-10.1.5	(SEQ ID NO: 620)	145
RGVI D3-10.3.5	(SEQ ID NO: 621)	146
GELL D3-10.1.6	(SEQ ID NO: 626)	147
GVII D3-10.3.6	(SEQ ID NO: 627)	148
ELLy D3-10.1.7	(SEQ ID NO: 630)	149
SYYN D3-10.2.7	(SEQ ID NO: 631)	150
VLwL D3-16.1.1	(SEQ ID NO: 632)	151
YYDY D3-16.2.1	(SEQ ID NO: 633)	152
IMIT D3-16.3.1	(SEQ ID NO: 634)	153
LwLR D3-16.1.2	(SEQ ID NO: 641)	154
YDYV D3-16.2.2	(SEQ ID NO: 642)	155
MITF D3-16.3.2	(SEQ ID NO: 643)	156
wLRL D3-16.1.3	(SEQ ID NO: 650)	157
DYVW D3-16.2.3	(SEQ ID NO: 651)	158
ITFG D3-16.3.3	(SEQ ID NO: 652)	159
LRLG D3-16.1.4	(SEQ ID NO: 659)	160
YVWG D3-16.2.4	(SEQ ID NO: 660)	161
TFGG D3-16.3.4	(SEQ ID NO: 661)	162
RLGE D3-16.1.5	(SEQ ID NO: 668)	163
VWGS D3-16.2.5	(SEQ ID NO: 669)	164
FGGV D3-16.3.5	(SEQ ID NO: 670)	165
LGEL D3-16.1.6	(SEQ ID NO: 677)	166
WGSY D3-16.2.6	(SEQ ID NO: 678)	167
GGVI D3-16.3.6	(SEQ ID NO: 679)	168
GELS D3-16.1.7	(SEQ ID NO: 686)	169
GSYR D3-16.2.7	(SEQ ID NO: 687)	170
GVIV D3-16.3.7	(SEQ ID NO: 688)	171
ELSL D3-16.1.8	(SEQ ID NO: 694)	172
SYRY D3-16.2.8	(SEQ ID NO: 695)	173
VIVI D3-16.3.8	(SEQ ID NO: 696)	174
LSLY D3-16.1.9	(SEQ ID NO: 699)	175
YRYT D3-16.2.9	(SEQ ID NO: 700)	176
VLLw D3-22.1.1	(SEQ ID NO: 701)	177
YYYD D3-22.2.1	(SEQ ID NO: 702)	178
ITMI D3-22.3.1	(SEQ ID NO: 703)	179
LLwy D3-22.1.2	(SEQ ID NO: 710)	180
YYDS D3-22.2.2	(SEQ ID NO: 711)	181
TMIV D3-22.3.2	(SEQ ID NO: 712)	182
Lwyy D3-22.1.3	(SEQ ID NO: 719)	183
YDSS D3-22.2.3	(SEQ ID NO: 720)	184
MIVV D3-22.3.3	(SEQ ID NO: 721)	185
wyyW D3-22.1.4	(SEQ ID NO: 728)	186
DSSG D3-22.2.4	(SEQ ID NO: 729)	187
yyWL D3-22.1.5	(SEQ ID NO: 736)	188
SSGY D3-22.2.5	(SEQ ID NO: 737)	189
VVVI D3-22.3.5	(SEQ ID NO: 738)	190
yWLL D3-22.1.6	(SEQ ID NO: 744)	191
VVIT D3-22.3.6	(SEQ ID NO: 745)	192
WLLL D3-22.1.7	(SEQ ID NO: 748)	193
GYYY D3-22.2.7	(SEQ ID NO: 749)	194
wLQy D4-4.1.1	(SEQ ID NO: 750)	195
DYSN D4-4.2.1	(SEQ ID NO: 751)	196
TTVT D4-4.3.1	(SEQ ID NO: 752)	197
LQyL D4-4.1.2	(SEQ ID NO: 755)	198
YSNY D4-4.2.2	(SEQ ID NO: 756)	199
wLRw D4-17.1.1	(SEQ ID NO: 757)	200
DYGD D4-17.2.1	(SEQ ID NO: 758)	201
LRwL D4-17.1.2	(SEQ ID NO: 761)	202
YGDY D4-17.2.2	(SEQ ID NO: 762)	203
wLRW D4-23.1.1	(SEQ ID NO: 763)	204
DYGG D4-23.2.1	(SEQ ID NO: 764)	205
TTVV D4-23.3.1	(SEQ ID NO: 765)	206
LRWy D4-23.1.2	(SEQ ID NO: 771)	207
YGGN D4-23.2.2	(SEQ ID NO: 772)	208
TVVT D4-23.3.2	(SEQ ID NO: 773)	209
RWyL D4-23.1.3	(SEQ ID NO: 776)	210
GGNS D4-23.2.3	(SEQ ID NO: 777)	211
VDTA D5-5.1.1	(SEQ ID NO: 778)	212
WIQL D5-5.2.1	(SEQ ID NO: 779)	213
GYSY D5-5.3.1	(SEQ ID NO: 780)	214
DTAM D5-5.1.2	(SEQ ID NO: 787)	215
IQLW D5-5.2.2	(SEQ ID NO: 788)	216
YSYG D5-5.3.2	(SEQ ID NO: 789)	217
TAMV D5-5.1.3	(SEQ ID NO: 793)	218
QLWL D5-5.2.3	(SEQ ID NO: 794)	219
SYGY D5-5.3.3	(SEQ ID NO: 795)	220
VDIV D5-12.1.1	(SEQ ID NO: 796)	221
WIyW D5-12.2.1	(SEQ ID NO: 797)	222
GYSG D5-12.3.1	(SEQ ID NO: 798)	223
DIVA D5-12.1.2	(SEQ ID NO: 805)	224
IyWL D5-12.2.2	(SEQ ID NO: 806)	225
YSGY D5-12.3.2	(SEQ ID NO: 807)	226
IVAT D5-12.1.3	(SEQ ID NO: 814)	227
yWLR D5-12.2.3	(SEQ ID NO: 815)	228
SGYD D5-12.3.3	(SEQ ID NO: 816)	229
VATI D5-12.1.4	(SEQ ID NO: 820)	230
WLRL D5-12.2.4	(SEQ ID NO: 821)	231
GYDY D5-12.3.4	(SEQ ID NO: 822)	232
VEMA D5-24.1.1	(SEQ ID NO: 823)	233
yRWL D5-24.2.1	(SEQ ID NO: 824)	234
RDGY D5-24.3.1	(SEQ ID NO: 825)	235
EMAT D5-24.1.2	(SEQ ID NO: 832)	236
RWLQ D5-24.2.2	(SEQ ID NO: 833)	237
DGYN D5-24.3.2	(SEQ ID NO: 834)	238
MATI D5-24.1.3	(SEQ ID NO: 838)	239
WLQL D5-24.2.3	(SEQ ID NO: 839)	240
GYNY D5-24.3.3	(SEQ ID NO: 840)	241
EYSS D6-6.1.1	(SEQ ID NO: 841)	242
SIAA D6-6.2.1	(SEQ ID NO: 842)	243
VyQL D6-6.3.1	(SEQ ID NO: 843)	244
YSSS D6-6.1.2	(SEQ ID NO: 848)	245
IAAR D6-6.2.2	(SEQ ID NO: 849)	246
yQLV D6-6.3.2	(SEQ ID NO: 850)	247
SSSS D6-6.1.3	(SEQ ID NO: 852)	248
GYSS D6-13.1.1	(SEQ ID NO: 853)	249
GIAA D6-13.2.1	(SEQ ID NO: 854)	250
VyQQ D6-13.3.1	(SEQ ID NO: 855)	251
IAAA D6-13.2.2	(SEQ ID NO: 862)	252
yQQL D6-13.3.2	(SEQ ID NO: 863)	253
SSSW D6-13.1.3	(SEQ ID NO: 868)	254
AAAG D6-13.2.3	(SEQ ID NO: 869)	255
QQLV D6-13.3.3	(SEQ ID NO: 870)	256
SSWY D6-13.1.4	(SEQ ID NO: 872)	257
GIAV D6-19.2.1	(SEQ ID NO: 873)	258
VyQW D6-19.3.1	(SEQ ID NO: 874)	259
YSSG D6-19.1.2	(SEQ ID NO: 881)	260
IAVA D6-19.2.2	(SEQ ID NO: 882)	261
yQWL D6-19.3.2	(SEQ ID NO: 883)	262
SSGW D6-19.1.3	(SEQ ID NO: 888)	263
AVAG D6-19.2.3	(SEQ ID NO: 889)	264
QWLV D6-19.3.3	(SEQ ID NO: 890)	265
SGWY D6-19.1.4	(SEQ ID NO: 941)	266

TABLE 13

Pentamers that can be extracted from human
D segments

GTTGT D1-1.1.1	(SEQ ID NO: 260)	1
VQLER D1-1.2.1	(SEQ ID NO: 261)	2
YNWND D1-1.3.1	(SEQ ID NO: 262)	3
GITGT D1-7.1.1	(SEQ ID NO: 268)	4
VyLEL D1-7.2.1	(SEQ ID NO: 269)	5
YNWNY D1-7.3.1	(SEQ ID NO: 270)	6
VyLER D1-20.2.1	(SEQ ID NO: 274)	7
GIVGA D1-26.1.1	(SEQ ID NO: 279)	8
VyWEL D1-26.2.1	(SEQ ID NO: 280)	9
YSGSY D1-26.3.1	(SEQ ID NO: 281)	10
IVGAT D1-26.1.2	(SEQ ID NO: 288)	11
yWELL D1-26.2.2	(SEQ ID NO: 289)	12
SGSYY D1-26.3.2	(SEQ ID NO: 290)	13
RILyy D2-2.1.1	(SEQ ID NO: 297)	14
GYCSS D2-2.2.1	(SEQ ID NO: 298)	15
DIVVV D2-2.3.1	(SEQ ID NO: 299)	16
ILyyY D2-2.1.2	(SEQ ID NO: 306)	17
YCSST D2-2.2.2	(SEQ ID NO: 307)	18
IVVVP D2-2.3.2	(SEQ ID NO: 308)	19
LyyYQ D2-2.1.3	(SEQ ID NO: 315)	20
CSSTS D2-2.2.3	(SEQ ID NO: 316)	21
VVVPA D2-2.3.3	(SEQ ID NO: 317)	22
yyYQL D2-2.1.4	(SEQ ID NO: 324)	23
SSTSC D2-2.2.4	(SEQ ID NO: 325)	24
VVPAA D2-2.3.4	(SEQ ID NO: 326)	25
yYQLL D2-2.1.5	(SEQ ID NO: 333)	26
STSCY D2-2.2.5	(SEQ ID NO: 334)	27
VPAAI D2-2.3.5	(SEQ ID NO: 335)	28
YQLLY D2-2.1.6	(SEQ ID NO: 341)	29
TSCYT D2-2.2.6	(SEQ ID NO: 342)	30
RILYy D2-8.1.1	(SEQ ID NO: 348)	31
GYCTN D2-8.2.1	(SEQ ID NO: 349)	32
DIVLM D2-8.3.1	(SEQ ID NO: 350)	33
ILYyW D2-8.1.2	(SEQ ID NO: 357)	34
YCTNG D2-8.2.2	(SEQ ID NO: 358)	35
IVLMV D2-8.3.2	(SEQ ID NO: 359)	36
LYyWC D2-8.1.3	(SEQ ID NO: 366)	37
CTNGV D2-8.2.3	(SEQ ID NO: 367)	38
VLMVY D2-8.3.3	(SEQ ID NO: 368)	39
YyWCM D2-8.1.4	(SEQ ID NO: 375)	40
TNGVC D2-8.2.4	(SEQ ID NO: 376)	41
LMVYA D2-8.3.4	(SEQ ID NO: 377)	42
yWCML D2-8.1.5	(SEQ ID NO: 384)	43
NGVCY D2-8.2.5	(SEQ ID NO: 385)	44
MVYAI D2-8.3.5	(SEQ ID NO: 386)	45
WCMLY D2-8.1.6	(SEQ ID NO: 392)	46
GVCYT D2-8.2.6	(SEQ ID NO: 393)	47
RILyW D2-15.1.1	(SEQ ID NO: 396)	48
GYCSG D2-15.2.1	(SEQ ID NO: 397)	49
ILyWW D2-15.1.2	(SEQ ID NO: 403)	50
YCSGG D2-15.2.2	(SEQ ID NO: 404)	51
IVVVV D2-15.3.2	(SEQ ID NO: 405)	52
LyWWy D2-15.1.3	(SEQ ID NO: 412)	53
CSGGS D2-15.2.3	(SEQ ID NO: 413)	54
VVVVA D2-15.3.3	(SEQ ID NO: 414)	55
yWWyL D2-15.1.4	(SEQ ID NO: 421)	56
SGGSC D2-15.2.4	(SEQ ID NO: 422)	57
VVVAA D2-15.3.4	(SEQ ID NO: 423)	58
WWyLL D2-15.1.5	(SEQ ID NO: 430)	59
GGSCY D2-15.2.5	(SEQ ID NO: 431)	60
VVAAT D2-15.3.5	(SEQ ID NO: 432)	61
WyLLL D2-15.1.6	(SEQ ID NO: 438)	62
GSCYS D2-15.2.6	(SEQ ID NO: 439)	63
SILWW D2-21.1.1	(SEQ ID NO: 445)	64
AYCGG D2-21.2.1	(SEQ ID NO: 446)	65
HIVVV D2-21.3.1	(SEQ ID NO: 447)	66
ILWWw D2-21.1.2	(SEQ ID NO: 453)	67
YCGGD D2-21.2.2	(SEQ ID NO: 454)	68
IVVVT D2-21.3.2	(SEQ ID NO: 455)	69
LWWwL D2-21.1.3	(SEQ ID NO: 462)	70
CGGDC D2-21.2.3	(SEQ ID NO: 463)	71
VVVTA D2-21.3.3	(SEQ ID NO: 464)	72
WWwLL D2-21.1.4	(SEQ ID NO: 471)	73
GGDCY D2-21.2.4	(SEQ ID NO: 472)	74
VVTAI D2-21.3.4	(SEQ ID NO: 473)	75
WwLLF D2-21.1.5	(SEQ ID NO: 479)	76
GDCYS D2-21.2.5	(SEQ ID NO: 480)	77
VLRFL D3-3.1.1	(SEQ ID NO: 486)	78
YYDFW D3-3.2.1	(SEQ ID NO: 487)	79
ITIFG D3-3.3.1	(SEQ ID NO: 488)	80
LRFLE D3-3.1.2	(SEQ ID NO: 495)	81
YDFWS D3-3.2.2	(SEQ ID NO: 496)	82
TIFGV D3-3.3.2	(SEQ ID NO: 497)	83
RFLEW D3-3.1.3	(SEQ ID NO: 504)	84
DFWSG D3-3.2.3	(SEQ ID NO: 505)	85
IFGVV D3-3.3.3	(SEQ ID NO: 506)	86
FLEWL D3-3.1.4	(SEQ ID NO: 513)	87
FWSGY D3-3.2.4	(SEQ ID NO: 514)	88
FGVVI D3-3.3.4	(SEQ ID NO: 515)	89
LEWLL D3-3.1.5	(SEQ ID NO: 522)	90
WSGYY D3-3.2.5	(SEQ ID NO: 523)	91
GVVII D3-3.3.5	(SEQ ID NO: 524)	92
EWLLY D3-3.1.6	(SEQ ID NO: 530)	93
SGYYT D3-3.2.6	(SEQ ID NO: 531)	94
VLRYF D3-9.1.1	(SEQ ID NO: 536)	95
YYDIL D3-9.2.1	(SEQ ID NO: 537)	96
ITIFy D3-9.3.1	(SEQ ID NO: 538)	97
LRYFD D3-9.1.2	(SEQ ID NO: 545)	98
YDILT D3-9.2.2	(SEQ ID NO: 546)	99
TIFyL D3-9.3.2	(SEQ ID NO: 547)	100
RYFDW D3-9.1.3	(SEQ ID NO: 554)	101
DILTG D3-9.2.3	(SEQ ID NO: 555)	102
IFyLV D3-9.3.3	(SEQ ID NO: 556)	103
YFDWL D3-9.1.4	(SEQ ID NO: 563)	104
ILTGY D3-9.2.4	(SEQ ID NO: 564)	105
FyLVI D3-9.3.4	(SEQ ID NO: 565)	106
FDWLL D3-9.1.5	(SEQ ID NO: 572)	107
LTGYY D3-9.2.5	(SEQ ID NO: 573)	108
yLVII D3-9.3.5	(SEQ ID NO: 574)	109
DWLLy D3-9.1.6	(SEQ ID NO: 580)	110
TGYYN D3-9.2.6	(SEQ ID NO: 581)	111
VLLWF D3-10.1.1	(SEQ ID NO: 587)	112
YYYGS D3-10.2.1	(SEQ ID NO: 588)	113
ITMVR D3-10.3.1	(SEQ ID NO: 589)	114
LLWFG D3-10.1.2	(SEQ ID NO: 596)	115
YYGSG D3-10.2.2	(SEQ ID NO: 597)	116
TMVRG D3-10.3.2	(SEQ ID NO: 598)	117
LWFGE D3-10.1.3	(SEQ ID NO: 605)	118
YGSGS D3-10.2.3	(SEQ ID NO: 606)	119
MVRGV D3-10.3.3	(SEQ ID NO: 607)	120
WFGEL D3-10.1.4	(SEQ ID NO: 614)	121
GSGSY D3-10.2.4	(SEQ ID NO: 615)	122
VRGVI D3-10.3.4	(SEQ ID NO: 616)	123
FGELL D3-10.1.5	(SEQ ID NO: 622)	124
RGVII D3-10.3.5	(SEQ ID NO: 623)	125
GELLy D3-10.1.6	(SEQ ID NO: 628)	126
GSYYN D3-10.2.6	(SEQ ID NO: 629)	127
VLwLR D3-16.1.1	(SEQ ID NO: 635)	128
YYDYV D3-16.2.1	(SEQ ID NO: 636)	129
IMITF D3-16.3.1	(SEQ ID NO: 637)	130
LwLRL D3-16.1.2	(SEQ ID NO: 644)	131
YDYVW D3-16.2.2	(SEQ ID NO: 645)	132
MITFG D3-16.3.2	(SEQ ID NO: 646)	133
wLRLG D3-16.1.3	(SEQ ID NO: 653)	134
DYVWG D3-16.2.3	(SEQ ID NO: 654)	135
ITFGG D3-16.3.3	(SEQ ID NO: 655)	136
LRLGE D3-16.1.4	(SEQ ID NO: 662)	137
YVWGS D3-16.2.4	(SEQ ID NO: 663)	138
TFGGV D3-16.3.4	(SEQ ID NO: 664)	139
RLGEL D3-16.1.5	(SEQ ID NO: 671)	140
VWGSY D3-16.2.5	(SEQ ID NO: 672)	141
FGGVI D3-16.3.5	(SEQ ID NO: 673)	142
LGELS D3-16.1.6	(SEQ ID NO: 680)	143
WGSYR D3-16.2.6	(SEQ ID NO: 681)	144
GGVIV D3-16.3.6	(SEQ ID NO: 682)	145
GELSL D3-16.1.7	(SEQ ID NO: 689)	146
GSYRY D3-16.2.7	(SEQ ID NO: 690)	147
GVIVI D3-16.3.7	(SEQ ID NO: 691)	148
ELSLY D3-16.1.8	(SEQ ID NO: 697)	149
SYRYT D3-16.2.8	(SEQ ID NO: 698)	150
VLLwy D3-22.1.1	(SEQ ID NO: 704)	151
YYYDS D3-22.2.1	(SEQ ID NO: 705)	152
ITMIV D3-22.3.1	(SEQ ID NO: 706)	153
LLwyy D3-22.1.2	(SEQ ID NO: 713)	154
YYDSS D3-22.2.2	(SEQ ID NO: 714)	155
TMIVV D3-22.3.2	(SEQ ID NO: 715)	156
LwyyW D3-22.1.3	(SEQ ID NO: 722)	157
YDSSG D3-22.2.3	(SEQ ID NO: 723)	158
MIVVV D3-22.3.3	(SEQ ID NO: 724)	159
wyyWL D3-22.1.4	(SEQ ID NO: 730)	160
DSSGY D3-22.2.4	(SEQ ID NO: 731)	161
IVVVI D3-22.3.4	(SEQ ID NO: 732)	162
yyWLL D3-22.1.5	(SEQ ID NO: 739)	163
SSGYY D3-22.2.5	(SEQ ID NO: 740)	164
VVVIT D3-22.3.5	(SEQ ID NO: 741)	165
yWLLL D3-22.1.6	(SEQ ID NO: 746)	166
SGYYY D3-22.2.6	(SEQ ID NO: 747)	167
wLQyL D4-4.1.1	(SEQ ID NO: 753)	168
DYSNY D4-4.2.1	(SEQ ID NO: 754)	169
wLRwL D4-17.1.1	(SEQ ID NO: 759)	170
DYGDY D4-17.2.1	(SEQ ID NO: 760)	171
wLRWy D4-23.1.1	(SEQ ID NO: 766)	172
DYGGN D4-23.2.1	(SEQ ID NO: 767)	173
TTVVT D4-23.3.1	(SEQ ID NO: 768)	174
LRWyL D4-23.1.2	(SEQ ID NO: 774)	175
YGGNS D4-23.2.2	(SEQ ID NO: 775)	176
VDTAM D5-5.1.1	(SEQ ID NO: 781)	177
WIQLW D5-5.2.1	(SEQ ID NO: 782)	178
GYSYG D5-5.3.1	(SEQ ID NO: 783)	179
DTAMV D5-5.1.2	(SEQ ID NO: 790)	180
IQLWL D5-5.2.2	(SEQ ID NO: 791)	181
YSYGY D5-5.3.2	(SEQ ID NO: 792)	182
VDIVA D5-12.1.1	(SEQ ID NO: 799)	183
WIyWL D5-12.2.1	(SEQ ID NO: 800)	184
GYSGY D5-12.3.1	(SEQ ID NO: 801)	185
DIVAT D5-12.1.2	(SEQ ID NO: 808)	186
IyWLR D5-12.2.2	(SEQ ID NO: 809)	187
YSGYD D5-12.3.2	(SEQ ID NO: 810)	188
IVATI D5-12.1.3	(SEQ ID NO: 817)	189
yWLRL D5-12.2.3	(SEQ ID NO: 818)	190
SGYDY D5-12.3.3	(SEQ ID NO: 819)	191
VEMAT D5-24.1.1	(SEQ ID NO: 826)	192
yRWLQ D5-24.2.1	(SEQ ID NO: 827)	193
RDGYN D5-24.3.1	(SEQ ID NO: 828)	194
EMATI D5-24.1.2	(SEQ ID NO: 835)	195
RWLQL D5-24.2.2	(SEQ ID NO: 836)	196
DGYNY D5-24.3.2	(SEQ ID NO: 837)	197
EYSSS D6-6.1.1	(SEQ ID NO: 844)	198
SIAAR D6-6.2.1	(SEQ ID NO: 845)	199
VyQLV D6-6.3.1	(SEQ ID NO: 846)	200
YSSSS D6-6.1.2	(SEQ ID NO: 851)	201
GYSSS D6-13.1.1	(SEQ ID NO: 856)	202
GIAAA D6-13.2.1	(SEQ ID NO: 857)	203
VyQQL D6-13.3.1	(SEQ ID NO: 858)	204
YSSSW D6-13.1.2	(SEQ ID NO: 864)	205
IAAAG D6-13.2.2	(SEQ ID NO: 865)	206
yQQLV D6-13.3.2	(SEQ ID NO: 866)	207
SSSWY D6-13.1.3	(SEQ ID NO: 871)	208
GYSSG D6-19.1.1	(SEQ ID NO: 875)	209
GIAVA D6-19.2.1	(SEQ ID NO: 876)	210
VyQWL D6-19.3.1	(SEQ ID NO: 877)	211
YSSGW D6-19.1.2	(SEQ ID NO: 884)	212
IAVAG D6-19.2.2	(SEQ ID NO: 885)	213
yQWLV D6-19.3.2	(SEQ ID NO: 886)	214
SSGWY D6-19.1.3	(SEQ ID NO: 891)	215

TABLE 14

All hexamers that can be extracted from
human D segments

GIVGAT D1-26.1.1	(SEQ ID NO: 282)	1
VyWELL D1-26.2.1	(SEQ ID NO: 283)	2
YSGSYY D1-26.3.1	(SEQ ID NO: 284)	3
RILyyY D2-2.1.1	(SEQ ID NO: 300)	4
GYCSST D2-2.2.1	(SEQ ID NO: 301)	5
DIVVVP D2-2.3.1	(SEQ ID NO: 302)	6
ILyyYQ D2-2.1.2	(SEQ ID NO: 309)	7
YCSSTS D2-2.2.2	(SEQ ID NO: 310)	8
IVVVPA D2-2.3.2	(SEQ ID NO: 311)	9
LyyYQL D2-2.1.3	(SEQ ID NO: 318)	10
CSSTSC D2-2.2.3	(SEQ ID NO: 319)	11
VVVPAA D2-2.3.3	(SEQ ID NO: 320)	12
yyYQLL D2-2.1.4	(SEQ ID NO: 327)	13
SSTSCY D2-2.2.4	(SEQ ID NO: 328)	14
VVPAAI D2-2.3.4	(SEQ ID NO: 329)	15
yYQLLY D2-2.1.5	(SEQ ID NO: 336)	16
STSCYT D2-2.2.5	(SEQ ID NO: 337)	17
RILYyW D2-8.1.1	(SEQ ID NO: 351)	18
GYCTNG D2-8.2.1	(SEQ ID NO: 352)	19
DIVLMV D2-8.3.1	(SEQ ID NO: 353)	20
ILYyWC D2-8.1.2	(SEQ ID NO: 360)	21
YCTNGV D2-8.2.2	(SEQ ID NO: 361)	22
IVLMVY D2-8.3.2	(SEQ ID NO: 362)	23
LYyWCM D2-8.1.3	(SEQ ID NO: 369)	24
CTNGVC D2-8.2.3	(SEQ ID NO: 370)	25
VLMVYA D2-8.3.3	(SEQ ID NO: 371)	26
YyWCML D2-8.1.4	(SEQ ID NO: 378)	27
TNGVCY D2-8.2.4	(SEQ ID NO: 379)	28
LMVYAI D2-8.3.4	(SEQ ID NO: 380)	29
yWCMLY D2-8.1.5	(SEQ ID NO: 387)	30
NGVCYT D2-8.2.5	(SEQ ID NO: 388)	31
RILyWW D2-15.1.1	(SEQ ID NO: 398)	32
GYCSGG D2-15.2.1	(SEQ ID NO: 399)	33
DIVVVV D2-15.3.1	(SEQ ID NO: 400)	34
ILyWWy D2-15.1.2	(SEQ ID NO: 406)	35
YCSGGS D2-15.2.2	(SEQ ID NO: 407)	36
IVVVVA D2-15.3.2	(SEQ ID NO: 408)	37
LyWWyL D2-15.1.3	(SEQ ID NO: 415)	38
CSGGSC D2-15.2.3	(SEQ ID NO: 416)	39
VVVVAA D2-15.3.3	(SEQ ID NO: 417)	40
yWWyLL D2-15.1.4	(SEQ ID NO: 424)	41
SGGSCY D2-15.2.4	(SEQ ID NO: 425)	42
VVVAAT D2-15.3.4	(SEQ ID NO: 426)	43
WWyLLL D2-15.1.5	(SEQ ID NO: 433)	44
GGSCYS D2-15.2.5	(SEQ ID NO: 434)	45
SILWWw D2-21.1.1	(SEQ ID NO: 448)	46
AYCGGD D2-21.2.1	(SEQ ID NO: 449)	47
HIVVVT D2-21.3.1	(SEQ ID NO: 450)	48
ILWWwL D2-21.1.2	(SEQ ID NO: 456)	49
YCGGDC D2-21.2.2	(SEQ ID NO: 457)	50
IVVVTA D2-21.3.2	(SEQ ID NO: 458)	51
LWWwLL D2-21.1.3	(SEQ ID NO: 465)	52
CGGDCY D2-21.2.3	(SEQ ID NO: 466)	53
VVVTAI D2-21.3.3	(SEQ ID NO: 467)	54
WWwLLF D2-21.1.4	(SEQ ID NO: 474)	55
GGDCYS D2-21.2.4	(SEQ ID NO: 475)	56
VLRFLE D3-3.1.1	(SEQ ID NO: 489)	57
YYDFWS D3-3.2.1	(SEQ ID NO: 490)	58
ITIFGV D3-3.3.1	(SEQ ID NO: 491)	59
LRFLEW D3-3.1.2	(SEQ ID NO: 498)	60
YDFWSG D3-3.2.2	(SEQ ID NO: 499)	61
TIFGVV D3-3.3.2	(SEQ ID NO: 500)	62
RFLEWL D3-3.1.3	(SEQ ID NO: 507)	63
DFWSGY D3-3.2.3	(SEQ ID NO: 508)	64
IFGVVI D3-3.3.3	(SEQ ID NO: 509)	65
FLEWLL D3-3.1.4	(SEQ ID NO: 516)	66
FWSGYY D3-3.2.4	(SEQ ID NO: 517)	67
FGVVII D3-3.3.4	(SEQ ID NO: 518)	68
LEWLLY D3-3.1.5	(SEQ ID NO: 525)	69
WSGYYT D3-3.2.5	(SEQ ID NO: 526)	70
VLRYFD D3-9.1.1	(SEQ ID NO: 539)	71
YYDILT D3-9.2.1	(SEQ ID NO: 540)	72
ITIFyL D3-9.3.1	(SEQ ID NO: 541)	73
LRYFDW D3-9.1.2	(SEQ ID NO: 548)	74
YDILTG D3-9.2.2	(SEQ ID NO: 549)	75
TIFyLV D3-9.3.2	(SEQ ID NO: 550)	76
RYFDWL D3-9.1.3	(SEQ ID NO: 557)	77
DILTGY D3-9.2.3	(SEQ ID NO: 558)	78
IFyLVI D3-9.3.3	(SEQ ID NO: 559)	79
YFDWLL D3-9.1.4	(SEQ ID NO: 566)	80
ILTGYY D3-9.2.4	(SEQ ID NO: 567)	81
FyLVII D3-9.3.4	(SEQ ID NO: 568)	82
FDWLLy D3-9.1.5	(SEQ ID NO: 575)	83
LTGYYN D3-9.2.5	(SEQ ID NO: 576)	84
VLLWFG D3-10.1.1	(SEQ ID NO: 590)	85
YYYGSG D3-10.2.1	(SEQ ID NO: 591)	86
ITMVRG D3-10.3.1	(SEQ ID NO: 592)	87
LLWFGE D3-10.1.2	(SEQ ID NO: 599)	88
YYGSGS D3-10.2.2	(SEQ ID NO: 600)	89
TMVRGV D3-10.3.2	(SEQ ID NO: 601)	90
LWFGEL D3-10.1.3	(SEQ ID NO: 608)	91
YGSGSY D3-10.2.3	(SEQ ID NO: 609)	92
MVRGVI D3-10.3.3	(SEQ ID NO: 610)	93
WFGELL D3-10.1.4	(SEQ ID NO: 617)	94
GSGSYY D3-10.2.4	(SEQ ID NO: 618)	95
VRGVII D3-10.3.4	(SEQ ID NO: 619)	96
FGELLy D3-10.1.5	(SEQ ID NO: 624)	97
SGSYYN D3-10.2.5	(SEQ ID NO: 625)	98
VLwLRL D3-16.1.1	(SEQ ID NO: 638)	99
YYDYVW D3-16.2.1	(SEQ ID NO: 639)	100
IMITFG D3-16.3.1	(SEQ ID NO: 640)	101
LwLRLG D3-16.1.2	(SEQ ID NO: 647)	102
YDYVWG D3-16.2.2	(SEQ ID NO: 648)	103
MITFGG D3-16.3.2	(SEQ ID NO: 649)	104
wLRLGE D3-16.1.3	(SEQ ID NO: 656)	105
DYVWGS D3-16.2.3	(SEQ ID NO: 657)	106
ITFGGV D3-16.3.3	(SEQ ID NO: 658)	107
LRLGEL D3-16.1.4	(SEQ ID NO: 665)	108
YVWGSY D3-16.2.4	(SEQ ID NO: 666)	109
TFGGVI D3-16.3.4	(SEQ ID NO: 667)	110
RLGELS D3-16.1.5	(SEQ ID NO: 674)	111
VWGSYR D3-16.2.5	(SEQ ID NO: 675)	112
FGGVIV D3-16.3.5	(SEQ ID NO: 676)	113
LGELSL D3-16.1.6	(SEQ ID NO: 683)	114
WGSYRY D3-16.2.6	(SEQ ID NO: 684)	115
GGVIVI D3-16.3.6	(SEQ ID NO: 685)	116
GELSLY D3-16.1.7	(SEQ ID NO: 692)	117
GSYRYT D3-16.2.7	(SEQ ID NO: 693)	118
VLLwyy D3-22.1.1	(SEQ ID NO: 707)	119
YYYDSS D3-22.2.1	(SEQ ID NO: 708)	120
ITMIVV D3-22.3.1	(SEQ ID NO: 709)	121
LLwyyW D3-22.1.2	(SEQ ID NO: 716)	122
YYDSSG D3-22.2.2	(SEQ ID NO: 717)	123
TMIVVV D3-22.3.2	(SEQ ID NO: 718)	124
LwyyWL D3-22.1.3	(SEQ ID NO: 725)	125
YDSSGY D3-22.2.3	(SEQ ID NO: 726)	126
MIVVVI D3-22.3.3	(SEQ ID NO: 727)	127
wyyWLL D3-22.1.4	(SEQ ID NO: 733)	128
DSSGYY D3-22.2.4	(SEQ ID NO: 734)	129
IVVVIT D3-22.3.4	(SEQ ID NO: 735)	130
yyWLLL D3-22.1.5	(SEQ ID NO: 742)	131
SSGYYY D3-22.2.5	(SEQ ID NO: 743)	132
wLRWyL D4-23.1.1	(SEQ ID NO: 769)	133
DYGGNS D4-23.2.1	(SEQ ID NO: 770)	134
VDTAMV D5-5.1.1	(SEQ ID NO: 784)	135
WIQLWL D5-5.2.1	(SEQ ID NO: 785)	136
GYSYGY D5-5.3.1	(SEQ ID NO: 786)	137
VDIVAT D5-12.1.1	(SEQ ID NO: 802)	138
WIyWLR D5-12.2.1	(SEQ ID NO: 803)	139
GYSGYD D5-12.3.1	(SEQ ID NO: 804)	140
DIVATI D5-12.1.2	(SEQ ID NO: 811)	141
IyWLRL D5-12.2.2	(SEQ ID NO: 812)	142
YSGYDY D5-12.3.2	(SEQ ID NO: 813)	143
VEMATI D5-24.1.1	(SEQ ID NO: 829)	144
yRWLQL D5-24.2.1	(SEQ ID NO: 830)	145
RDGYNY D5-24.3.1	(SEQ ID NO: 831)	146
EYSSSS D6-6.1.1	(SEQ ID NO: 847)	147
GYSSSW D6-13.1.1	(SEQ ID NO: 859)	148
GIAAAG D6-13.2.1	(SEQ ID NO: 860)	149
VyQQLV D6-13.3.1	(SEQ ID NO: 861)	150
YSSSWY D6-13.1.2	(SEQ ID NO: 867)	151
GYSSGW D6-19.1.1	(SEQ ID NO: 878)	152
GIAVAG D6-19.2.1	(SEQ ID NO: 879)	153
VyQWLV D6-19.3.1	(SEQ ID NO: 880)	154
YSSGWY D6-19.1.2	(SEQ ID NO: 887)	155

Example 3: CDR3 of Length 6-20

Insertion of D segments into synthetic HC CDR3s can lead to greater stability and lower immunogenicity. Libraries are designed at the amino-acid level by joining a VH to an optional filler of some length which is joined to a D segment an optional second filler and a JH. For libraries of length six or eight, a full-length JH may follow VH and a short filler. Table 77 shows the frequency of D segments in a sampling of 1419 Abs selected from FAB-310 or FAB-410 for binding to one target or another. In the sample, 1099 Abs had no detectable D segment (i.e., less that 70% match). Where D segments are used, the D segments D1-1.3, D1-26.3, D2-2.2, D2-8.2, D2-15.2, D2-21.2, D3-16.2, D3-22.2, D3-3.2, D3-9.1, D3-9.2, D3-10.2, D3-16.2, D4-4.2, D4-4.3, D4-11.2, D4-4.2, D4-17.2, D4-23.2, D5-5.3, D5-12.3, D5-18.3, D6-6.1, D6-6.2, D6-13.1, D6-13.2, D6-19.1, D6-19.2, and D7-27.1 are preferred.
Once the parental amino-acid sequence has been designed, it can be diversified in several ways: error-prone PCR, wobbling, and dobbling. Table 14 shows a number of hexamers that can be derived from human D regions. In one embodiment, the hexamers that contain cysteine residues are excluded. In one embodiment, the fragments of D regions that contain stops are excluded. In one embodiment, any TAG codon found in the D region is replaced by a codon picked from the set comprising TCG, TTG, TGG, CAG, AAG, TAT, and GAG. In one embodiment, any TAA codon found in the D region is replaced by a codon picked form the set comprising TCA, TTA, CAA, AAA, TAT, and GAA. In one embodiment, any TGA of the D region is replaced by a codon picked from the set comprising TGG, TCA, TTA, AGA, and GGA.
Table 21 shows exemplary parental amino-acid sequences for CDR3s from 6 to 20 amino acids. These parental sequences can be combined with diversity in HC CDR1 and CDR2 to form a library. The utility is likely to improve if the CDR3 regions are diversified by, for example, wobbling, dobbling, or error-prone PCR of the CDR3s. In Table 21, sequence 6a comprises the end of VH from 3-23 fused to whole JH1. Sequence 6b contains the end of 3-23 joined to a Y joined to D4-17 (RF 2) joined to the FR4 region of JH1. Sequence 6c contains the end of 3-23 followed by D5-5 (RF 3) followed by the FR4 part of JH1. Sequence 6d contains the end of 3-23 joined to SY joined to the whole JH4. Table 21 shows the level of doping that would be appropriate for the wobbling of the CDR3; other levels could be used as well. Other D regions or fragments of D regions could be used. Other JH sequences could be used.

TABLE 21

Parental amino-acid sequences for HC CDR3s of 6-20 AAs.

		level of		SEQ
Length	Parental sequence	doping	Comment	ID NO:

6a	yycakAEYFQHwgqgtlvtvss	70:10:10:10	JH1(whole)	226

6b	yycakYDYGDYwgqgtlvtvss	70:10:10:10	Y::D4-17(2)::FR4 of JH1	227

6c	yycakGYSYGYwgqgtlvtvss	70:10:10:10	D5-5(3)::FR4 of JH1	228

6d	yycakSYYFDYwgqgtlvtvss	70:10:10:10	SY::JH4(whole)	229

8a	yycakYYAEYFQHwgqgtlvtvss	73:9:9:9	YY:JH1(whole)	230

8b	yycakYGYSSSWYwgqgtlvtvss	73:9:9:9	Y::D6-13(1)::FR4 of JH1	231

8c	yycakYGDYYFDYwgqgtlvtvss	73:9:9:9	D4-17(2)[2-5]::JH4(whole)	232

10a	yycakYYYDSSGYYYwgqgtlvtvss	73:9:9:9	D3-22(2)::Fr4 of JH1	233

10b	yycakGYcSSTScYTwgqgtlvtvss	73:9:9:9	D2-2(2)::Fr4 of JH1	234

10c	yycakYYSSAEYFQHwgqgtlvtvss	73:9:9:9	YYSS::JH1(whole)	235
			(SEQ ID NO: 942)

10d	yycakGYSYGYYFDYwgqgtlvtvss	73:9:9:9	D5-5(3)::JH4(whole)	236

12a	yycakYYYDSSGYYYQHwgqgtlvtvss	85:5:5:5	D3-22(2)::QH::Fr4 of JH1	237

12b	yycakGYcSSTScYTQHwgqgtlvtvss	85:5:5:5	D2-2(2)::QH::Fr4 of JH1	238

12c	yycakYDGSYSAEYFQHwgqgtlvtvss	85:5:5:5	YDGSYS::JH1(whole)	239
			(SEQ ID NO: 943)

12d	yycakYYDYVWGSYRYTwgqgtlvtvss	85:5:5:5	D3-16(2)::Fr of JH1	240

12e	yycakGYSYGYYWYFDLwgrgtlvtvss	85:5:5:5	D5-5(3)::JH2(whole)	241

14a	yycakYYYDSSGYYYYFQHwgqgtlvtvss	73:9:9:9	D3-22(2)::YFQH::Fr of JH1	242
			(SEQ ID NO: 944)

14b	yycakGYcSSTScYTYFQHwgqgtlvtvss	73:9:9:9	D2-2(2)::YFQH::Fr of JH1	243
			(SEQ ID NO: 944)

14c	yycakSYGYcSSTScYTQHwgqgtlvtvss	73:9:9:9	SY::D2-2(2)::QH::Fr of JH1	244

14d	yycakSYRYSGYSAEYFQHwgqgtlvtvss	73:9:9:9	SYRYSGYS::JH1(whole)	245
			(SEQ ID NO: 945)

14e	yycakAYcGGDcYSNWFDPwgqgtlvtvss	73:9:9:9	D2-21(2)::JH5(whole)	246

15a	yycakSDGYYYDSSGYYYDYwgqgtlvtvss	73:9:9:9	SD::D3-22.2::JH4(101ff)	930

15b	yycakGSGYCSGGSCYSFDYwgqgtlvtvss	73:9:9:9	GS::D2-15.2::JH4(100ff)	931

15c	yycakGGRGYSSGWYRAFDIwgqgtmvtvss	73:9:9:9	GGR::D6-19.1::R::JH3(all)	932

16a	yycakYYYDSSGYYYAEYFQHwgqgtlvtvss	73:9:9:9	D3-22(2)::JH1(whole)	247

16b	yycakGYcSSTScYTAEYFQHwgqgtlvtvss	73:9:9:9	D2-2(2)::JH1(whole)	248

16c	yycakSYDSYRSYGSAEYFQHwgqgtlvtvss	73:9:9:9	SYDSYRSYGS::JH1(whole)	249
			(SEQ ID NO: 946)

16d	yycakSYSYGYcSSTScYTQHwgqgtlvtvss	73:9:9:9	SYSY::D2-2(2)::QH::Fr JH1	250
			(SEQ ID NO: 947)

17a	yycakSRPGYSSSWYYYYGMDVwgqgttvtvss	73:9:9:9	SRP::6-13.1::JH6(−1Y)	933

18a	yycakGYCSGGSCYSYYYYGMDVwgqgttvtvss	73:9:9:9	2-15.2::JH6(−1Y)	221

18b	yycakDGYCSGGSCYSYYYGMDVwgqgttvtvss	73:9:9:9	D::2-15.2::JH6(−2Ys)	222

19a	yycakDGYYYDSSGYYYRGYYFDYwgqgtlvtvss	73:9:9:9	D::D3-22.2::RGY::JH4(all)	223

20a	yycakYSSYYYYDSSGYYYAEYFQHwgqgtlvtvss	73:9:9:9	YSSY::D3-22(2)::JH1(whole)	251
			(SEQ ID NO: 948)

20b	yycakSYYSGYcSSTScYTAEYFQHwgqgtlvtvss	73:9:9:9	SYYS::D2-2(2)::JH1(whole)	252
			(SEQ ID NO: 949)

20c	yycakSGYcSSTScYTYYSAEYFQHwgqgtlvtvss	73:9:9:9	S::D2-2(2)::YYS::JH1(whole)	253

20d	yycakYYYYDYVWGSYRYTSNWFDPwgqgtlvtvss	73:9:9:9	Y::D3-16(2)::S::JH5(whole)	254

20e	yycakYYYYDYVWGSYRYTSSYFDYwgqgtlvtvss	73:9:9:9	Y::D3-16(2)::SS::JH4(whole)	255

TABLE 22

HC display cassette

The amino-acid sequence shown in Table 22 is SEQ ID NO: 892.

The DNA sequence shown in Table 22 is SEQ ID NO: 893.

!		Signal for VH-CH1-IIIstump
!		1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
!		M K Y L L P T A A A G L L L L
	946	atg aaa tac cta ttg cct acg gca gcc gct gga ttg tta tta ctc
!

!		16 17 18 19 20 21 22
!		A A Q P A M A
	991	gcG GCC cag ccG GCC atg gcc
!		SfiI.............
!		NgoMI...(1/2)
!		NcoI....
!
!	VH

!		FR1(DP47/V3-23)---------------
!		1 2 3 4 5 6 7 8
!		E V Q L L E S G
	1012	gaa\|gtt\|CAA\|TTG\|tta\|gag\|tct\|ggt\|
!		\| MfeI \|
!

!		--------------FR1--------------------------------------------
!		9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
!		G G L V Q P G G S L R L S C A
	1036	\|ggc\|ggt\|ctt\|gtt\|cag\|cct\|ggt\|ggt\|tct\|tta\|cgt\|ctt\|tct\|tgc\|gct\|
!

!		----FR1-------------------->\|...CDR1............\|---FR2------
!		24 25 26 27 28 29 30 31 32 33 34 35 36 37 38
!		A S G F T F S S Y A M S W V R
	1081	\|gct\|TCC\|GGA\|ttc\|act\|ttc\|tct\|tCG\|TAC\|Gct\|atg\|tct\|tgg\|gtt\|cgC\|
!		\| BspEI \| \| BsiWI\| \|BstXI.
!

!		--------FR2-------------------------------->\|...CDR2.........
!		39 40 41 42 43 44 45 46 47 48 49 50 51 52 52a
!		Q A P G K G L E W V S A I S G
	1126	\|CAa\|gct\|ccT\|GGt\|aaa\|ggt\|ttg\|gag\|tgg\|gtt\|tct\|gct\|atc\|tct\|ggt\|

!	...BstXI \|

!

!		....CDR2............................................\|---FR3---
!		53 54 55 56 57 58 59 60 61 62 63 64 65 66 67
!		S G G S T Y Y A D S V K G R F
	1171	\|tct\|ggt\|ggc\|agt\|act\|tac\|tat\|gct\|gac\|tcc\|gtt\|aaa\|ggt\|cgc\|ttc\|
!
!

!		--------FR3--------------------------------------------------
!		68 69 70 71 72 73 74 75 76 77 78 79 80 81 82
!		T I S R D N S K N T L Y L Q M
	1216	\|act\|atc\|TCT\|AGA\|gac\|aac\|tct\|aag\|aat\|act\|ctc\|tac\|ttg\|cag\|atg\|
!		\| XbaI \|
!

!		---FR3---------------------------------------------------->\|
!		82a 82b 82c 83 84 85 86 87 88 89 90 91 92 93 94
!		N S L R A E D T A V Y Y C A K
	1261	\|aac\|agC\|TTA\|AGg\|gct\|gag\|gac\|aCT\|GCA\|Gtc\|tac\|tat\|tgc\|gct\|aaa\|
!		\|AflII \| \| PstI \|(2/2)
!

!		.......CDR3.................................\|----FR4--------
!		95 96 97 98 98a 98b 98c 99 100 101 102 103 104 105 106
!		D Y E G T G Y A F D I W G Q G
	1306	\|gac\|tat\|gaa\|ggt\|act\|ggt\|tat\|gct\|ttc\|gaC\|ATA\|TGg\|ggt\|caa\|ggt\|
!		\| NdeI \|
!

!		--------------FR4---------->\|
!		107 108 109 110 111 112 113
!		T M V T V S S
	1351	\|act\|atG\|GTC\|ACC\|gtc\|tct\|agt
!		\| BstEII \| c tcg ag = XhoI.
!
!	CH1

!		A S T K G P S V F P L A P S S
	1372	gcc tcc acc aag ggc cca tcg gtc ttc ccG CTA GCa ccc tcc tcc
!		NheI....
!

!		151 152 153 154 155 156 157 158 159 160 161 162 163 164 165
!		K S T S G G T A A L G C L V K
	1417	aag agc acc tct ggg ggc aca gcg gcc ctg ggc tgc ctg gtc aag
!

!		166 167 168 169 170 171 172 173 174 175 176 177 178 179 180
!		D Y F P E P V T V S W N S G A
	1462	gac tac ttc ccc gaa ccg gtg acg gtg tcg tgg aac tca ggc gcc
!

!		181 182 183 184 185 186 187 188 189 190 191 192 193 194 195
!		L T S G V H T F P A V L Q S S
	1507	ctg acc agc ggc gtc cac acc ttc ccg gct gtc cta cag tcc tca
!

!		196 197 198 199 200 201 202 203 204 205 206 207 208 209 210
!		G L Y S L S S V V T V P S S S
	1552	gga ctc tac tcc ctc agc agc gta gtg acc gtg ccc tCC Agc agc
!		BstXI........
!
!		211 212 213 214 215 216 217 218 219 220 221 222 223 224 225
!		L G T Q T Y I C N V N H K P S
	1597	tTG Ggc acc cag acc tac atc tgc aac gtg aat cac aag ccc agc

!	BstXI........

!

!		226 227 228 229 230 231 232 233 234 235 236 237 238
!		N T K V D K K V E P K S C
	1642	aac acc aag gtg gac aaG AAA GTT GAG CCC AAA TCT TGT
!

!		139 140 141 His tag.............. cMyc tag......................
!		A A A H H H H H H G A A E Q K L I
	1681	GCG GCC GCa cat cat cat cac cat cac ggg gcc gca gaa caa aaa ctc atc
!		NotI......
!		EagI....
!

!		..................................
!		S E E D L N G A A E A S S A S N A S
	1732	tca gaa gag gat ctg aat ggg GCC gca gaG GCt agt tct gct agt aAC GCG Tct
!		BglI..........(3/4) MluI....
!

!	Domain 3 (IIIstump)-----------------------------------------------------

!		S G D F D Y E K M A N A N K G A
	1786	tcc ggt gat ttt gat tat gaa aag atg gca aac gct aat aag ggg gct
!

!		M T E N A D E N A L Q S D A K G
	1834	atg acc gaa aat gcc gat gaa aac gcg cta cag tct gac gct aaa ggc
!

!		K L D S V A T D Y G A A I D G F
	1882	aaa ctt gat tct gtc gct act gat tac ggt gct gct atc gat ggt ttc
!

!		I G D V S G L A N G N G A T G D
	1930	att ggt gac gtt tcc ggc ctt gct aat ggt aat ggt gct act ggt gat
!

!		F A G S N S Q M A Q V G D G D N
	1978	ttt gct ggc tct aat tcc caa atg gct caa gtc ggt gac ggt gat aat
!

!		S P L M N N F R Q Y L P S L P Q
	2026	tca cct tta atg aat aat ttc cgt caa tat tta cct tcc ctc cct caa
!

!		S V E C R P F V F G A G K P Y E
	2074	tcg gtt gaa tgt cgc cct ttt gtc ttt ggc gct ggt aaa cca tat gaa
!

!		F S I D C D K I N L F R
	2122	ttt tct att gat tgt gac aaa ata aac tta ttc cgt
!		End Domain 3
!

!		G V F A F L L Y V A T F M Y V F140
	2158	ggt gtc ttt gcg ttt ctt tta tat gtt gcc acc ttt atg tat gta ttt
!		start transmembrane segment
!

!		S T F A N I L
	2206	tct acg ttt gct aac ata ctg
!

!		R N K E S (SEQ ID NO: 892)
	2227	cgt aat aag gag tct TAA tga aAC GCG Tga tga GAATTC (SEQ ID NO: 893)
!		Intracellular anchor. MluI.... EcoRI.

TABLE 25

The DNA sequence of DY3F85LC containing a sample germline
O12 kappa light chain. The antibody sequences shown
are of the form of actual antibody, but have not been
identified as binding to a particular antigen. On each line,
everything after an exclamation point (!) is commentary.
The DNA of DY3F85LC is SEQ ID NO: 950

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

1	AATGCTACTA CTATTAGTAG AATTGATGCC ACCTTTTCAG CTCGCGCCCC AAATGAAAAT

61	ATAGCTAAAC AGGTTATTGA CCATTTGCGA AATGTATCTA ATGGTCAAAC TAAATCTACT

121	CGTTCGCAGA ATTGGGAATC AACTGTTATA TGGAATGAAA CTTCCAGACA CCGTACTTTA

181	GTTGCATATT TAAAACATGT TGAGCTACAG CATTATATTC AGCAATTAAG CTCTAAGCCA

241	TCCGCAAAAA TGACCTCTTA TCAAAAGGAG CAATTAAAGG TACTCTCTAA TCCTGACCTG

301	TTGGAGTTTG CTTCCGGTCT GGTTCGCTTT GAAGCTCGAA TTAAAACGCG ATATTTGAAG

361	TCTTTCGGGC TTCCTCTTAA TCTTTTTGAT GCAATCCGCT TTGCTTCTGA CTATAATAGT

421	CAGGGTAAAG ACCTGATTTT TGATTTATGG TCATTCTCGT TTTCTGAACT GTTTAAAGCA

481	TTTGAGGGGG ATTCAATGAA TATTTATGAC GATTCCGCAG TATTGGACGC TATCCAGTCT

541	AAACATTTTA CTATTACCCC CTCTGGCAAA ACTTCTTTTG CAAAAGCCTC TCGCTATTTT

601	GGTTTTTATC GTCGTCTGGT AAACGAGGGT TATGATAGTG TTGCTCTTAC TATGCCTCGT

661	AATTCCTTTT GGCGTTATGT ATCTGCATTA GTTGAATGTG GTATTCCTAA ATCTCAACTG

721	ATGAATCTTT CTACCTGTAA TAATGTTGTT CCGTTAGTTC GTTTTATTAA CGTAGATTTT

781	TCTTCCCAAC GTCCTGACTG GTATAATGAG CCAGTTCTTA AAATCGCATA AGGTAATTCA

841	CAATGATTAA AGTTGAAATT AAACCATCTC AAGCCCAATT TACTACTCGT TCTGGTGTTT

901	CTCGTCAGGG CAAGCCTTAT TCACTGAATG AGCAGCTTTG TTACGTTGAT TTGGGTAATG

961	AATATCCGGT TCTTGTCAAG ATTACTCTTG ATGAAGGTCA GCCAGCCTAT GCGCCTGGTC

1021	TGTACACCGT TCATCTGTCC TCTTTCAAAG TTGGTCAGTT CGGTTCCCTT ATGATTGACC

1081	GTCTGCGCCT CGTTCCGGCT AAGTAACATG GAGCAGGTCG CGGATTTCGA CACAATTTAT

1141	CAGGCGATGA TACAAATCTC CGTTGTACTT TGTTTCGCGC TTGGTATAAT CGCTGGGGGT

1201	CAAAGATGAG TGTTTTAGTG TATTCTTTTG CCTCTTTCGT TTTAGGTTGG TGCCTTCGTA

1261	GTGGCATTAC GTATTTTACC CGTTTAATGG AAACTTCCTC ATGAAAAAGT CTTTAGTCCT

1321	CAAAGCCTCT GTAGCCGTTG CTACCCTCGT TCCGATGCTG TCTTTCGCTG CTGAGGGTGA

1381	CGATCCCGCA AAAGCGGCCT TTAACTCCCT GCAAGCCTCA GCGACCGAAT ATATCGGTTA

1441	TGCGTGGGCG ATGGTTGTTG TCATTGTCGG CGCAACTATC GGTATCAAGC TGTTTAAGAA

1501	ATTCACCTCG AAAGCAAGCT GATAAACCGA TACAATTAAA GGCTCCTTTT GGAGCCTTTT

1561	TTTTGGAGAT TTTCAACGTG AAAAAATTAT TATTCGCAAT TCCTTTAGTT GTTCCTTTCT

1621	ATTCTCACTC CGCTGAAACT GTTGAAAGTT GTTTAGCAAA ATCCCATACA GAAAATTCAT

1681	TTACTAACGT CTGGAAAGAC GACAAAACTT TAGATCGTTA CGCTAACTAT GAGGGCTGTC

1741	TGTGGAATGC TACAGGCGTT GTAGTTTGTA CTGGTGACGA AACTCAGTGT TACGGTACAT

1801	GGGTTCCTAT TGGGCTTGCT ATCCCTGAAA ATGAGGGTGG TGGCTCTGAG GGTGGCGGTT

1861	CTGAGGGTGG CGGTTCTGAG GGTGGCGGTA CTAAACCTCC TGAGTACGGT GATACACCTA

1921	TTCCGGGCTA TACTTATATC AACCCTCTCG ACGGCACTTA TCCGCCTGGT ACTGAGCAAA

1981	ACCCCGCTAA TCCTAATCCT TCTCTTGAGG AGTCTCAGCC TCTTAATACT TTCATGTTTC

2041	AGAATAATAG GTTCCGAAAT AGGCAGGGGG CATTAACTGT TTATACGGGC ACTGTTACTC

2101	AAGGCACTGA CCCCGTTAAA ACTTATTACC AGTACACTCC TGTATCATCA AAAGCCATGT

2161	ATGACGCTTA CTGGAACGGT AAATTCAGAG ACTGCGCTTT CCATTCTGGC TTTAATGAGG

2221	ATTTATTTGT TTGTGAATAT CAAGGCCAAT CGTCTGACCT GCCTCAACCT CCTGTCAATG

2281	CTGGCGGCGG CTCTGGTGGT GGTTCTGGTG GCGGCTCTGA GGGTGGTGGC TCTGAGGGTG

2341	GCGGTTCTGA GGGTGGCGGC TCTGAGGGAG GCGGTTCCGG TGGTGGCTCT GGTTCCGGTG

2401	ATTTTGATTA TGAAAAGATG GCAAACGCTA ATAAGGGGGC TATGACCGAA AATGCCGATG

2461	AAAACGCGCT ACAGTCTGAC GCTAAAGGCA AACTTGATTC TGTCGCTACT GATTACGGTG

2521	CTGCTATCGA TGGTTTCATT GGTGACGTTT CCGGCCTTGC TAATGGTAAT GGTGCTACTG

2581	GTGATTTTGC TGGCTCTAAT TCCCAAATGG CTCAAGTCGG TGACGGTGAT AATTCACCTT

2641	TAATGAATAA TTTCCGTCAA TATTTACCTT CCCTCCCTCA ATCGGTTGAA TGTCGCCCTT

2701	TTGTCTTTGG CGCTGGTAAA CCATATGAAT TTTCTATTGA TTGTGACAAA ATAAACTTAT

2761	TCCGTGGTGT CTTTGCGTTT CTTTTATATG TTGCCACCTT TATGTATGTA TTTTCTACGT

2821	TTGCTAACAT ACTGCGTAAT AAGGAGTCTT AATCATGCCA GTTCTTTTGG GTATTCCGTT

2881	ATTATTGCGT TTCCTCGGTT TCCTTCTGGT AACTTTGTTC GGCTATCTGC TTACTTTTCT

2941	TAAAAAGGGC TTCGGTAAGA TAGCTATTGC TATTTCATTG TTTCTTGCTC TTATTATTGG

3001	GCTTAACTCA ATTCTTGTGG GTTATCTCTC TGATATTAGC GCTCAATTAC CCTCTGACTT

3061	TGTTCAGGGT GTTCAGTTAA TTCTCCCGTC TAATGCGCTT CCCTGTTTTT ATGTTATTCT

3121	CTCTGTAAAG GCTGCTATTT TCATTTTTGA CGTTAAACAA AAAATCGTTT CTTATTTGGA

3181	TTGGGATAAA TAATATGGCT GTTTATTTTG TAACTGGCAA ATTAGGCTCT GGAAAGACGC

3241	TCGTTAGCGT TGGTAAGATT CAGGATAAAA TTGTAGCTGG GTGCAAAATA GCAACTAATC

3301	TTGATTTAAG GCTTCAAAAC CTCCCGCAAG TCGGGAGGTT CGCTAAAACG CCTCGCGTTC

3361	TTAGAATACC GGATAAGCCT TCTATATCTG ATTTGCTTGC TATTGGGCGC GGTAATGATT

3421	CCTACGATGA AAATAAAAAC GGCTTGCTTG TTCTCGATGA GTGCGGTACT TGGTTTAATA

3481	CCCGTTCTTG GAATGATAAG GAAAGACAGC CGATTATTGA TTGGTTTCTA CATGCTCGTA

3541	AATTAGGATG GGATATTATT TTTCTTGTTC AGGACTTATC TATTGTTGAT AAACAGGCGC

3601	GTTCTGCATT AGCTGAACAT GTTGTTTATT GTCGTCGTCT GGACAGAATT ACTTTACCTT

3661	TTGTCGGTAC TTTATATTCT CTTATTACTG GCTCGAAAAT GCCTCTGCCT AAATTACATG

3721	TTGGCGTTGT TAAATATGGC GATTCTCAAT TAAGCCCTAC TGTTGAGCGT TGGCTTTATA

3781	CTGGTAAGAA TTTGTATAAC GCATATGATA CTAAACAGGC TTTTTCTAGT AATTATGATT

3841	CCGGTGTTTA TTCTTATTTA ACGCCTTATT TATCACACGG TCGGTATTTC AAACCATTAA

3901	ATTTAGGTCA GAAGATGAAA TTAACTAAAA TATATTTGAA AAAGTTTTCT CGCGTTCTTT

3961	GTCTTGCGAT TGGATTTGCA TCAGCATTTA CATATAGTTA TATAACCCAA CCTAAGCCGG

4021	AGGTTAAAAA GGTAGTCTCT CAGACCTATG ATTTTGATAA ATTCACTATT GACTCTTCTC

4081	AGCGTCTTAA TCTAAGCTAT CGCTATGTTT TCAAGGATTC TAAGGGAAAA TTAATTAATA

4141	GCGACGATTT ACAGAAGCAA GGTTATTCAC TCACATATAT TGATTTATGT ACTGTTTCCA

4201	TTAAAAAAGG TAATTCAAAT GAAATTGTTA AATGTAATTA ATTTTGTTTT CTTGATGTTT

4261	GTTTCATCAT CTTCTTTTGC TCAGGTAATT GAAATGAATA ATTCGCCTCT GCGCGATTTT

4321	GTAACTTGGT ATTCAAAGCA ATCAGGCGAA TCCGTTATTG TTTCTCCCGA TGTAAAAGGT

4381	ACTGTTACTG TATATTCATC TGACGTTAAA CCTGAAAATC TACGCAATTT CTTTATTTCT

4441	GTTTTACGTG CAAATAATTT TGATATGGTA GGTTCTAACC CTTCCATAAT TCAGAAGTAT

4501	AATCCAAACA ATCAGGATTA TATTGATGAA TTGCCATCAT CTGATAATCA GGAATATGAT

4561	GATAATTCCG CTCCTTCTGG TGGTTTCTTT GTTCCGCAAA ATGATAATGT TACTCAAACT

4621	TTTAAAATTA ATAACGTTCG GGCAAAGGAT TTAATACGAG TTGTCGAATT GTTTGTAAAG

4681	TCTAATACTT CTAAATCCTC AAATGTATTA TCTATTGACG GCTCTAATCT ATTAGTTGTT

4741	AGTGCTCCTA AAGATATTTT AGATAACCTT CCTCAATTCC TTTCAACTGT TGATTTGCCA

4801	ACTGACCAGA TATTGATTGA GGGTTTGATA TTTGAGGTTC AGCAAGGTGA TGCTTTAGAT

4861	TTTTCATTTG CTGCTGGCTC TCAGCGTGGC ACTGTTGCAG GCGGTGTTAA TACTGACCGC

4921	CTCACCTCTG TTTTATCTTC TGCTGGTGGT TCGTTCGGTA TTTTTAATGG CGATGTTTTA

4981	GGGCTATCAG TTCGCGCATT AAAGACTAAT AGCCATTCAA AAATATTGTC TGTGCCACGT

5041	ATTCTTACGC TTTCAGGTCA GAAGGGTTCT ATCTCTGTTG GCCAGAATGT CCCTTTTATT

5101	ACTGGTCGTG TGACTGGTGA ATCTGCCAAT GTAAATAATC CATTTCAGAC GATTGAGCGT

5161	CAAAATGTAG GTATTTCCAT GAGCGTTTTT CCTGTTGCAA TGGCTGGCGG TAATATTGTT

5221	CTGGATATTA CCAGCAAGGC CGATAGTTTG AGTTCTTCTA CTCAGGCAAG TGATGTTATT

5281	ACTAATCAAA GAAGTATTGC TACAACGGTT AATTTGCGTG ATGGACAGAC TCTTTTACTC

5341	GGTGGCCTCA CTGATTATAA AAACACTTCT CAGGATTCTG GCGTACCGTT CCTGTCTAAA

5401	ATCCCTTTAA TCGGCCTCCT GTTTAGCTCC CGCTCTGATT CTAACGAGGA AAGCACGTTA

5461	TACGTGCTCG TCAAAGCAAC CATAGTACGC GCCCTGTAGC GGCGCATTAA GCGCGGCGGG

5521	TGTGGTGGTT ACGCGCAGCG TGACCGCTAC ACTTGCCAGC GCCCTAGCGC CCGCTCCTTT

5581	CGCTTTCTTC CCTTCCTTTC TCGCCACGTT CGCCGGCTTT CCCCGTCAAG CTCTAAATCG

5641	GGGGCTCCCT TTAGGGTTCC GATTTAGTGC TTTACGGCAC CTCGACCCCA AAAAACTTGA

5701	TTTGGGTGAT GGTTCACGTA GTGGGCCATC GCCCTGATAG ACGGTTTTTC GCCCTTTGAC

5761	GTTGGAGTCC ACGTTCTTTA ATAGTGGACT CTTGTTCCAA ACTGGAACAA CACTCAACCC

5821	TATCTCGGGC TATTCTTTTG ATTTATAAGG GATTTTGCCG ATTTCGGAAC CACCATCAAA

5881	CAGGATTTTC GCCTGCTGGG GCAAACCAGC GTGGACCGCT TGCTGCAACT CTCTCAGGGC

5941	CAGGCGGTGA AGGGCAATCA GCTGTTGCCC GTCTCACTGG TGAAAAGAAA AACCACCCTG

6001	GATCCAAGCT TGCAGGTGGC ACTTTTCGGG GAAATGTGCG CGGAACCCCT ATTTGTTTAT

6061	TTTTCTAAAT ACATTCAAAT ATGTATCCGC TCATGAGACA ATAACCCTGA TAAATGCTTC

6121	AATAATATTG AAAAAGGAAG AGTATGAGTA TTCAACATTT CCGTGTCGCC CTTATTCCCT

6181	TTTTTGCGGC ATTTTGCCTT CCTGTTTTTG CTCACCCAGA AACGCTGGTG AAAGTAAAAG

6241	ATGCTGAAGA TCAGTTGGGC GCACTAGTGG GTTACATCGA ACTGGATCTC AACAGCGGTA

6301	AGATCCTTGA GAGTTTTCGC CCCGAAGAAC GTTTTCCAAT GATGAGCACT TTTAAAGTTC

6361	TGCTATGTGG CGCGGTATTA TCCCGTATTG ACGCCGGGCA AGAGCAACTC GGTCGCCGCA

6421	TACACTATTC TCAGAATGAC TTGGTTGAGT ACTCACCAGT CACAGAAAAG CATCTTACGG

6481	ATGGCATGAC AGTAAGAGAA TTATGCAGTG CTGCCATAAC CATGAGTGAT AACACTGCGG

6541	CCAACTTACT TCTGACAACG ATCGGAGGAC CGAAGGAGCT AACCGCTTTT TTGCACAACA

6601	TGGGGGATCA TGTAACTCGC CTTGATCGTT GGGAACCGGA GCTGAATGAA GCCATACCAA

6661	ACGACGAGCG TGACACCACG ATGCCTGTAG CAATGGCAAC AACGTTGCGC AAACTATTAA

6721	CTGGCGAACT ACTTACTCTA GCTTCCCGGC AACAATTAAT AGACTGGATG GAGGCGGATA

6781	AAGTTGCAGG ACCACTTCTG CGCTCGGCCC TTCCGGCTGG CTGGTTTATT GCTGATAAAT

6841	CTGGAGCCGG TGAGCGTGGG TCTCGCGGTA TCATTGCAGC ACTGGGGCCA GATGGTAAGC

6901	CCTCCCGTAT CGTAGTTATC TACACGACGG GGAGTCAGGC AACTATGGAT GAACGAAATA

6961	GACAGATCGC TGAGATAGGT GCCTCACTGA TTAAGCATTG GTAACTGTCA GACCAAGTTT

7021	ACTCATATAT ACTTTAGATT GATTTAAAAC TTCATTTTTA ATTTAAAAGG ATCTAGGTGA

7081	AGATCCTTTT TGATAATCTC ATGACCAAAA TCCCTTAACG TGAGTTTTCG TTCCACTGTA

7141	CGTAAGACCC CCAAGCTTGT CGACTGAATG GCGAATGGCG CTTTGCCTGG TTTCCGGCAC

7201	CAGAAGCGGT GCCGGAAAGC TGGCTGGAGT GCGATCTTCC TGACGCTCGA GCGCAACGCA
!	XhoI...

7261	ATTAATGTGA GTTAGCTCAC TCATTAGGCA CCCCAGGCTT TACACTTTAT GCTTCCGGCT

7321	CGTATGTTGT GTGGAATTGT GAGCGGATAA CAATTTCACA CAGGAAACAG CTATGACCAT

7381	GATTACGCCA AGCTTTGGAG CCTTTTTTTT GGAGATTTTC AAC

TABLE 30

DNA sequence of DY3FHC87 (SEQ ID NO: 894)

1	aatgctacta ctattagtag aattgatgcc accttttcag ctcgcgcccc aaatgaaaat

61	atagctaaac aggttattga ccatttgcga aatgtatcta atggtcaaac taaatctact

121	cgttcgcaga attgggaatc aactgttata tggaatgaaa cttccagaca ccgtacttta

181	gttgcatatt taaaacatgt tgagctacag cattatattc agcaattaag ctctaagcca

241	tccgcaaaaa tgacctctta tcaaaaggag caattaaagg tactctctaa tcctgacctg

301	ttggagtttg cttccggtct ggttcgcttt gaagctcgaa ttaaaacgcg atatttgaag

361	tctttcgggc ttcctcttaa tctttttgat gcaatccgct ttgcttctga ctataatagt

421	cagggtaaag acctgatttt tgatttatgg tcattctcgt tttctgaact gtttaaagca

481	tttgaggggg attcaatgaa tatttatgac gattccgcag tattggacgc tatccagtct

541	aaacatttta ctattacccc ctctggcaaa acttcttttg caaaagcctc tcgctatttt

601	ggtttttatc gtcgtctggt aaacgagggt tatgatagtg ttgctcttac tatgcctcgt

661	aattcctttt ggcgttatgt atctgcatta gttgaatgtg gtattcctaa atctcaactg

721	atgaatcttt ctacctgtaa taatgttgtt ccgttagttc gttttattaa cgtagatttt

781	tcttcccaac gtcctgactg gtataatgag ccagttctta aaatcgcata aggtaattca

841	caatgattaa agttgaaatt aaaccatctc aagcccaatt tactactcgt tctggtgttt

901	ctcgtcaggg caagccttat tcactgaatg agcagctttg ttacgttgat ttgggtaatg

961	aatatccggt tcttgtcaag attactcttg atgaaggtca gccagcctat gcgcctggtc

1021	tgtacaccgt tcatctgtcc tctttcaaag ttggtcagtt cggttccctt atgattgacc

1081	gtctgcgcct cgttccggct aagtaacatg gagcaggtcg cggatttcga cacaatttat

1141	caggcgatga tacaaatctc cgttgtactt tgtttcgcgc ttggtataat cgctgggggt

1201	caaagatgag tgttttagtg tattcttttg cctctttcgt tttaggttgg tgccttcgta

1261	gtggcattac gtattttacc cgtttaatgg aaacttcctc atgaaaaagt ctttagtcct

1321	caaagcctct gtagccgttg ctaccctcgt tccgatgctg tctttcgctg ctgagggtga

1381	cgatcccgca aaagcggcct ttaactccct gcaagcctca gcgaccgaat atatcggtta

1441	tgcgtgggcg atggttgttg tcattgtcgg cgcaactatc ggtatcaagc tgtttaagaa

1501	attcacctcg aaagcaagct gataaaccga tacaattaaa ggctcctttt ggagcctttt

1561	tttttggaga ttttcaacgt gaaaaaatta ttattcgcaa ttcctttagt tgttcctttc

1621	tattctcact ccgctgaaac tgttgaaagt tgtttagcaa aatcccatac agaaaattca

1681	tttactaacg tctggaaaga cgacaaaact ttagatcgtt acgctaacta tgagggctgt

1741	ctgtggaatg ctacaggcgt tgtagtttgt actggtgacg aaactcagtg ttacggtaca

1801	tgggttccta ttgggcttgc tatccctgaa aatgagggtg gtggctctga gggtggcggt

1861	tctgagggtg gcggttctga gggtggcggt actaaacctc ctgagtacgg tgatacacct

1921	attccgggct atacttatat caaccctctc gacggcactt atccgcctgg tactgagcaa

1981	aaccccgcta atcctaatcc ttctcttgag gagtctcagc ctcttaatac tttcatgttt

2041	cagaataata ggttccgaaa taggcagggg gcattaactg tttatacggg cactgttact

2101	caaggcactg accccgttaa aacttattac cagtacactc ctgtatcatc aaaagccatg

2161	tatgacgctt actggaacgg taaattcaga gactgcgctt tccattctgg ctttaatgag

2221	gatttatttg tttgtgaata tcaaggccaa tcgtctgacc tgcctcaacc tcctgtcaat

2281	gctggcggcg gctctggtgg tggttctggt ggcggctctg agggtggtgg ctctgagggt

2341	ggcggttctg agggtggcgg ctctgaggga ggcggttccg gtggtggctc tggttccggt

2401	gattttgatt atgaaaagat ggcaaacgct aataaggggg ctatgaccga aaatgccgat

2461	gaaaacgcgc tacagtctga cgctaaaggc aaacttgatt ctgtcgctac tgattacggt

2521	gctgctatcg atggtttcat tggtgacgtt tccggccttg ctaatggtaa tggtgctact

2581	ggtgattttg ctggctctaa ttcccaaatg gctcaagtcg gtgacggtga taattcacct

2641	ttaatgaata atttccgtca atatttacct tccctccctc aatcggttga atgtcgccct

2701	tttgtctttg gcgctggtaa accatatgaa ttttctattg attgtgacaa aataaactta

2761	ttccgtggtg tctttgcgtt tcttttatat gttgccacct ttatgtatgt attttctacg

2821	tttgctaaca tactgcgtaa taaggagtct taatcatgcc agttcttttg ggtattccgt

2881	tattattgcg tttcctcggt ttccttctgg taactttgtt cggctatctg cttacttttc

2941	ttaaaaaggg cttcggtaag atagctattg ctatttcatt gtttcttgct cttattattg

3001	ggcttaactc aattcttgtg ggttatctct ctgatattag cgctcaatta ccctctgact

3061	ttgttcaggg tgttcagtta attctcccgt ctaatgcgct tccctgtttt tatgttattc

3121	tctctgtaaa ggctgctatt ttcatttttg acgttaaaca aaaaatcgtt tcttatttgg

3181	attgggataa ataatatggc tgtttatttt gtaactggca aattaggctc tggaaagacg

3241	ctcgttagcg ttggtaagat tcaggataaa attgtagctg ggtgcaaaat agcaactaat

3301	cttgatttaa ggcttcaaaa cctcccgcaa gtcgggaggt tcgctaaaac gcctcgcgtt

3361	cttagaatac cggataagcc ttctatatct gatttgcttg ctattgggcg cggtaatgat

3421	tcctacgatg aaaataaaaa cggcttgctt gttctcgatg agtgcggtac ttggtttaat

3481	acccgttctt ggaatgataa ggaaagacag ccgattattg attggtttct acatgctcgt

3541	aaattaggat gggatattat ttttcttgtt caggacttat ctattgttga taaacaggcg

3601	cgttctgcat tagctgaaca tgttgtttat tgtcgtcgtc tggacagaat tactttacct

3661	tttgtcggta ctttatattc tcttattact ggctcgaaaa tgcctctgcc taaattacat

3721	gttggcgttg ttaaatatgg cgattctcaa ttaagcccta ctgttgagcg ttggctttat

3781	actggtaaga atttgtataa cgcatatgat actaaacagg ctttttctag taattatgat

3841	tccggtgttt attcttattt aacgccttat ttatcacacg gtcggtattt caaaccatta

3901	aatttaggtc agaagatgaa attaactaaa atatatttga aaaagttttc tcgcgttctt

3961	tgtcttgcga ttggatttgc atcagcattt acatatagtt atataaccca acctaagccg

4021	gaggttaaaa aggtagtctc tcagacctat gattttgata aattcactat tgactcttct

4081	cagcgtctta atctaagcta tcgctatgtt ttcaaggatt ctaagggaaa attaattaat

4141	agcgacgatt tacagaagca aggttattca ctcacatata ttgatttatg tactgtttcc

4201	attaaaaaag gtaattcaaa tgaaattgtt aaatgtaatt aattttgttt tcttgatgtt

4261	tgtttcatca tcttcttttg ctcaggtaat tgaaatgaat aattcgcctc tgcgcgattt

4321	tgtaacttgg tattcaaagc aatcaggcga atccgttatt gtttctcccg atgtaaaagg

4381	tactgttact gtatattcat ctgacgttaa acctgaaaat ctacgcaatt tctttatttc

4441	tgttttacgt gcaaataatt ttgatatggt aggttctaac ccttccataa ttcagaagta

4501	taatccaaac aatcaggatt atattgatga attgccatca tctgataatc aggaatatga

4561	tgataattcc gctccttctg gtggtttctt tgttccgcaa aatgataatg ttactcaaac

4621	ttttaaaatt aataacgttc gggcaaagga tttaatacga gttgtcgaat tgtttgtaaa

4681	gtctaatact tctaaatcct caaatgtatt atctattgac ggctctaatc tattagttgt

4741	tagtgctcct aaagatattt tagataacct tcctcaattc ctttcaactg ttgatttgcc

4801	aactgaccag atattgattg agggtttgat atttgaggtt cagcaaggtg atgctttaga

4861	tttttcattt gctgctggct ctcagcgtgg cactgttgca ggcggtgtta atactgaccg

4921	cctcacctct gttttatctt ctgctggtgg ttcgttcggt atttttaatg gcgatgtttt

4981	agggctatca gttcgcgcat taaagactaa tagccattca aaaatattgt ctgtgccacg

5041	tattcttacg ctttcaggtc agaagggttc tatctctgtt ggccagaatg tcccttttat

5101	tactggtcgt gtgactggtg aatctgccaa tgtaaataat ccatttcaga cgattgagcg

5161	tcaaaatgta ggtatttcca tgagcgtttt tcctgttgca atggctggcg gtaatattgt

5221	tctggatatt accagcaagg ccgatagttt gagttcttct actcaggcaa gtgatgttat

5281	tactaatcaa agaagtattg ctacaacggt taatttgcgt gatggacaga ctcttttact

5341	cggtggcctc actgattata aaaacacttc tcaggattct ggcgtaccgt tcctgtctaa

5401	aatcccttta atcggcctcc tgtttagctc ccgctctgat tctaacgagg aaagcacgtt

5461	atacgtgctc gtcaaagcaa ccatagtacg cgccctgtag cggcgcatta agcgcggcgg

5521	gtgtggtggt tacgcgcagc gtgaccgcta cacttgccag cgccctagcg cccgctcctt

5581	tcgctttctt cccttccttt ctcgccacgt tcgccggctt tccccgtcaa gctctaaatc

5641	gggggctccc tttagggttc cgatttagtg ctttacggca cctcgacccc aaaaaacttg

5701	atttgggtga tggttcacgt agtgggccat cgccctgata gacggttttt cgccctttga

5761	cgttggagtc cacgttcttt aatagtggac tcttgttcca aactggaaca acactcaacc

5821	ctatctcggg ctattctttt gatttataag ggattttgcc gatttcggaa ccaccatcaa

5881	acaggatttt cgcctgctgg ggcaaaccag cgtggaccgc ttgctgcaac tctctcaggg

5941	ccaggcggtg aagggcaatc agctgttgcc cgtctcactg gtgaaaagaa aaaccaccct

6001	ggatccaagc ttgcaggtgg cacttttcgg ggaaatgtgc gcggaacccc tatttgttta

6061	tttttctaaa tacattcaaa tatgtatccg ctcatgagac aataaccctg ataaatgctt

6121	caataatatt gaaaaaggaa gagtatgagt attcaacatt tccgtgtcgc ccttattccc

6181	ttttttgcgg cattttgcct tcctgttttt gctcacccag aaacgctggt gaaagtaaaa

6241	gatgctgaag atcagttggg cgcactagtg ggttacatcg aactggatct caacagcggt

6301	aagatccttg agagttttcg ccccgaagaa cgttttccaa tgatgagcac ttttaaagtt

6361	ctgctatgtg gcgcggtatt atcccgtatt gacgccgggc aagagcaact cggtcgccgc

6421	atacactatt ctcagaatga cttggttgag tactcaccag tcacagaaaa gcatcttacg

6481	gatggcatga cagtaagaga attatgcagt gctgccataa ccatgagtga taacactgcg

6541	gccaacttac ttctgacaac gatcggagga ccgaaggagc taaccgcttt tttgcacaac

6601	atgggggatc atgtaactcg ccttgatcgt tgggaaccgg agctgaatga agccatacca

6661	aacgacgagc gtgacaccac gatgcctgta gcaatggcaa caacgttgcg caaactatta

6721	actggcgaac tacttactct agcttcccgg caacaattaa tagactggat ggaggcggat

6781	aaagttgcag gaccacttct gcgctcggcc cttccggctg gctggtttat tgctgataaa

6841	tctggagccg gtgagcgtgg gtctcgcggt atcattgcag cactggggcc agatggtaag

6901	ccctcccgta tcgtagttat ctacacgacg gggagtcagg caactatgga tgaacgaaat

6961	agacagatcg ctgagatagg tgcctcactg attaagcatt ggtaactgtc agaccaagtt

7021	tactcatata tactttagat tgatttaaaa cttcattttt aatttaaaag gatctaggtg

7081	aagatccttt ttgataatct catgaccaaa atcccttaac gtgagttttc gttccactgt

7141	acgtaagacc cccaagcttg tcgactgaat ggcgaatggc gctttgcctg gtttccggca

7201	ccagaagcgg tgccggaaag ctggctggag tgcgatcttc ctgacgctcg agcgcaacgc

7261	aattaatgtg agttagctca ctcattaggc accccaggct ttacacttta tgcttccggc

7321	tcgtatgttg tgtggaattg tgagcggata acaatttcac acaggaaaca gctatgacca

7381	tgattacgcc aagctttgga gccttttttt tggagatttt caacatgaaa tacctattgc

7441	ctacggcagc cgctggattg ttattactcg cGGCCcagcc GGCCatggcc gaagttcaat

7501	tgttagagtc tggtggcggt cttgttcagc ctggtggttc tttacgtctt tcttgcgctg

7561	cttccggatt cactttctct tcgtacgcta tgtcttgggt tcgccaagct cctggtaaag

7621	gtttggagtg ggtttctgct atctctggtt ctggtggcag tacttactat gctgactccg

7681	ttaaaggtcg cttcactatc tctagagaca actctaagaa tactctctac ttgcagatga

7741	acagcttaag ggctgaggac actgcagtct actattgcgc taaagcctat cgtccttctt

7801	atcatgacat atggggtcaa ggtactatgg tcaccgtctc tagtgcctcc accaagggcc

7861	catcggtctt cccgctagca ccctcctcca agagcacctc tgggggcaca gcggccctgg

7921	gctgcctggt caaggactac ttccccgaac cggtgacggt gtcgtggaac tcaggcgccc

7981	tgaccagcgg cgtccacacc ttcccggctg tcctacagtc ctcaggactc tactccctca

8041	gcagcgtagt gaccgtgccc tccagcagct tgggcaccca gacctacatc tgcaacgtga

8101	atcacaagcc cagcaacacc aaggtggaca agaaagttga gcccaaatct tgtgcggccg

8161	cacatcatca tcaccatcac ggggccgcag aacaaaaact catctcagaa gaggatctga

8221	atggggccgc agaggctagc tctgctagtg gcgacttcga ctacgagaaa atggctaatg

8281	ccaacaaagg cgccatgact gagaacgctg acgagaatgc tttgcaaagc gatgccaagg

8341	gtaagttaga cagcgtcgcg accgactatg gcgccgccat cgacggcttt atcggcgatg

8401	tcagtggttt ggccaacggc aacggagcca ccggagactt cgcaggttcg aattctcaga

8461	tggcccaggt tggagatggg gacaacagtc cgcttatgaa caactttaga cagtaccttc

8521	cgtctcttcc gcagagtgtc gagtgccgtc cattcgtttt cggtgccggc aagccttacg

8581	agttcagcat cgactgcgat aagatcaatc ttttccgcgg cgttttcgct ttcttgctat

8641	acgtcgctac tttcatgtac gttttcagca ctttcgccaa tattttacgc aacaaagaaa

8701	gctagtgatc tcctaggaag cccgcctaat gagcgggctt tttttttctg gtatgcatcc

8761	tgaggccgat actgtcgtcg tcccctcaaa ctggcagatg cacggttacg atgcgcccat

8821	ctacaccaac gtgacctatc ccattacggt caatccgccg tttgttccca cggagaatcc

8881	gacgggttgt tactcgctca catttaatgt tgatgaaagc tggctacagg aaggccagac

8941	gcgaattatt tttgatggcg ttcctattgg ttaaaaaatg agctgattta acaaaaattt

9001	aatgcgaatt ttaacaaaat attaacgttt acaatttaaa tatttgctta tacaatcttc

9061	ctgtttttgg ggcttttctg attatcaacc ggggtacata tgattgacat gctagtttta

9121	cgattaccgt tcatcgattc tcttgtttgc tccagactct caggcaatga cctgatagcc

9181	tttgtagatc tctcaaaaat agctaccctc tccggcatta atttatcagc tagaacggtt

9241	gaatatcata ttgatggtga tttgactgtc tccggccttt ctcacccttt tgaatcttta

9301	cctacacatt actcaggcat tgcatttaaa atatatgagg gttctaaaaa tttttatcct

9361	tgcgttgaaa taaaggcttc tcccgcaaaa gtattacagg gtcataatgt ttttggtaca

9421	accgatttag ctttatgctc tgaggcttta ttgcttaatt ttgctaattc tttgccttgc

9481	ctgtatgatt tattggatgt t

TABLE 35

DNA sequence of pMID21: 5957 bp (SEQ ID NO: 895)

1	gacgaaaggg cctcgtgata cgcctatttt tataggttaa tgtcatgata ataatggttt

61	cttagacgtc aggtggcact tttcggggaa atgtgcgcgg aacccctatt tgtttatttt

121	tctaaataca ttcaaatatg tatccgctca tgagacaata accctgataa atgcttcaat

181	aatattgaaa aaggaagagt atgagtattc aacatttccg tgtcgccctt attccctttt

241	ttgcggcatt ttgccttcct gtttttgctc acccagaaac gctggtgaaa gtaaaagatg

301	ctgaagatca gttgggtgcc cgagtgggtt acatcgaact ggatctcaac agcggtaaga

361	tccttgagag ttttcgcccc gaagaacgtt ttccaatgat gagcactttt aaagttctgc

421	tatgtggcgc ggtattatcc cgtattgacg ccgggcaaga gcaactcggt cgccgcatac

481	actattctca gaatgacttg gttgagtact caccagtcac agaaaagcat cttacggatg

541	gcatgacagt aagagaatta tgcagtgctg ccataaccat gagtgataac actgcggcca

601	acttacttct gacaacgatc ggaggaccga aggagctaac cgcttttttg cacaacatgg

661	gggatcatgt aactcgcctt gatcgttggg aaccggagct gaatgaagcc ataccaaacg

721	acgagcgtga caccacgatg cctgtagcaa tggcaacaac gttgcgcaaa ctattaactg

781	gcgaactact tactctagct tcccggcaac aattaataga ctggatggag gcggataaag

841	ttgcaggacc acttctgcgc tcggcccttc cggctggctg gtttattgct gataaatctg

901	gagccggtga gcgtgggtct cgcggtatca ttgcagcact ggggccagat ggtaagccct

961	cccgtatcgt agttatctac acgacgggga gtcaggcaac tatggatgaa cgaaatagac

1021	agatcgctga gataggtgcc tcactgatta agcattggta actgtcagac caagtttact

1081	catatatact ttagattgat ttaaaacttc atttttaatt taaaaggatc taggtgaaga

1141	tcctttttga taatctcatg accaaaatcc cttaacgtga gttttcgttc cactgagcgt

1201	cagaccccgt agaaaagatc aaaggatctt cttgagatcc tttttttctg cgcgtaatct

1261	gctgcttgca aacaaaaaaa ccaccgctac cagcggtggt ttgtttgccg gatcaagagc

1321	taccaactct ttttccgaag gtaactggct tcagcagagc gcagatacca aatactgttc

1381	ttctagtgta gccgtagtta ggccaccact tcaagaactc tgtagcaccg cctacatacc

1441	tcgctctgct aatcctgtta ccagtggctg ctgccagtgg cgataagtcg tgtcttaccg

1501	ggttggactc aagacgatag ttaccggata aggcgcagcg gtcgggctga acggggggtt

1561	cgtgcataca gcccagcttg gagcgaacga cctacaccga actgagatac ctacagcgtg

1621	agctatgaga aagcgccacg cttcccgaag ggagaaaggc ggacaggtat ccggtaagcg

1681	gcagggtcgg aacaggagag cgcacgaggg agcttccagg gggaaacgcc tggtatcttt

1741	atagtcctgt cgggtttcgc cacctctgac ttgagcgtcg atttttgtga tgctcgtcag

1801	gggggcggag cctatggaaa aacgccagca acgcggcctt tttacggttc ctggcctttt

1861	gctggccttt tgctcacatg ttctttcctg cgttatcccc tgattctgtg gataaccgta

1921	ttaccgcctt tgagtgagct gataccgctc gccgcagccg aacgaccgag cgcagcgagt

1981	cagtgagcga ggaagcggaa gagcgcccaa tacgcaaacc gcctctcccc gcgcgttggc

2041	cgattcatta atgcagctgg cacgacaggt ttcccgactg gaaagcgggc agtgagcgca

2101	acgcaattaa tgtgagttag ctcactcatt aggcacccca ggctttacac tttatgcttc

2161	cggctcgtat gttgtgtgga attgtgagcg gataacaatt tcacacagga aacagctatg

2221	accatgatta cgccaagctt tggagccttt tttttggaga ttttcaacgt gaaaaaatta

2281	ttattcgcaa ttcctttagt tgttcctttc tattctcaca gtgcacaggt ccaactgcag

2341	gagctcgaga tcaaacgtgg aactgtggct gcaccatctg tcttcatctt cccgccatct

2401	gatgagcagt tgaaatctgg aactgcctct gttgtgtgcc tgctgaataa cttctatccc

2461	agagaggcca aagtacagtg gaaggtggat aacgccctcc aatcgggtaa ctcccaggag

2521	agtgtcacag agcaggacag caaggacagc acctacagcc tcagcagcac cctgacgctg

2581	agcaaagcag actacgagaa acacaaagtc tacgcctgcg aagtcaccca tcagggcctg

2641	agttcaccgg tgacaaagag cttcaacagg ggagagtgtt aataaggcgc gcctaaccat

2701	ctatttcaag gaacagtctt aatgaaaaag cttttattca tgatcccgtt agttgtaccg

2761	ttcgtggccc agccggcctc tgctgaagtt caattgttag agtctggtgg cggtcttgtt

2821	cagcctggtg gttctttacg tctttcttgc gctgcttccg gagcttcaga tctgtttgcc

2881	tttttgtggg gtggtgcaga tcgcgttacg gagatcgacc gactgcttga gcaaaagcca

2941	cgcttaactg ctgatcaggc atgggatgtt attcgccaaa ccagtcgtca ggatcttaac

3001	ctgaggcttt ttttacctac tctgcaagca gcgacatctg gtttgacaca gagcgatccg

3061	cgtcgtcagt tggtagaaac attaacacgt tgggatggca tcaatttgct taatgatgat

3121	ggtaaaacct ggcagcagcc aggctctgcc atcctgaacg tttggctgac cagtatgttg

3181	aagcgtaccg tagtggctgc cgtacctatg ccatttgata agtggtacag cgccagtggc

3241	tacgaaacaa cccaggacgg cccaactggt tcgctgaata taagtgttgg agcaaaaatt

3301	ttgtatgagg cggtgcaggg agacaaatca ccaatcccac aggcggttga tctgtttgct

3361	gggaaaccac agcaggaggt tgtgttggct gcgctggaag atacctggga gactctttcc

3421	aaacgctatg gcaataatgt gagtaactgg aaaacaccgg caatggcctt aacgttccgg

3481	gcaaataatt tctttggtgt accgcaggcc gcagcggaag aaacgcgtca tcaggcggag

3541	tatcaaaacc gtggaacaga aaacgatatg attgttttct caccaacgac aagcgatcgt

3601	cctgtgcttg cctgggatgt ggtcgcaccc ggtcagagtg ggtttattgc tcccgatgga

3661	acagttgata agcactatga agatcagctg aaaatgtacg aaaattttgg ccgtaagtcg

3721	ctctggttaa cgaagcagga tgtggaggcg cataaggagt tctagagaca actctaagaa

3781	tactctctac ttgcagatga acagcttaag tctgagcatt cggtccgggc aacattctcc

3841	aaactgacca gacgacacaa acggcttacg ctaaatcccg cgcatgggat ggtaaagagg

3901	tggcgtcttt gctggcctgg actcatcaga tgaaggccaa aaattggcag gagtggacac

3961	agcaggcagc gaaacaagca ctgaccatca actggtacta tgctgatgta aacggcaata

4021	ttggttatgt tcatactggt gcttatccag atcgtcaatc aggccatgat ccgcgattac

4081	ccgttcctgg tacgggaaaa tgggactgga aagggctatt gccttttgaa atgaacccta

4141	aggtgtataa cccccagcag ctagccatat tctctcggtc accgtctcaa gcgcctccac

4201	caagggccca tcggtcttcc cgctagcacc ctcctccaag agcacctctg ggggcacagc

4261	ggccctgggc tgcctggtca aggactactt ccccgaaccg gtgacggtgt cgtggaactc

4321	aggcgccctg accagcggcg tccacacctt cccggctgtc ctacagtcta gcggactcta

4381	ctccctcagc agcgtagtga ccgtgccctc ttctagcttg ggcacccaga cctacatctg

4441	caacgtgaat cacaagccca gcaacaccaa ggtggacaag aaagttgagc ccaaatcttg

4501	tgcggccgca catcatcatc accatcacgg ggccgcagaa caaaaactca tctcagaaga

4561	ggatctgaat ggggccgcag aggctagttc tgctagtaac gcgtcttccg gtgattttga

4621	ttatgaaaag atggcaaacg ctaataaggg ggctatgacc gaaaatgccg atgaaaacgc

4681	gctacagtct gacgctaaag gcaaacttga ttctgtcgct actgattacg gtgctgctat

4741	cgatggtttc attggtgacg tttccggcct tgctaatggt aatggtgcta ctggtgattt

4801	tgctggctct aattcccaaa tggctcaagt cggtgacggt gataattcac ctttaatgaa

4861	taatttccgt caatatttac cttccctccc tcaatcggtt gaatgtcgcc cttttgtctt

4921	tggcgctggt aaaccatatg aattttctat tgattgtgac aaaataaact tattccgtgg

4981	tgtctttgcg tttcttttat atgttgccac ctttatgtat gtattttcta cgtttgctaa

5041	catactgcgt aataaggagt cttaatgaaa cgcgtgatga gaattcactg gccgtcgttt

5101	tacaacgtcg tgactgggaa aaccctggcg ttacccaact taatcgcctt gcagcacatc

5161	cccctttcgc cagctggcgt aatagcgaag aggcccgcac cgatcgccct tcccaacagt

5221	tgcgcagcct gaatggcgaa tggcgcctga tgcggtattt tctccttacg catctgtgcg

5281	gtatttcaca ccgcatacgt caaagcaacc atagtacgcg ccctgtagcg gcgcattaag

5341	cgcggcgggt gtggtggtta cgcgcagcgt gaccgctaca cttgccagcg ccttagcgcc

5401	cgctcctttc gctttcttcc cttcctttct cgccacgttc gccggctttc cccgtcaagc

5461	tctaaatcgg gggctccctt tagggttccg atttagtgct ttacggcacc tcgaccccaa

5521	aaaacttgat ttgggtgatg gttcacgtag tgggccatcg ccctgataga cggtttttcg

5581	ccctttgacg ttggagtcca cgttctttaa tagtggactc ttgttccaaa ctggaacaac

5641	actcaactct atctcgggct attcttttga tttataaggg attttgccga tttcggtcta

5701	ttggttaaaa aatgagctga tttaacaaaa atttaacgcg aattttaaca aaatattaac

5761	gtttacaatt ttatggtgca gtctcagtac aatctgctct gatgccgcat agttaagcca

5821	gccccgacac ccgccaacac ccgctgacgc gccctgacgg gcttgtctgc tcccggcatc

5881	cgcttacaga caagctgtga ccgtctccgg gagctgcatg tgtcagaggt tttcaccgtc

5941	atcaccgaaa cgcgcga

TABLE 36

pM21J containing IIIss::A27::Ckappa
Number of bases 5225 (SEQ ID NO: 921)

GACGAAAGGG CCTCGTGATA CGCCTATTTT TATAGGTTAA TGTCATGATA ATAATGGTTT	60

CTTAGACGTC AGGTGGCACT TTTCGGGGAA ATGTGCGCGG AACCCCTATT TGTTTATTTT	120

TCTAAATACA TTCAAATATG TATCCGCTCA TGAGACAATA ACCCTGATAA ATGCTTCAAT	180

AATATTGAAA AAGGAAGAGT ATGAGTATTC AACATTTCCG TGTCGCCCTT ATTCCCTTTT	240

TTGCGGCATT TTGCCTTCCT GTTTTTGCTC ACCCAGAAAC GCTGGTGAAA GTAAAAGATG	300

CTGAAGATCA GTTGGGTGCC CGAGTGGGTT ACATCGAACT GGATCTCAAC AGCGGTAAGA	360

TCCTTGAGAG TTTTCGCCCC GAAGAACGTT TTCCAATGAT GAGCACTTTT AAAGTTCTGC	420

TATGTGGCGC GGTATTATCC CGTATTGACG CCGGGCAAGA GCAACTCGGT CGCCGCATAC	480

ACTATTCTCA GAATGACTTG GTTGAGTACT CACCAGTCAC AGAAAAGCAT CTTACGGATG	540

GCATGACAGT AAGAGAATTA TGCAGTGCTG CCATAACCAT GAGTGATAAC ACTGCGGCCA	600

ACTTACTTCT GACAACGATC GGAGGACCGA AGGAGCTAAC CGCTTTTTTG CACAACATGG	660

GGGATCATGT AACTCGCCTT GATCGTTGGG AACCGGAGCT GAATGAAGCC ATACCAAACG	720

ACGAGCGTGA CACCACGATG CCTGTAGCAA TGGCAACAAC GTTGCGCAAA CTATTAACTG	780

GCGAACTACT TACTCTAGCT TCCCGGCAAC AATTAATAGA CTGGATGGAG GCGGATAAAG	840

TTGCAGGACC ACTTCTGCGC TCGGCCCTTC CGGCTGGCTG GTTTATTGCT GATAAATCTG	900

GAGCCGGTGA GCGTGGGTCT CGCGGTATCA TTGCAGCACT GGGGCCAGAT GGTAAGCCCT	960

CCCGTATCGT AGTTATCTAC ACGACGGGGA GTCAGGCAAC TATGGATGAA CGAAATAGAC	1020

AGATCGCTGA GATAGGTGCC TCACTGATTA AGCATTGGTA ACTGTCAGAC CAAGTTTACT	1080

CATATATACT TTAGATTGAT TTAAAACTTC ATTTTTAATT TAAAAGGATC TAGGTGAAGA	1140

TCCTTTTTGA TAATCTCATG ACCAAAATCC CTTAACGTGA GTTTTCGTTC CACTGAGCGT	1200

CAGACCCCGT AGAAAAGATC AAAGGATCTT CTTGAGATCC TTTTTTTCTG CGCGTAATCT	1260

GCTGCTTGCA AACAAAAAAA CCACCGCTAC CAGCGGTGGT TTGTTTGCCG GATCAAGAGC	1320

TACCAACTCT TTTTCCGAAG GTAACTGGCT TCAGCAGAGC GCAGATACCA AATACTGTTC	1380

TTCTAGTGTA GCCGTAGTTA GGCCACCACT TCAAGAACTC TGTAGCACCG CCTACATACC	1440

TCGCTCTGCT AATCCTGTTA CCAGTGGCTG CTGCCAGTGG CGATAAGTCG TGTCTTACCG	1500

GGTTGGACTC AAGACGATAG TTACCGGATA AGGCGCAGCG GTCGGGCTGA ACGGGGGGTT	1560

CGTGCATACA GCCCAGCTTG GAGCGAACGA CCTACACCGA ACTGAGATAC CTACAGCGTG	1620

AGCTATGAGA AAGCGCCACG CTTCCCGAAG GGAGAAAGGC GGACAGGTAT CCGGTAAGCG	1680

GCAGGGTCGG AACAGGAGAG CGCACGAGGG AGCTTCCAGG GGGAAACGCC TGGTATCTTT	1740

ATAGTCCTGT CGGGTTTCGC CACCTCTGAC TTGAGCGTCG ATTTTTGTGA TGCTCGTCAG	1800

GGGGGCGGAG CCTATGGAAA AACGCCAGCA ACGCGGCCTT TTTACGGTTC CTGGCCTTTT	1860

GCTGGCCTTT TGCTCACATG TTCTTTCCTG CGTTATCCCC TGATTCTGTG GATAACCGTA	1920

TTACCGCCTT TGAGTGAGCT GATACCGCTC GCCGCAGCCG AACGACCGAG CGCAGCGAGT	1980

CAGTGAGCGA GGAAGCGGAA GAGCGCCCAA TACGCAAACC GCCTCTCCCC GCGCGTTGGC	2040

CGATTCATTA ATGCAGCTGG CACGACAGGT TTCCCGACTG GAAAGCGGGC AGTGAGCGCA	2100

ACGCAATTAA TGTGAGTTAG CTCACTCATT AGGCACCCCA GGCTTTACAC TTTATGCTTC	2160

CGGCTCGTAT GTTGTGTGGA ATTGTGAGCG GATAACAATT TCACACAGGA AACAGCTATG	2220

ACCATGATTA CGCCAAGCTT TGGAGCCTTT TTTTTGGAGA TTTTCAACAT GAAGAAACTG	2280

CTGTCTGCTA TCCCACTAGT TGTCCCTTTC TATTCTCATA GTGAAATCGT TCTGACCCAG	2340

TCCCCGGGGA CCCTGTCTCT GTCTCCGGGT GAACGTGCTA CGCTGAGCTG TCGTGCTTCT	2400

CAATCCGTTA GCTCCTCTTA TTTAGCTTGG TATCAGCAAA AGCCGGGTCA AGCTCCGCGG	2460

CTGTTGATCT ATGGTGCCTC TAGTCGTGCT ACTGGCATCC CTGATCGTTT CTCTGGCTCT	2520

GGCTCCGGAA CCGATTTCAC TCTGACCATT TCTCGTCTCG AGCCGGAAGA TTTCGCTGTC	2580

TACTATTGTC AACAGTATGG TTCTAGTCCG CTGACTTTCG GTGGCGGTAC CAAAGTCGAA	2640

ATCAAGCGTG GAACTGTGGC TGCACCATCT GTCTTCATCT TCCCGCCATC TGATGAGCAG	2700

TTGAAATCTG GAACTGCCTC TGTTGTGTGC CTGCTGAATA ACTTCTATCC CAGAGAGGCC	2760

AAAGTACAGT GGAAGGTGGA TAACGCCCTC CAATCGGGTA ACTCCCAGGA GAGTGTCACA	2820

GAGCAGGACA GCAAGGACAG CACCTACAGC CTCAGCAGCA CCCTGACTCT GTCCAAAGCA	2880

GACTACGAGA AACACAAAGT CTACGCCTGC GAAGTCACCC ATCAGGGCCT GAGTTCACCG	2940

GTGACAAAGA GCTTCAACAG GGGAGAGTGT TAATAAGGCG CGCCAATTTA ACCATCTATT	3000

TCAAGGAACA GTCTTAATGA AGAAGCTCCT CTTTGCTATC CCGCTCGTCG TTCCTTTTGT	3060

GGCCCAGCCG GCCATGGCCG AAGTTCAATT GTTAGAGTCT GGTGGCGGTC TTGTTCAGCC	3120

TGGTGGTTCT TTACGTCTTT CTTGCGCTGC TTCCGGATTC ACTTTCTCTC GTTACAAGAT	3180

GAAGTGGGTT CGCCAAGCTC CTGGTAAAGG TTTGGAGTGG GTTTCTGTTA TCTATCCTTC	3240

TGGTGGCGGT ACTGGTTATG CTGACTCCGT TAAAGGTCGC TTCACTATCT CTAGAGACAA	3300

CTCTAAGAAT ACTCTCTACT TGCAGATGAA CAGCTTAAGG GCTGAGGACA CTGCAGTCTA	3360

CTATTGTGCG AGAGTCAATT ACTATGATAG TAGTGGTTAC GGTCCTATAG CTCCTGGACT	3420

TGACTACTGG GGCCAGGGAA CCCTGGTCAC CGTCTCAAGC GCCTCCACCA AGGGTCCGTC	3480

GGTCTTCCCG CTAGCACCCT CCTCCAAGAG CACCTCTGGG GGCACAGCGG CCCTGGGCTG	3540

CCTGGTCAAG GACTACTTCC CCGAACCGGT GACGGTGTCG TGGAACTCAG GCGCCCTGAC	3600

CAGCGGCGTC CACACCTTCC CGGCTGTCCT ACAGTCTAGC GGACTCTACT CCCTCAGCAG	3660

CGTAGTGACC GTGCCCTCTT CTAGCTTGGG CACCCAGACC TACATCTGCA ACGTGAATCA	3720

CAAGCCCAGC AACACCAAGG TGGACAAGAA AGTTGAGCCC AAATCTTGTG CGGCCGCACA	3780

TCATCATCAC CATCACGGGG CCGCAGAACA AAAACTCATC TCAGAAGAGG ATCTGAATGG	3840

GGCCGCAGAG GCTAGTTCTG CTAGTAACGC GTCTTCCGGT GATTTTGATT ATGAAAAGAT	3900

GGCAAACGCT AATAAGGGGG CTATGACCGA AAATGCCGAT GAAAACGCGC TACAGTCTGA	3960

CGCTAAAGGC AAACTTGATT CTGTCGCTAC TGATTACGGT GCTGCTATCG ATGGTTTCAT	4020

TGGTGACGTT TCCGGCCTTG CTAATGGTAA TGGTGCTACT GGTGATTTTG CTGGCTCTAA	4080

TTCCCAAATG GCTCAAGTCG GTGACGGTGA TAATTCACCT TTAATGAATA ATTTCCGTCA	4140

ATATTTACCT TCCCTCCCTC AATCGGTTGA ATGTCGCCCT TTTGTCTTTG GCGCTGGTAA	4200

ACCATATGAA TTTTCTATTG ATTGTGACAA AATAAACTTA TTCCGTGGTG TCTTTGCGTT	4260

TCTTTTATAT GTTGCCACCT TTATGTATGT ATTTTCTACG TTTGCTAACA TACTGCGTAA	4320

TAAGGAGTCT TAATGAAACG CGTGATGAGA ATTCACTGGC CGTCGTTTTA CAACGTCGTG	4380

ACTGGGAAAA CCCTGGCGTT ACCCAACTTA ATCGCCTTGC AGCACATCCC CCTTTCGCCA	4440

GCTGGCGTAA TAGCGAAGAG GCCCGCACCG ATCGCCCTTC CCAACAGTTG CGCAGCCTGA	4500

ATGGCGAATG GCGCCTGATG CGGTATTTTC TCCTTACGCA TCTGTGCGGT ATTTCACACC	4560

GCATACGTCA AAGCAACCAT AGTACGCGCC CTGTAGCGGC GCATTAAGCG CGGCGGGTGT	4620

GGTGGTTACG CGCAGCGTGA CCGCTACACT TGCCAGCGCC TTAGCGCCCG CTCCTTTCGC	4680

TTTCTTCCCT TCCTTTCTCG CCACGTTCGC CGGCTTTCCC CGTCAAGCTC TAAATCGGGG	4740

GCTCCCTTTA GGGTTCCGAT TTAGTGCTTT ACGGCACCTC GACCCCAAAA AACTTGATTT	4800

GGGTGATGGT TCACGTAGTG GGCCATCGCC CTGATAGACG GTTTTTCGCC CTTTGACGTT	4860

GGAGTCCACG TTCTTTAATA GTGGACTCTT GTTCCAAACT GGAACAACAC TCAACTCTAT	4920

CTCGGGCTAT TCTTTTGATT TATAAGGGAT TTTGCCGATT TCGGTCTATT GGTTAAAAAA	4980

TGAGCTGATT TAACAAAAAT TTAACGCGAA TTTTAACAAA ATATTAACGT TTACAATTTT	5040

ATGGTGCAGT CTCAGTACAA TCTGCTCTGA TGCCGCATAG TTAAGCCAGC CCCGACACCC	5100

GCCAACACCC GCTGACGCGC CCTGACGGGC TTGTCTGCTC CCGGCATCCG CTTACAGACA	5160

AGCTGTGACC GTCTCCGGGA GCTGCATGTG TCAGAGGTTT TCACCGTCAT CACCGAAACG	5220

CGCGA	5225

TABLE 40

pLCSK23 (SEQ ID NO: 896)

1	GACGAAAGGG CCTGCTCTGC CAGTGTTACA ACCAATTAAC CAATTCTGAT TAGAAAAACT

61	CATCGAGCAT CAAATGAAAC TGCAATTTAT TCATATCAGG ATTATCAATA CCATATTTTT

121	GAAAAAGCCG TTTCTGTAAT GAAGGAGAAA ACTCACCGAG GCAGTTCCAT AGGATGGCAA

181	GATCCTGGTA TCGGTCTGCG ATTCCGACTC GTCCAACATC AATACAACCT ATTAATTTCC

241	CCTCGTCAAA AATAAGGTTA TCAAGTGAGA AATCACCATG AGTGACGACT GAATCCGGTG

301	AGAATGGCAA AAGCTTATGC ATTTCTTTCC AGACTTGTTC AACAGGCCAG CCATTACGCT

361	CGTCATCAAA ATCACTCGCA TCAACCAAAC CGTTATTCAT TCGTGATTGC GCCTGAGCGA

421	GACGAAATAC GCGATCGCTG TTAAAAGGAC AATTACAAAC AGGAATTGAA TGCAACCGGC

481	GCAGGAACAC TGCCAGCGCA TCAACAATAT TTTCACCTGA ATCAGGATAT TCTTCTAATA

541	CCTGGAATGC TGTTTTCCCG GGGATCGCAG TGGTGAGTAA CCATGCATCA TCAGGAGTAC

601	GGATAAAATG CTTGATGGTC GGAAGAGGCA TAAATTCCGT CAGCCAGTTT AGTCTGACCA

661	TCTCATCTGT AACATCATTG GCAACGCTAC CTTTGCCATG TTTCAGAAAC AACTCTGGCG

721	CATCGGGCTT CCCATACAAT CGATAGATTG TCGCACCTGA TTGCCCGACA TTATCGCGAG

781	CCCATTTATA CCCATATAAA TCAGCATCCA TGTTGGAATT TAATCGCGGC CTCGAGCAAG

841	ACGTTTCCCG TTGAATATGG CTCATAACAC CCCTTGTATT ACTGTTTATG TAAGCAGACA

901	GTTTTATTGT TCATGATGAT ATATTTTTAT CTTGTGCAAT GTAACATCAG AGATTTTGAG

961	ACACAACGTG GCTTTCCCCC CCCCCCCCTG CAGGTCTCGG GCTATTCCTG TCAGACCAAG

1021	TTTACTCATA TATACTTTAG ATTGATTTAA AACTTCATTT TTAATTTAAA AGGATCTAGG

1081	TGAAGATCCT TTTTGATAAT CTCATGACCA AAATCCCTTA ACGTGAGTTT TCGTTCCACT

1141	GAGCGTCAGA CCCCGTAGAA AAGATCAAAG GATCTTCTTG AGATCCTTTT TTTCTGCGCG

1201	TAATCTGCTG CTTGCAAACA AAAAAACCAC CGCTACCAGC GGTGGTTTGT TTGCCGGATC

1261	AAGAGCTACC AACTCTTTTT CCGAAGGTAA CTGGCTTCAG CAGAGCGCAG ATACCAAATA

1321	CTGTTCTTCT AGTGTAGCCG TAGTTAGGCC ACCACTTCAA GAACTCTGTA GCACCGCCTA

1381	CATACCTCGC TCTGCTAATC CTGTTACCAG TGGCTGCTGC CAGTGGCGAT AAGTCGTGTC

1441	TTACCGGGTT GGACTCAAGA CGATAGTTAC CGGATAAGGC GCAGCGGTCG GGCTGAACGG

1501	GGGGTTCGTG CATACAGCCC AGCTTGGAGC GAACGACCTA CACCGAACTG AGATACCTAC

1561	AGCGTGAGCT ATGAGAAAGC GCCACGCTTC CCGAAGGGAG AAAGGCGGAC AGGTATCCGG

1621	TAAGCGGCAG GGTCGGAACA GGAGAGCGCA CGAGGGAGCT TCCAGGGGGA AACGCCTGGT

1681	ATCTTTATAG TCCTGTCGGG TTTCGCCACC TCTGACTTGA GCGTCGATTT TTGTGATGCT

1741	CGTCAGGGGG GCGGAGCCTA TGGAAAAACG CCAGCAACGC GGCCTTTTTA CGGTTCCTGG

1801	CCTTTTGCTG GCCTTTTGCT CACATGTTCT TTCCTGCGTT ATCCCCTGAT TCTGTGGATA

1861	ACCGTATTAC CGCCTTTGAG TGAGCTGATA CCGCTCGCCG CAGCCGAACG ACCGAGCGCA

1921	GCGAGTCAGT GAGCGAGGAA GCGGAAGAGC GCCCAATACG CAAACCGCCT CTCCCCGCGC

1981	GTTGGCCGAT TCATTAATGC AGCTGGCACG ACAGGTTTCC CGACTGGAAA GCGGGCAGTG

2041	AGCGCAACGC AATTAATGTG AGTTAGCTCA CTCATTAGGC ACCCCAGGCT TTACACTTTA

2101	TGCTTCCGGC TCGTATGTTG TGTGGAATTG TGAGCGGATA ACAATTTCAC ACAGGAAACA

2161	GCTATGACCA TGATTACGCC AAGCTTTGGA GCCTTTTTTT TGGAGATTTT CAACATGAAG

2221	AAGCTCCTCT TTGCTATCCC GCTCGTCGTT CCTTTTGTGG CCCAGCCGGC CATGGCCGAC

2281	ATCCAGATGA CCCAGTCTCC ATCCTCCCTG TCTGCATCTG TAGGAGACAG AGTCACCATC

2341	ACTTGCCGGG CAAGTCAGAG CATTAGCAGC TATTTAAATT GGTATCAGCA GAAACCAGGG

2401	AAAGCCCCTA AGCTCCTGAT CTATGCTGCA TCCAGTTTGC AAAGTGGGGT CCCATCAAGG

2461	TTCAGTGGCA GTGGATCTGG GACAGATTTC ACTCTCACCA TCAGCAGTCT GCAACCTGAA

2521	GATTTTGCAA CTTACTACTG TCAACAGAGT TACAGTACCC CTTTCACTTT CGGCCCTGGG

2581	ACCAAAGTGG ATATCAAACG TGGtACcGTG GCTGCACCAT CTGTCTTCAT CTTCCCGCCA

2641	TCTGATGAGC AGTTGAAATC TGGAACTGCC TCTGTTGTGT GCCTGCTGAA TAACTTCTAT

2701	CCCAGAGAGG CCAAAGTACA GTGGAAGGTG GATAACGCCC TCCAATCGGG TAACTCCCAG

2761	GAGAGTGTCA CAGAGCAGGA CAGCAAGGAC AGCACCTACA GCCTCAGCAG CACCCTGACG

2821	CTGAGCAAAG CAGACTACGA GAAACACAAA GTCTACGCCT GCGAAGTCAC CCATCAGGGC

2881	CTGAGTTCAC CGGTGACAAA GAGCTTCAAC AGGGGAGAGT GTGCGGCCGC TGGTAAGCCT

2941	ATCCCTAACC CTCTCCTCGG TCTCGATTCT ACGTGATAAC TTCACCGGTC AACGCGTGAT

3001	GAGAATTCAC TGGCCGTCGT TTTACAACGT CGTGACTGGG AAAACCCTGG CGTTACCCAA

3061	CTTAATCGCC TTGCAGCACA TCCCCCTTTC GCCAGCTGGC GTAATAGCGA AGAGGCCCGC

3121	ACCGATCGCC CTTCCCAACA GTTGCGCAGC CTGAATGGCG AATGGCGCCT GATGCGGTAT

3181	TTTCTCCTTA CGCATCTGTG CGGTATTTCA CACCGCATAC GTCAAAGCAA CCATAGTCTC

3241	AGTACAATCT GCTCTGATGC CGCATAGTTA AGCCAGCCCC GACACCCGCC AACACCCGCT

3301	GACGCGCCCT GACAGGCTTG TCTGCTCCCG GCATCCGCTT ACAGACAAGC TGTGACCGTC

3361	TCCGGGAGCT GCATGTGTCA GAGGTTTTCA CCGTCATCAC CGAAACGCGC GA

Example 4: Dobbling of CDRs

The following examples exemplify the use of dobbling in constructing synthetic libraries. The parental 3-23 heavy chain (HC) is diversified in CDR1, 2, and 3. This diversity is combined with a synthetically diversified A27 light chain (LC). The diversity will be as follows:

Example 4.1 HC CDR1

The following dobbling diversity allows 5,832 variants. See Table 50. At position 31, Ser is the germline (GL) amino-acid type. Hence we make Ser three times more likely then the other types. Since 18 types are allowed, Ser will be allowed 15% of the time and all the others are allowed at 5%. Thus, if there is no selection for the AA type at 31, we are more likely to isolate an Ab with Ser. Similarly, at 33 the GL AA type is Ala and we make Ala 3 times as likely (15%) as all the others (5%). At 35 Ser is the GL AA type and we make it three times as likely as the others. At all three positions, we have excluded Cys and Met. We exclude Cys because we do not want gratuitous disulfides or exposed unpaired cysteines that could adversely affect the solubility and reactivity of the Ab. We exclude Met because exposed methionines side groups are subject to oxidation which can alter binding properties and shelf life. We could make the germline amino-acid type 2, 3, 4, 5, 6, 8, or 10 times more likely than the other AA types.

TABLE 50

Diversity for CDR1 in 3-23

Position	Parental AA	Allowed

31	S (three-times more	ADEFGHKLNPQRSTVWY
	likely as the others)

33	A (3-X more likely)	ADEFGHKLNPQRSTVWY

35	S (3-X more likely)	ADEFGHKLNPQRSTVWY

Throughout this disclosure, the shown “Allowed” amino acids are the amino acids that can be used at a given position. For example, in Table 50, at position 31, allowed amino acids “ADEFGHKLNPQRSTVWY” are shown. This indicates that amino acids A, D, E, F, G, H, K, L, N, P, Q, R, S, T, V, W, and Y are all allowed at position 31.

Example 4.2: HC CDR2

In CDR2, we allow diversity at positions 50, 52, 52a, 56, and 58. At 50, 52, 56, and 58 we allow all amino-acid types except Cys and Met and we make the GL AA types more likely by three fold. We could make the GL AA type 2, 3, 4, 5, 6, 8, or 10 times more likely than the other AA types.

TABLE 51

HC CDR2: Diversity = 419,904

Position	Parental AA	Allowed

50	A (3-X more likely)	ADEFGHKLNPQRSTVWY

52	S (3-X more likely)	ADEFGHKLNPQRSTVWY

52a	G (3-X more likely)	GPSY

56	S (3-X more likely)	ADEFGHKLNPQRSTVWY

58	Y (3-X more likely)	ADEFGHKLNPQRSTVWY

Combined CDR1 and CDR2 diversity=2.45 E 9

Example 4.3 HC CDR3, Lengths 3, 4, 5

Very short CDR3 can be made by dobbling. Table 7 shows several parental sequences for CDR3 length 3. At 94 many VH3s have Arg and we have allowed this change, but Lys is made 3-X as likely. At 95, F is found at this position in JH1. We also allow Ser, Tyr, Asp, and Arg to allow small, large, plus charge, and minus charge. At 96, JH1 has Q. Since Q is very similar to Glu, we allow Glu as an acidic alternative plus Arg, Ser, Tyr, and Leu. At 97, His is the germline AA from JH1. We allow minus charge (D), plus charge (R), small polar (S), large hydrophobic (Y), and aliphatic (L). The parental sequence makes up 4.5% of the library, but this is combined with a large diversity in CDR1 and CDR2. The dobbling allows 360 sequences in all. The least likely sequences occur at 1 in 1792. The most likely (parental) sequence occurs about 1 in 22.

TABLE 60

A dobbled HC CDR3 of length 3
(V-3JH1 of Table 7) (‘KFQH’ disclosed
as SEQ ID NO: 951)

	Parental amino
Position	acid (source)	Allowed

94	K (VH 3-23)	KR (3:1)

95	F (JH1)	FSYDR (3:1:1:1:1)

96	Q (JH1)	QERSYL (3:1:1:1:1:1)

97	H (JH1)	HDRSYL (3:1:1:1:1:1)

103	W (JH1)	W

Table 61 shows a dobbled HC CDR3 of length 3. Here K94 is fixed as is W103. We have made the “parental” D segment amino acid five times as likely as the other allowed AA types.

TABLE 61

A dobbled HC CDR3 of length 3 from a D
fragment (V-3D1-1.1.2-JH1 of Table 7).
(‘KTTG’ disclosed as SEQ ID NO: 952)

Position	Parental	Allowed

94	K (V 3-23)	K

95	T (D1-1.1.2)	TYRDL (5:1:1:1:1)

96	T (D1-1.1.2)	TYRDL (5:1:1:1:1)

97	G (D1-1.1.2)	GSYRDL (5:1:1:1:1:1)

103	W (JH1)	W

In this example (Table 62, using V-4JH2 from Table 8), 94 is fixed as Lys. At 95, JH2 has Tyr and we have allowed Ser, Asp, Arg, and Leu so that size, charge, and hydrophobicity can alter to suit the antigen. JH2 has Phe at 96 and we have allowed Ser, Tyr, Asp, Arg, and Leu. At 97, JH2 has Asp and we have allowed Arg, Ser, Tyr, and Leu. At 98, JH2 has Leu and we have allowed Ser, Tyr, Asp, and Arg. This pattern allows 750 distinct sequences, of which the parental is the most likely (1 in 18). The least likely sequences occur at 1 in 4608 or 256 times less likely than the most likely.

TABLE 62

HC CDR3 length 4 from JH2 (V-4JH2 in Table 7)
(‘KYFDL’ disclosed as SEQ ID NO: 953)

Position	Parental AA (source)	Allowed

94	K (VH 3-23)	K

95	Y (JH2)	YSDRL (4:1:1:1:1)

96	F (JH2)	FSYDRL (4:1:1:1:1:1)

97	D (JH2)	DRSYL (4:1:1:1:1)

98	L (JH2)	LSYDR (4:1:1:1:1)

103	W (JH2)	W

In Table 63, there is a dobbling of V-4D3-10.1a-JH2 from Table 8. At 94, we allow Lys and Arg with Lys (the parental) four times as likely as Arg. At 95, D3-10.1a (i.e., D3-10 in the first reading frame and starting a AA 1) has Leu; we allow SYDR as well with Leu 4-X as likely as each of the other AA types. At 96, D3-10.1a has Leu again and we allow the same menu. At 97, D3-10.1a has Trp and we allow Ser, Tyr, Asp, and Arg with Trp 4-X as likely. At 98, D3-10.1a has Phe and we allow Ser, Tyr, Asp, and Arg as well.

TABLE 63

HC CDR3 of length four from V-4D3-10.1a in
Table 8 (‘KLLWF’ disclosed as SEQ ID NO: 954)

Position	Parental AA (source)	Allowed

94	K (VH 3-23)	KR (4:1)

95	L (D3-10.1a)	LSYDR (4:1:1:1:1)

96	L (D3-10.1a)	LSYDR (4:1:1:1:1)

97	W (D3-10.1a)	WSYDR (4:1:1:1:1)

98	F (D3-10.1a)	FSYDR (4:1:1:1:1)

103	W	W

Example 4.4: HC CDR3 length 10 to 20

HC CDR3
Two sublibraries, both with CDR3 of length 16:

TABLE 52

Library 1: Diversity = 5 E 11, the “parental” sequence
occurs at 1 in 1.5 E6. (‘KYYYDSSGYYYAEYFQHW’
disclosed as SEQ ID NO: 955)

Position	“Parental” AA (source)	Allowed

94	K (3-X more likely) (3-23)	KR (3:1)

95	Y (3-X more likely) (D2-21(2))	YSRDL (3:1:1:1:1)

96	Y (3-X more likely) (D2-21(2))	YSRDL (3:1:1:1:1)

97	Y (3-X more likely) (D2-21(2))	YSRDL (3:1:1:1:1)

98	D (3-X more likely) (D2-21(2))	DYSRL (3:1:1:1:1)

99	S (3-X more likely) (D2-21(2))	SYRDL (3:1:1:1:1)

100	S (3-X more likely) (D2-21(2))	SYRDL (3:1:1:1:1)

101	G (3-X more likely) (D2-21(2))	GASYRDL (3:1:1:1:1:1:1)

102	Y (3-X more likely) (D2-21(2))	YSRDL (3:1:1:1:1)

102a	Y (3-X more likely) (D2-21(2))	YSRDL (3:1:1:1:1)

102b	Y (3-X more likely) (D2-21(2))	YSRDL (3:1:1:1:1)

102c	A (3-X more likely) (JH1)	ASYRD (3:1:1:1:1)

102d	E (3-X more likely) (JH1)	ERSYL (3:1:1:1:1)

102e	Y (3-X more likely) (JH1)	YSRDL (3:1:1:1:1)

102f	F (3-X more likely) (JH1)	FYSRD (3:1:1:1:1)

102g	Q (3-X more likely) (JH1)	QERSY (3:1:1:1:1)

102h	H (3-X more likely) (JH1)	HERSYL (3:1:1:1:1:1)

103	W (JH1, fixed)	W

TABLE 53

Library 2: CDR3 length 16; Diversity is 3.0 E 10 and the
parental sequence occurs once in 3.7 E 5.
(‘KGYCSSTSCYTAEYFQHW’ disclosed as SEQ ID NO: 956)

Position	“Parental” AA (source)	Allowed

94	K (3-X more likely) (3-23)	KR (3:1)

95	G (3-X more likely) (D2-2(2))	GSYDRL (3:1:1:1:1:1)

96	Y (3-X more likely) (D2-2(2))	YSDRL (3:1:1:1:1)

97	C (fixed) (D2-2(2))	C

98	S (3-X more likely) (D2-2(2))	SYRDL (3:1:1:1:1)

99	S (3-X more likely) (D2-2(2))	SYRDL (3:1:1:1:1)

100	T (3-X more likely) (D2-2(2))	TYRDL (3:1:1:1:1)

101	S (3-X more likely) (D2-2(2))	SYRDL (3:1:1:1:1)

102	C (fixed) (D2-2(2))	C

102a	Y (3-X more likely) (D2-2(2))	YSDRL (3:1:1:1:1)

102b	T (3-X more likely) (D2-2(2))	TYRDL (3:1:1:1:1)

102c	A (3-X more likely) (JH1)	ASYDRL (3:1:1:1:1:1)

102d	E (3-X more likely) (JH1)	ERSYL (3:1:1:1:1)

102e	Y (3-X more likely) (JH1)	YSDRL (3:1:1:1:1)

102f	F (3-X more likely) (JH1)	FYSRDL (3:1:1:1:1:1)

102g	Q (3-X more likely) (JH1)	QERSYL (3:1:1:1:1:1)

102h	H (3-X more likely) (JH1)	HDRSYL (3:1:1:1:1:1)

103	W ((JH1))	W

Table 65 shows a dobbling variegation of SEQ ID NO: 898. The total diversity allowed is 2.1 E 13. A synthesis that produces 1. E 8, 3. E 8, 5. E 8, 1. E 9, or 5. E 9 will sample the diversity adequately. The design of SEQ ID NO: 898 was discussed above. In dobbling SEQ ID NO: 898, is to allow the parental AA type at three-fold above other AA types at most positions. At positions where the parental is Tyr, then we use Tyr and Ser at equal amounts with Leu at one half that frequency. The Cys residues are fixed. Each parental AA type is allowed to go to one of Arg, Asp, Ser, Tyr, or Leu (Leu might be omitted if the parental is hydrophobic, such as Phe). The parental sequence will occur once in 1. E 8 members. The least likely sequences will occur once in 9.5 E 16. It is not important that the library actually contain the parental sequence, only that it contains many sequences that resemble the parent. Thus, a library that contains 1. E 7, 5. E7, 1.E8, 3. E8, 1. E 9, or 5. E 9, when combined with diversity in HC CDR1, HC CDR2, LC CDR1, LC CDR2, and LC CDR3 will provide a library that will contain many valuable Abs.

TABLE 65

Dobbling of Design 1 with SEQ ID NO: 898
as parent (‘KDYGYCSSTSCYTYGYSYAEYFQHW’
disclosed as SEQ ID NO: 957)

Position	Parental (source)	Allowed

94	K (VH 3-23)	K

95	D (No source)	DSYL (3:1:1:1)

96	Y (No source)	YSL (2:2:1)

97	G (D2-2.2)	GSYDRL (3:1:1:1:1:1)

98	Y (D2-2.2)	YSL (2:2:1)

99	C (D2-2.2)	C

100	S (D2-2.2)	SYDRL (3:1:1:1:1)

101	S (D2-2.2)	SYDRL (3:1:1:1:1)

102	T (D2-2.2)	TYDRL (3:1:1:1:1)

102a	S (D2-2.2)	SYDRL (3:1:1:1:1)

102b	C (D2-2.2)	C

102c	Y (D2-2.2)	YSL (2:2:1)

102d	T (D2-2.2)	TYDRL (3:1:1:1:1)

102e	Y (No source)	YDSL (3:1:1:1)

102f	G (No source)	GSYRD (3:1:1:1:1)

102g	Y (No source)	YSL (2:2:1)

102h	S (No source)	SYDRL (3:1:1:1)

102i	Y (No source)	YSL (2:2:1)

102j	A (JH1)	ASYDR (3:1:1:1:1)

102k	E (JH1)	ERSYL (3:1:1:1:1)

102l	Y (JH1)	YSL (2:2:1)

102m	F (JH1)	FSYDR (3:1:1:1:1)

102n	Q (JH1)	QYSDRL (3:1:1:1:1:1)

102p	H (JH1)	HSYDRL (3:1:1:1:1:1)

103	W (JH1, FR4)	W

Example 4.5 Dobbling of yycakGSGYCSGGSCYSFDYwgqgtlvtvss (SEQ ID NO:931)

Table 80 shows the dobbling of SEQ ID NO:931, an example of an HC CDR3 of length 15. Position 94 is part of FR3 and is held constant. Positions 95 and 96 have “parental” amino-acid types picked from the highly used set of (YGDRS) and are G95 and S96. The next ten positions are taken from D2-15.2 (a moderately highly used D segment containing a disulfide-closed loop). The final three positions are from the JH4 positions 100, 101, and 102 as shown in Table 3. At each position, we make the parental amino-acid type three times more likely than the other allowed types. The Cys residues are fixed. At 102e, Phe is three times more likely as are YGSRD (i.e., Phe is three times more likely as are any of amino acids Y, G, S, R, or D). The diversity allowed is 1.46 E 9. The parental sequence is expected at 1 in 6.9 E 4. Each of the singly substituted sequences is about ⅓ as likely; the doubly substituted ones are 1/9 as likely and so on. The sequences that are composed entirely of other AA types occur at only 1 in 1.1 E 11.
Each of the other sequences in Table 21 can be dobbled in the same way.

TABLE 80

Dobbling of yycakGSGYCSGGSCYSFDYwgqgtlvtvss
(SEQ ID NO: 931)
(‘KGSGYCSGGSCYSFDYW’ disclosed as SEQ ID NO: 958)

Position	Parental (source)	Allowed

94	K (VH 3-23)	K

95	G (No source)	GYSRD (3:1:1:1:1)

96	S (No source)	SGYRD (3:1:1:1:1)

97	G (D2-15.2)	GYSRD (3:1:1:1:1)

98	Y (D2-15.2)	YGSRD (3:1:1:1:1)

99	C (D2-15.2)	C

100	S (D2-15.2)	SGYRD (3:1:1:1:1)

101	G (D2-15.2)	GYSRD (3:1:1:1:1)

102	G (D2-15.2)	GYSRD (3:1:1:1:1)

102a	S (D2-15.2)	SGYRD (3:1:1:1:1)

102b	C (D2-15.2)	C

102c	Y (D2-15.2)	YGSRD (3:1:1:1:1)

102d	S (D2-15.2)	SGYRD (3:1:1:1:1)

102e	F (JH4)	FYGSRD (3:1:1:1:1:1)

102f	D (JH4)	DGSRY (3:1:1:1:1)

102g	Y (JH4)	YGSRD (3:1:1:1:1)

103	W (JH4, FR4)	W

Example 5: Synthetic Light Chain Diversity

To make whole antibodies, we need to combine a library of heavy chains with a library of light chains (LC). In natural Abs, it is often observed that HC does most of the binding and many libraries have given little attention to the LC or have obtained LC diversity from human donors. To have enough diversity to give good binders to almost any target, we have designed a diversification program that exceeds what the human immune system usually provides. Nevertheless, the program is designed to yield fully functional LC that have the same kind of changes as seen in natural Abs, only a few more. Vkappa III A27 was picked as the LC.
From a library that comprises donated kappa and lambda LCs, a collection of 1266 Abs were typed. Among VKIIIs, A27 is most often seen (Table 66) and pairs well with HC 3-23.
The CDRs of A27 contain 12, 7, and 9 amino acids. Putting diversity at all of these positions might not work well: a) there might be many unstable or non-functional members, and b) diversity at some positions might not help improve binding. We have reduced the number of variable positions from 28 to 16.
We have studied the 3D structure of 1QLR which has an A27 LC. The 1GLR structure is publicly available in the RCDB Protein Data Base. From this, the residues marked in Table 68 look useful to vary. The T56 is about 10 A from a His in HC CDR3. Variation at 56 may be useful. G24 is only about 7 A from an atom in HC CDR3. Germline is R24; thus, variation at 24 may be useful.
Table 69 shows a display cassette that we designed for use in pMID21. Thus, the restriction enzymes picked do not have other sites in pMID21. SpeI is in the iii signal sequence and allows the entire LC to be inserted or removed. XmaI, PpuMI, EcoO109I, and BlpI precede CDR1. SacII is in FR2, separating CDR1 from CDR2. Alternatively, an AvrII site could be inserted at the same position. BspEI and XhoI sites are in FR3 and a KpnI site is in FR4.
We gathered 155 A27 sequences and analyzed what happens in the CDRs. Table 70 shows the analysis. In Table 70, we show what is found in the Abs from our library and what we would put at each position.

TABLE 68

where to vary A27

!
!		22 3 3 5 5 89 9
!		45 0a 4 0 5 90 5
!	1QLR	GASQSVS_NYLA DASSRAT QQYGSSPLT
!	A27	RASQSVSSSYLA GASSRAT QQYGSSPLT
		** * * * * ******

	GASQSVS is (SEQ ID NO: 922)

	NYLA (SEQ ID NO: 959)

	DASSRAT is (SEQ ID NO: 923)

	QQYGSSPLY is (SEQ ID NO: 924)

	QQYGSSPLT (SEQ ID NO: 966)

	RASQSVSSSYLA is (SEQ ID NO: 925)

	GASSRAT is (SEQ ID NO: 926)

Table 68 shows where the CDRs of A27 would be variegated.

TABLE 67

Compare VKIII AA seqs

VK3 is (SEQ ID NO: 927)

A27 is (SEQ ID NO: 960)

A11 is (SEQ ID NO: 961)

L2 is (SEQ ID NO: 962)

L16 is (SEQ ID NO: 962)

L6 is (SEQ ID NO: 963)

L20 is (SEQ ID NO: 964)

L25 is (SEQ ID NO: 965)

	FR1....................CDR1........FR2............CDR2...FR3
	1 2 3 4 5 6
	1234567890123456789012345678901a23456789012345678901234567890
VK3	DIVLTQSPATLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGVPA
A27	E-------G-------------------------------------------------I-D
A11	E----------------------G------------------L-------D-------I-D
L2	E--M--------V------------------#N--------------------T----I--
L16	E--M--------V------------------#N--------------------T----I--
L6	E------------------------------#------------------D--N----I--
L20	E--------------------------G---#------------------D--N----I--
L25	E--M------------------------------S------------------T----I--

		.............................CDR3.....FR4.........
		1
		7 8 9 0
		1234567890123456789012345678901234567890123456789
	VK3	RFSGSGSGTDFTLTISSLEPEDFAVYYCQQHYTTPPTFGQGTKVEIKRT
	A27	----------------R-------------YGSS-
	A11	----------------R-------------YGSS-
	L2	---------E--------QS----------YNNW-
	L16	---------E--------QS----------YNNW-
	L6	------------------------------RSNW-
	L20	-------P----------------------RSNWH
	L25	------------------Q-----------D-NL-

VK3 differs from A27 by E1D, G9A, I58V, D60A, R77S.

A27 and L6 differ by G9A(FR1), Δ31a(in CDR1), G50D(CDR2),

S53N(CDR2), G92S(CDR3), S93N(CDR3), S94W(CDR3)

VK3 from U.S. Pat. No. 7,264,963.

CDR1
R24, A25, and S26 are too far from the combining site to help and were held constant. The side group of V29 is buried; this position was held constant as Val. At the other positions, we allowed Y or S and a charge flip-flop (RE or RD, depending on where the sample had more of E or D at the position in question) plus other types that were frequently seen. We used an Excel spread sheet to determine that this pattern of variegation would give the parental sequence at 0.8% if the “other” AAs were substituted at 5%, at 0.1% if the “other” AAs were substituted at 6.5%, and at 0.02% if “other” was at 9%. In the sample of 155, 17 have one AA deleted (including 1QLR); thus, we will arrange to have S30a deleted in ˜8% of the members.
CDR2
From inspection of 1QLR, we see that CDR2 is somewhat remote from the combining site. There have even been suggestions that we keep the residues in this CDR constant. Studying the 3D structure suggests that variegation at G50, S53, and T56 could be useful. S53 is the most variable in the sample of 155, but this does not prove that these changes are useful. In 1QLR, G50 has been mutated to R50. The side group of T56 is pointed toward HC CDR3 and is about 11 A from an atom in HC CDR3.
CDR3
Q89 and Q90 are buried and nature does not vary them often; these residues are not varied. Y91 is packed against HC CDR3 and changes here would alter the combining site and do occur. At G92, φ=−80 and ψ=−15 so putting in a non-Gly is feasible; nature does it in 47/155 cases. S93 is very often varied or deleted. S94 is highly exposed and is highly varied. P95 is exposed and varied. L96 packs against HC CDR3: changes here will affect the binding site and do occur in nature. T97 is buried and has been held constant/the amino acid is not varied.
The parental sequence appears at 0.000246 or 1 in 4.06 E3. The allowed diversity is about 2.1 E 12. With two 8% deletions, 84.6% of the members will be full length, 7.4% will have short CDR1 and full-length CDR3, 7.4% will have full-length CDR1 and short CDR3, and 0.6% will have both deletions.
Other germlines were not in the sample.

TABLE 66

Distribution of VLs in 1266 selected LCs.

Kappas	Lambdas

O12	VKI	313		1a	VL1	9
O18	VKI	1		1e	VL1	7
A20	VKI	26		1c	VL1	55
A30	VKI	26		1g	VL1	46
L14	VKI	2		1b	VL1	1	118
L1	VKI	5		2c	VL2	18
L15	VKI	1		2e	VL2	23
L5	VKI	83		2a2	VL2	79
L8	VKI	10		2d	VL2	1	121
L12	VKI	77	544	3r	VL3	56
O11	VKII	4		3j	VL3	4
A17	VKII	17		3l	VL3	31
A19	VKII	31	52	3h	VL3	22	113
A27	VKIII	155		4a	VL4	1	1
L2	VKIII	31		5c	VL5	1	1
L6	VKIII	88		6a	VL6	8	8
L25	VKIII	16	290	10a	VL10	6	6

B3

VKIV

12

Number of lambdas

368

Number of kappas	898	Total Abs in sample	1266

TABLE 69

A Display gene for A27 in pM21J.
IIIsignal::A27::Ckappa

The amino-acid sequence of Table 69 is (SEQ ID NO: 928).

The DNA sequence of Table 69 is (SEQ ID NO: 929).

!		signal sequence--------------------------------------------
!		1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
!		M K K L L S A I P L V V P F Y
	1	\|atg\|aaG\|aaA\|ctg\|ctg\|tct\|gct\|atc\|ccA\|CTA\|GTt\|gtc\|cct\|ttc\|tat\|
		SpeI....
!
!		Signal------- FR1-------------------------------------------
!		16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
!		S H S E1 I V3 L T5 Q S7 P G9 T L S12
	46	\|tct\|cat\|agt\|gaa\|atc\|gtt\|ctg\|acc\|cag\|tcC\|CCG\|GGG\|aCC\|Ctg\|tct\|
!		XmaI....
!		PpuMI....
!		EcoO109I.(1/2)
!
!		FR1--------------------------------------- CDR1-----------
!		31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
!		L13 S P G E R A T L S C23 R24 A S Q
	91	\|ctg\|tct\|ccg\|ggt\|gaa\|cgt\|gct\|acG\|CTg\|AGC\|tgt\|cgt\|gct\|tct\|caa\|
!		BlpI.....
!
!		CDR1-------------------------- FR2------------------------
!		46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
!		S28 V S S S30a Y L A34 W Y Q Q K P G
	136	\|tcc\|gtt\|agC\|TCC\|TCt\|tat\|tta\|gct\|tgg\|tat\|cag\|caa\|aag\|ccg\|ggt\|
!		BseRI...
!
!		FR2--------------------------- CDR2-----------------------
!		61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
!		Q A P R45 L L I Y G50 A S S R A T56
	181	\|caa\|gct\|CCG\|CGG\|ctg\|ttg\|atc\|tat\|ggt\|gcc\|tct\|agt\|cgt\|gct\|act\|
!		SacII..
!
!		FR3-------------------------------------------------------
!		76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
!		G I P D60 R F S G S65 G S G T D F
	226	\|ggc\|atc\|cct\|gat\|cgt\|ttc\|tct\|ggc\|tct\|ggc\|TCC\|GGA\|acc\|gat\|ttc\|
!		BspEI..
!
!		FR3-------------------------------------------------------
!		91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
!		T L T I S R L E P E D F A V Y
	271	\|act\|ctg\|acc\|att\|tct\|CGT\|CTC\|GAG\|ccg\|gaa\|gat\|ttc\|gct\|gtc\|tac\|
!		BsmBI..
!		XhoI...
!
!		FR3---- CDR3------------------------------ FR4-----------
!		106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
!		Y C Q89 Q Y G S S P95 L T F G G G
	316	\|tat\|tgt\|caa\|cag\|tat\|ggt\|tct\|agt\|ccg\|ctg\|act\|ttc\|ggt\|ggc\|GGT\|
!		KpnI...
!
!		FR4--------------------
!		121 122 123 124 125 126
!		T K V E I K
	361	\|ACC\|aaa\|gtc\|gaa\|atc\|aag
!		KpnI.
!
!		Ckappa-----------------------------------------------------
!		R G T V A A P S V F I F P P S
	379	cgt gga act gtg gCT GCA Cca tct GTC TTC atc ttc ccg cca tct
!		BsgI.... BbsI...
!
!		D E Q L K S G T A S V V C L L
	424	gat gag cag ttg aaa tct gga act gcc tct gtt gtg tgc ctg ctg
!
		N N F Y P R E A K V Q W K V D
!	469	aat aac ttc tat ccc aga gag gcc aaa gta cag tgg aag gtg gat
!
!		N A L Q S G N S Q E S V T E Q
	514	aac gcc ctc caa tcg ggt aac tcc cag gag agt gtc aca gag cag
!
!		D S K D S T Y S L S S T L T L
	559	gac agc aag gac agc acc tac agc ctc agc agc acc ctg act ctg
!
!		S K A D Y E K H K V Y A C E V
!	604	tcc aaa gca gac tac gag aaa cac aaa GTC TAC gcc tgc gaa gtc
!
!		T H Q G L S S P V T K S F N R
	649	acc cat cAG GGC CTg agt tCA CCG GTG aca aag agc ttc aac agg
!		AlwNI...... SgrAI.....
!		EcoO109I.(2/2) AgeI....
!
!		G E C . .
	694	gga gag tgt taa taa
!
	709	GG CGCGCCaatt
!		AscI.....
!		BssHII.

TABLE 70

Tally of mutations in CDRs of A27 Abs

CDR1 (‘RASQSVSSSYLA’ disclosed as SEQ ID NO: 925)

R24	1, 3G, 1T, 151-,	Fix

A25	2, 3T, 152-,	Fix

S26	3, 1R, 154-,	Fix

Q27	4, 3E, 1H, 1L, 1P, 4R, 145-,	9% ERYSL

S28	5, 1A, 2F, 2G, 1I, 2L, 5N, 1P, 1R, 10T, 1V, 1Y, 128-,	9% NTYERL

V29	6, 1F, 19I, 6L, 129-,	Fix

S30	7, 2A, 2D, 8G, 2H, 1I, 11N, 9R, 6T, 4V, 2Y, 108-,	9% DNRTY

530a	8, 1A, 2F, 6G, 1H, 6N, 1P, 10R, 6T, 3Y, 119-,	9% GNRTYD

	(8% delete 30a)

S31	9, 1A, 5D, 3F, 4G, 1H, 2I, 4K, 1L, 31N, 19R, 7T, 7Y, 70-,	9% DFGNRTY

Y32	10, 5F, 1K, 14L, 4N, 4Q, 2R, 85, 3V, 1W, 113-,	9% FDLNQRSY

L33	11, 16A, 1F, 4I, 1N, 1S, 8V, 1Y, 123-,	Fix

A34	12, 2G, 2L, 1N, 1S, 4V, 128-,	9% SY

-	13, 2A, 1G,

-	14, 1S,

-	15, 1S,

-	16, 1Y,

-	17, 1L,

-	18, 1A,

Note:

one antibody had an insertion of six AAs in CDR1! Two other Abs had a

single insertion. Seventeen Abs have a one AA deletion in CDR1.

CDR2 (‘GASSRAT’ disclosed as SEQ ID NO: 926)

G50	1, 10A, 11D, 1H, 2R, 2S, 1V, 7Y, 121-,	9% DRSYL

A51	2, 7G, 2I, 65, 7T, 2V, 131-,	Fix

S52	3, 6A, 3F, 1G, 1T, 144-,	Fix

S53	4, 1A, 1G, 1H, 5I, 2K, 16N, 7R, 16T, 106-,	9% NTSYER

R54	5, 1A, 1I, 1N, 1S, 3T, 1Y, 147-,	Fix

A55	6, 2P, 7R, 4S, 2V, 140-,	Fix

T56	7, 10A¹, 1G, 1H, 2P, 4S, 137-,	9% ERSY

_	8, 1A, 6T,

Note,

there are seven antibodies with an insertion of one AA.

CDR3 (showing “_” means that the Ab has a deletion in CDR3)

('QQYGSSPLT' disclosed as SEQ ID NO: 966)

Q89	1, 5H, 1L, 2M, 147-,	Fix

Q90	2, 1E, 1F, 13H, 2K, 2L, 4R, 1S, 1Y, 130-,	Fix

Y91	3, 2A, 8F, 2G, 2H, 1L, 1P, 13R, 4S, 122-,	9% FERS

G92	4, 10A, 3D, 2H, 1I, 1L, 2N, 6R, 12S, 2V, 3Y, 108-, 5_,	9% ADRSTY

S93	5, 1A, 2D, 2F, 6G, 2H, 3I, 2K, 2M, 14N, 1P, 1Q, 8R, 17T, 2Y, 86-, 6_,	9% DFNRTY

	(8% have 93 deleted)

S94	6, 3A, 6F, 1I, 3L, 3P, 2R, 2T, 11W, 117-, 7_,	9% WERYS

P95	7, 2A, 1E, 1G, 1K, 3L, 1M, 7R, 3S, 3T, 1V, 108-, 24_,	9% ERYS

L96	8, 2A, 2E, 3F, 3G, 1H, 1I, 3K, 7L, 2M, 24P ², 6Q, 28R, 3S, 3T, 7V, 2Y, 58-,	9% ERPYS

T97	9, 2A, 1F, 2G, 3I, 1K, 2L, 3M, 1N, 1R, 6S, 3V, 2Y, 128-,	Fix

_	10, 1A, 1S, 34-,

_	11, 1S, 7-,

_	12, 1A,

There is one Ab with an insertion of 3 AAs.

Five have deletions of 4 AAs, 1 has a 3 AA deletion, 1 has a 2 AA deletion,

and 17 have a one AA deletion.

TABLE 71

Allowed diversity in CDR1, 2, and 3 of A27::JK4.
(‘RASQSVSSSYLA’ disclosed as SEQ ID NO: 925;
‘GASSRAT’ disclosed as SEQ ID NO: 926;
‘QQYGSSPLT’ disclosed as SEQ ID NO: 966)

Position	parental	allowed

CDR1

42	(24)	R	fixed
43	(25)	A	fixed
44	(26)	S	fixed
45	(27)	4	ERYSL	55% Q 9% other
46	(28)	S	NTYERL	46% S 9% other
47	(29)	V	fixed
48	(30)	S	DNRTY	55% S 9% other
49	(30a)	S	GNRTYD	46% S 9% other

8% have 30a deleted

50	(31)	S	DFGNRTY	44% S 8% other
51	(32)	Y	FDLNQRSY	44% Y 7% other
52	(33)	L	fixed
53	(34)	A	SY	70% A 15% other

CDR2

69	(50)	G	DRSYL	55% G 9% other
70	(51)	A	Fixed
71	(52)	S	Fixed
72	(53)	S	NTSYER	52% S 8% other
73	(54)	R	Fixed
74	(55)	A	Fixed
75	(56)	T	ERSY	64% T 9% other

CDR3

108	(89)	Q	fixed
109	(90)	Q	fixed
110	(91)	Y	FERS	64% Y 9% other
111	(92)	G	ADRSTY	52% G 8% other
112	(93)	S	DFNRTY	52% S 8% other
113	(94)	S	WERYS	55% S 9% other
114	(95)	P	ERYS	64% P 9% other

8% have P95 deleted

115	(96)	L	ERPYS	55% L 9% other
116	(97)	T	fixed

The parental sequence appears at 5.32 E-5 or 1 in 1.88 E 4.
Sequences with a single substitution have a probability between 1.1 E-5 and 7.5 E-6.
Sequences that have none of the parental AAs occurs at 1 in 6.7 E 16.
The allowed diversity is about 2.35 E 12.

TABLE 75

Frequencies of amino acids in HC CDR3s.

				Rel
AA	Number	%	Rel up	down

Y	3428	15.64	50.41	1.00
G	3244	14.80	47.71	0.95
D	2622	11.96	38.56	0.76
S	1777	8.11	26.13	0.52
R	1337	6.10	19.66	0.39
F	1328	6.06	19.53	0.39
A	1213	5.53	17.84	0.35
V	1141	5.20	16.78	0.33
L	816	3.72	12.00	0.24
I	745	3.40	10.96	0.22
P	726	3.31	10.68	0.21
T	586	2.67	8.62	0.17
W	566	2.58	8.32	0.17
M	560	2.55	8.24	0.16
N	462	2.11	6.79	0.13
E	363	1.66	5.34	0.11
K	355	1.62	5.22	0.10
H	327	1.49	4.81	0.10
Q	259	1.18	3.81	0.08
C	68	0.31	1.00	0.02
Total	21923

TABLE 76

Length distribution of HC CDR3

	Number
	of
Length	Antibodies	Sum	Median

1	0
2	0
3	2	2
4	21	23
5	16	39
6	100	139
7	36	175
8	78	253
9	155	408
10	153	561
11	134	695	11.12
12	123	818
13	133	951
14	92	1043
15	87	1130
16	71	1201
17	59	1260
18	41	1301
19	40	1341
20	22	1363
21	21	1384
22	15	1399
23	7	1406
24	7	1413
25	1	1414
26	1	1415
27	3	1418
28	0	1418
29	0	1418
30	1	1419
	1419	709.5

TABLE 77

Utilization of D-segments
(cut off at 0.70 match)

				SEQ ID NO:

3-22.2	38	YYYDSSGYYY	88

4-17.2	27	DYGDY	195

3-3.2	25	YYDFWSGYYT	177

6-19.1	25	GYSSGWY	218

7-27.1	19	LTG	221

5-5.3	18	GYSYGY	786

6-13.1	18	GYSSSWY	215

5-12.3	13	GYSGYDY	205

6-13.2	10	GIAAAG	216

1-26.3	9	YSGSYY	284

2-15.2	9	GYCSGGSCYS	136

4-4.3	9	TTVT	190

3-10.2	8	YYYGSGSYYN	81

1-1.3	7	YNWND	262

4-4.2	7	DYSNY	754

2-2.2	6	GYCSSTSCYT	70

3-16.2	6	YYDYVWGSYRYT	104

6-6.1	6	EYSSSS	212

6-19.2	6	GIAVAG	219

3-9.1	5	VLRYFDWLL@	179

4-23.2	5	DYGGNS	198

6-6.2	5	SIAAR	213

1-7.3	4	YNWNY	270

2-2.3	4	DIVVVPAAI	168

4-23.3	4	TTVVT	199

1-7.1	3	GITGT	268

1-26.1	3	GIVGAT	282

7-27.3	3	NWG	223

3-10.1	2	VLLWFGELL@	182

3-10.2	2	ITMVRGVII	183

5-5.1	2	VDTAMV	200

5-5.2	2	WIQLWL	201

5-12.1	2	VDIVATI	203

5-24.3	2	RDGYNY	211

1-1.1	1	GTTGT	260

2-21.3	1	HIVVVTAI	175

3-3.3	1	ITIFGVVII	178

5-24.2	1	*RWLQL	210

6-6.3	1	V*QLV	214

6-19.3	1	V*QWLV	220

TABLE 78

D segment utilization (0.667 cutoff)

	Name	Number	Sequence	SEQ ID NO:	%

None	935			0.517

7-27.1	158	LTG	221	0.087

7-27.3	98	NWG	223	0.054

5-5.3	72	GYSYGY	786	0.040

1-26.3	67	YSGSYY	166	0.037

3-22.2	46	YYYDSSGYYY	187	0.025

4-17.2	38	DYGDY	195	0.021

3-3.2	37	YYDFWSGYYT	177	0.020

7-27.2	37	@LG	222	0.020

6-19.1	33	GYSSGWY	218	0.018

6-13.2	31	GIAAAG	860	0.017

6-13.1	22	GYSSSWY	215	0.012

6-6.1	18	EYSSSS	847	0.010

6-19.2	18	GIAVAG	879	0.010

4-23.2	17	DYGGNS	198	0.009

5-12.3	17	GYSGYDY	205	0.009

5-24.3	14	RDGYNY	211	0.008

2-15.2	13	GYCSGGSCYS	136	0.007

1-26.1	11	GIVGAT	164	0.006

4-4.3	11	TTVT	190	0.006

1-1.3	9	YNWND	262	0.005

2-2.2	9	GYCSSTSCYT	70	0.005

3-16.2	9	YYDYVWGSYRYT	104	0.005

2-2.3	8	DIVVVPAAI	168	0.004

3-10.2	8	YYYGSGSYYN	81	0.004

4-4.2	8	DYSNY	192	0.004

1-7.3	7	YNWNY	270	0.004

3-3.3	6	ITIFGVVII	178	0.003

6-6.2	6	SIAAR	213	0.003

3-9.1	5	VLRYFDWLL@	179	0.003

3-10.2	5	ITMVRGVII	183	0.003

6-19.3	5	V*QWLV	220	0.003

1-7.1	4	GITGT	268	0.002

4-23.3	4	TTVVT	768	0.002

1-1.1	3	GTTGT	156	0.002

5-5.1	3	VDTAMV	200	0.002

5-24.2	3	*RWLQL	210	0.002

3-10.1	2	VLLWFGELL@	182	0.001

5-5.2	2	WIQLWL	201	0.001

5-12.1	2	VDIVATI	203	0.001

1-26.2	1	V*WELL	165	0.001

2-21.2	1	AYCGGDCYS	174	0.001

2-21.3	1	HIVVVTAI	175	0.001

3-3.1	1	VLRFLEWLLY	176	0.001

3-16.2	1	IMITFGGVIVI	185	0.001

6-6.3	1	V*QLV	214	0.001

6-13.3	1	V*QQLV	217	0.001

TABLE 78

Utilization of JH segments

	JH1	17
	JH2	31
	JH3	452
	JH4	636
	JH5	32
	JH6	251

Example 6: Wobbled DNA for HC CDR3 16d

Table 400 shows a segment of DNA from an XbaI site in FR3 to a BstEII site in FR4. The HC CDR3 consists of SYSY::D2-2(2)::QH (‘SYSY’ disclosed as SEQ ID NO: 947) followed by the FR4 region of JH1. The QH is found in the germline of JH1. In V-D-J joining, immune cells often edit the ends of V, D, and J. Thus the construction corresponds to what is very possible in actual immunoglobulin gene construction and maturation. By wobbling the synthesis, we obtain a large collection of genes that resemble what would come from joining 3-23 to either a D region or to a little edited JH1 followed by some mutations. In library 16d, there are two cysteines that presumably form a disulfide, these are not wobbled.
Table 500 shows the expected distribution of amino-acid types at each position in the 16d library. The wobble doping was set at 73:9:9:9. The most likely sequence is the one shown in Table 21 and should be present at a frequency of 4.8 E-5. Only 55% of the sequences are stop free and 74% are free of ochre or opel. If the library is expressed in supE cells, this is the important number. It would be valuable to remove the sequences with stop codons as discussed elsewhere herein. One can see that those positions that start as S are predicted to have S 54% of the time and Y 5.4% while those that start as Y have Y 44% of the time and S 7.2%. At each position there are 7-9 AA types that appear at >1%. There are 14 variegated positions. The sequences that will be most effectively sampled number about 8¹⁴=4.3 E 12.

TABLE 400

Cassette for display of wobbled HC CDR3 16d

!		--------FR3--------------------------------------------------
!		68 69 70 71 72 73 74 75 76 77 78 79 80 81 82
!		T I S R D N S K N T L Y L Q M
	1216	\|act\|atc\|TCT\|AGA\|gac\|aac\|tct\|aag\|aat\|act\|ctc\|tac\|ttg\|cag\|atg\|
!		\| XbaI \|

!

!		---FR3----------------------------------------------------->\|
!		82a 82b 82c 83 84 85 86 87 88 89 90 91 92 93 94
!		N S L R A E D T A V Y Y C A K
	1261	\|aac\|agC\|TTA\|AGg\|gct\|gag\|gac\|act\|gca\|gtc\|tac\|tat\|tgc\|gct\|aaa\|
!		\|AflII \|

!
!	e = 0.73 A + 0.09 C + 0.09 G + 0.09 T
!	q = 0.09 A + 0.73 C + 0.09 G + 0.09 T
!	j = 0.09 A + 0.09 C + 0.73 G + 0.09 T
!	z = 0.09 A + 0.09 C + 0.09 G + 0.73 T
!	The values 0.73 and 0.09 are picked so that 0.73 + 3 * 0.09 = 1.0
!	Other ratios could be used.
!

!		102 102 102 102 102 102 102 102
!		95 96 97 98 99 100 101 102 a b c d e f g h
!		S Y S Y G Y c S S T S c Y T Q H
		zqz zez zqz zez jjz zez TGT zqz zqz eqz zqz TGT zez eqz qej qez

!

!		--------------FR4------------------------->\|
!		103 104 105 106 107 108 109 110 111 112 113
!		W G Q G T L V T V S S (SEQ ID NO: 968)
		\|TGg\|ggt\|caa\|ggt\|act\|ttG\|GTC\|ACC\|gtc\|tct\|agt (SEQ ID NO: 967)
!		\| BstEII \|
!

TABLE 500

Expected distribution of AA types in wobbled HC CDR3 16d

“.” = TGA or TAA; “b”= TAG

Amino acid disclosed as SEQ ID NO: 970

DNA sequence disclosed as SEQ ID NO: 969

S Y S Y G Y c S S T S c Y T Q H

zqz zez zqz zez jjz zez tgt zqz zqz eqz zqz tgt zez eqz qej qez

Nominal base purity = 0.7300 others = 0.0900

	s(zqz)	y(zez)	s(zqz)	y(zez)	g(jjz)	y(zez)	C(TGT)	s (zqz)	s(zqz)

1	s 5.4-01	y 4.4-01	s 5.4-01	y 4.4-01	g 5.3-01	y 4.4-01	c 1.000	s 5.4-01	s 5.4-01
2	p 6.6-02	s 7.2-02	p 6.6-02	s 7.2-02	r 7.8-02	s 7.2-02		p 6.6-02	p 6.6-02
3	a 6.6-02	f 5.4-02	a 6.6-02	f 5.4-02	a 6.6-02	f 5.4-02		a 6.6-02	a 6.6-02
4	t 6.6-02	h 5.4-02	t 6.6-02	h 5.4-02	v 6.6-02	h 5.4-02		t 6.6-02	t 6.6-02
5	f 5.4-02	n 5.4-02	f 5.4-02	n 5.4-02	s 6.2-02	n 5.4-02		f 5.4-02	f 5.4-02
6	c 5.4-02	c 5.4-02	c 5.4-02	c 5.4-02	c 5.4-02	c 5.4-02		c 5.4-02	c 5.4-02
7	y 5.4-02	d 5.4-02	y 5.4-02	d 5.4-02	d 5.4-02	d 5.4-02		y 5.4-02	y 5.4-02
8	l 2.0-02	. 5.4-02	l 2.0-02	. 5.4-02	e 1.2-02	. 5.4-02		l 2.0-02	l 2.0-02
9	. 1.2-02	b 4.8-02	. 1.2-02	b 4.8-02	l 9.6-03	b 4.8-02		. 1.2-02	. 1.2-02
10	r 9.6-03	l 2.0-02	r 9.6-03	l 2.0-02	t 8.1-03	l 2.0-02		r 9.6-03	r 9.6-03
11	g 8.1-03	k 1.2-02	g 8.1-03	k 1.2-02	p 8.1-03	k 1.2-02		g 8.1-03	g 8.1-03
12	v 8.1-03	q 1.2-02	v 8.1-03	q 1.2-02	i 7.4-03	q 1.2-02		v 8.1-03	v 8.1-03
13	i 7.4-03	e 1.2-02	i 7.4-03	e 1.2-02	. 6.6-03	e 1.2-02		i 7.4-03	i 7.4-03
14	h 6.6-03	r 9.6-03	h 6.6-03	r 9.6-03	f 6.6-03	r 9.6-03		h 6.6-03	h 6.6-03
15	n 6.6-03	t 8.1-03	n 6.6-03	t 8.1-03	h 6.6-03	t 8.1-03		n 6.6-03	n 6.6-03
16	d 6.6-03	v 8.1-03	d 6.6-03	v 8.1-03	y 6.6-03	v 8.1-03		d 6.6-03	d 6.6-03
17	w 5.9-03	a 8.1-03	w 5.9-03	a 8.1-03	n 6.6-03	a 8.1-03		w 5.9-03	w 5.9-03
18	b 5.9-03	g 8.1-03	b 5.9-03	g 8.1-03	w 5.9-03	g 8.1-03		b 5.9-03	b 5.9-03
19	q 1.5-03	p 8.1-03	q 1.5-03	p 8.1-03	q 1.5-03	p 8.1-03		q 1.5-03	q 1.5-03
20	k 1.5-03	i 7.4-03	k 1.5-03	i 7.4-03	k 1.5-03	i 7.4-03		k 1.5-03	k 1.5-03
21	e 1.5-03	w 5.9-03	e 1.5-03	w 5.9-03	m 7.3-04	w 5.9-03		e 1.5-03	e 1.5-03
22	m 7.3-04	m 7.3-04	m 7.3-04	m 7.3-04	b 7.3-04	m 7.3-04		m 7.3-04	m 7.3-04

	t(eqz)	s(zqz)	C(TGT)	y(zez)	t(eqz)	q(qej)	h(qez)

1	t 5.3-01	s 5.4-01	c 1.000	y 4.4-01	t 5.3-01	q 4.4-01	h 4.4-01
2	s 1.2-01	p 6.6-02		s 7.2-02	s 1.2-01	h 9.6-02	q 9.6-02
3	a 6.6-02	a 6.6-02		f 5.4-02	a 6.6-02	l 7.2-02	l 6.7-02
4	p 6.6-02	t 6.6-02		h 5.4-02	p 6.6-02	r 7.2-02	r 6.7-02
5	i 6.0-02	f 5.4-02		n 5.4-02	i 6.0-02	p 6.6-02	p 6.6-02
6	n 5.4-02	c 5.4-02		c 5.4-02	n 5.4-02	e 5.4-02	n 5.4-02
7	r 2.0-02	y 5.4-02		d 5.4-02	r 2.0-02	k 5.4-02	d 5.4-02
8	k 1.2-02	l 2.0-02		. 5.4-02	k 1.2-02	b 4.8-02	y 5.4-02
9	l 9.6-03	. 1.2-02		b 4.8-02	l 9.6-03	d 1.2-02	s 1.5-02
10	g 8.1-03	r 9.6-03		l 2.0-02	g 8.1-03	y 1.2-02	k 1.2-02
11	v 8.1-03	g 8.1-03		k 1.2-02	v 8.1-03	n 1.2-02	e 1.2-02
12	f 6.6-03	v 8.1-03		q 1.2-02	f 6.6-03	s 9.6-03	g 8.1-03
13	c 6.6-03	i 7.4-03		e 1.2-02	c 6.6-03	t 8.1-03	t 8.1-03
14	h 6.6-03	h 6.6-03		r 9.6-03	h 6.6-03	v 8.1-03	v 8.1-03
15	d 6.6-03	n 6.6-03		t 8.1-03	d 6.6-03	a 8.1-03	a 8.1-03
16	y 6.6-03	d 6.6-03		v 8.1-03	y 6.6-03	g 8.1-03	i 7.4-03
17	m 5.9-03	w 5.9-03		a 8.1-03	m 5.9-03	. 6.6-03	. 6.6-03
18	q 1.5-03	b 5.9-03		g 8.1-03	q 1.5-03	w 5.9-03	c 6.6-03
19	e 1.5-03	q 1.5-03		p 8.1-03	e 1.5-03	m 5.9-03	f 6.6-03
20	. 1.5-03	k 1.5-03		i 7.4-03	. 1.5-03	i 2.2-03	b 5.9-03
21	w 7.3-04	e 1.5-03		w 5.9-03	w 7.3-04	f 1.5-03	w 7.3-04
22	b 7.3-04	m 7.3-04		m 7.3-04	b 7.3-04	c 1.5-03	m 7.3-04

Most likely sequence has frequency = 4.8E−05

Fraction stop-free = 5.5E−01

Fraction (TAA&TGA)-free = 7.4E−01

		F %	F %	F %

D1	1-1	0.42	0.14	2.90
	1-7	0.42	0.28	1.24
	1-20	0.00	0.00	0.00
	1-26	0.00	0.97	1.80
D2	2-2	0.55	4.30	1.21
	2-8	0.00	0.67	0.41
	2-15	0.28	4.03	0.94
	2-21	0.00	2.22	0.94
D3	3-3	0.94	4.44	3.70
	3-9	0.67	1.82	0.00
	3-10	0.67	5.78	1.55
	3-16	1.08	2.49	0.67
	3-22	0.14	7.87	0.81
D4	4-4	0.28	0.69	0.28
	4-11	0.00	0.00	0.00
	4-17	0.00	4.03	2.76
	4-23	0.14	1.41	0.54
D5	5-5	1.34	0.40	4.30
	5-12	1.08	0.00	1.95
	5-18	0.00	0.00	0.00
	5-24	0.67	1.55	1.82
D6	6-6	1.21	1.55	0.13
	6-13	4.84	2.62	0.27
	6-19	6.66	1.95	0.54
D7	7-27	0.27	0.13	0.27

	Total fractional %	21.65	49.34	29.01

TABLE 800

!LC K1(O12)::JK1
!Amino acid disclosed as SEQ ID NO: 972
DNA sequence disclosed as SEQ ID NO: 971

!		..Leader seq. ->\|-------- FR1 ----------------------------->
!		1 2 3 4 5 6 7 8 9 10 11
!		G V H S A Q D I Q M T Q S P S S L
	1	\|ggT\|GTA\|CAc\|aGT\|GCT\|Cag\|gat\|att\|cag\|atg\|act\|caa\|tct\|ccC\|TCG\|AGt\|ctg\|
!		BsrGI... ApaLI... XhoI....

!		-------- FR1 ---------------------------------->\|--- CDR1 ->
!		12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
!		S A S V G D R V T I T C R A S
	46	\|tct\|gct\|tct\|gtc\|gGC\|GAT\|CGC\|gtt\|act\|att\|act\|tgt\|cgt\|gct\|tcc\|
!		SgfI......

!		---- CDR1 -------------------->\|---- FR2 ----------------->
!		27 28 29 30 31 32 33 34 35 36 37 38 39 40 41
!		Q S I S S Y L N W Y Q Q K P G
	91	\|cag\|tcc\|att\|tct\|agc\|tat\|ctg\|aat\|tGG\|TAC\|Cag\|caa\|aag\|ccg\|ggt\|
!		KpnI....
!
!		------ FR2 ------------------->\|-- CDR2 ------------------>
!		42 43 44 45 46 47 48 49 50 51 52 53 54 55 56
!		K A P K L L I Y A A S S L Q S
	136	\|aag\|gct\|ccg\|aaa\|ctg\|tta\|atc\|tat\|gcc\|gct\|tct\|agt\|ctg\|cag\|tct\|

!		---------- FR3 ------------------------------------------->
!		57 58 59 60 61 62 63 64 65 66 67 68 69 70 71
!		G V P S R F S G S G S G T D F
	181	\|ggt\|gtt\|ccg\|TCT\|AGA\|ttc\|tct\|ggc\|tct\|ggt\|tct\|ggt\|act\|gat\|ttt\|
!		XbaI...

!		---------- FR3 ------------------------------------------->
!		72 73 74 75 76 77 78 79 80 81 82 83 84 85 86
!		T L T I S S L Q P E D F A T Y
	226	\|act\|ctg\|act\|att\|tcc\|tct\|ctg\|caa\|ccg\|gag\|gac\|ttt\|gct\|acc\|tat\|

!		- FR3>\|---- CDR3 ------------------------>\|--- FR4 ------>
!		87 88 89 90 91 92 93 94 95 96 97 98 99 100 101
!		Y C Q Q S Y S T P W T F G Q G
	271	\|tac\|tgc\|caa\|cag\|tct\|tat\|agt\|act\|ccg\|tgg\|act\|ttc\|ggt\|caa\|ggc\|

!		---- FR4 -------------->\|---- Ckappa----------------------->
!		102 103 104 105 106 107 108 109 110 111 112 113 114 115 116
!		T K V E I K R T V A A P S V F
	316	\|act\|aaa\|gtt\|gag\|att\|aag\|CGT\|ACG\|gtg\|gct\|gct\|ccg\|tct\|gtc\|ttc\|
!		BsiWI..

TABLE 900

CDR1 diversity (SEQ ID NO: 973)

Diversity

Position	24	25	26	27	28	29	30	31	32	33	34
O12	R	A	S	Q	S	I	S	S	Y	L	N
diversity	2	2	1	1	3	1	2	2	4	1	3	576
allowed	Q	M			D		R	N	D		A
					G				W		G
									A

TABLE 1000

Big CDR1 diversity

Diversity

Position

24

25

26

27

28

29

30

31

32

33

34

O12

R

A

S

Q

S

I

S

Y

L

N

diversity

3

2

4

1

5

1

4

5

1

6

72000

allowed

Q

M

E

D

R

N

D

A

E

R

G

E

W

G

Y

R

Y

R

A

D

Y

R

Y

TABLE 1100

CDR2 diversity

								Diversity

POSITION	50	51	52	53	54	55	56
O12	A	A	S	S	L	Q	S
diversity	2	1	1	3	1	2	2	24
allowed	D			N		E	T
				T

TABLE 1200

Big CDR2 diversity

								Diversity

POSITION	50	51	52	53	54	55	56
O12	A	A	S	S	L	Q	S
diversity	4	1	4	6	1	4	5	1920
allowed	D		E	N		E	T
	R		R	T		R	Y
	Y		Y	E		Y	R
				R			E
				Y

TABLE 1300

CDR3 diversity

										div. tot.

Position	93	94	95	96	97	98	99	100	101
O12	Q	Q	S	Y	S	S	P	W	T
diversity	2	2	6	3	3	5	2	1	1	2160
allowed	L	K	Y	D	N	T	S
			H	N	Y	L
			F			Y
			A			F
			D

TABLE 1400

Big CDR3 diversity

										div. tot.

Position	93	94	95	96	97	98	99	100	101
O12	Q	Q	S	Y	S	S	P	W	T
diversity	6	1	7	7	6	5	2	6	1	105840
allowed	L		Y	D	N	T	S	F
	E		H	N	Y	L		Y
	R		F	R	D	Y		H
	Y		A	A	R	F		L
	A		D	L	A	E		I
			R	S		R

Example 7: Further Examples of Synthetic HC CDR3s

A collection of 22,063 Fabs with distinct CDR3 which had been selected from the FAB-310 or FAB-410 library and which were ELISA positive for at least one antigen were examined. The utilization of JH chains is shown in Table 1001; the FR4 part of each JH is shown bold. Table 1010 shows the utilization of amino acids in the HC CDR3s. Table 1020 shows the length distribution of CDR3. The median length is 11.5.
Table 1030 shows the utilization of D segments in the CDR3s. A D segment was identified is 70% of the amino acids matched; there were 5,654 cases (25.6%). The most used Ds were 3-3.2 (743, sequence: YYDFWSGYYT (SEQ ID NO: 177)), 3-22.2 (617, sequence: YYYDSSGYYY (SEQ ID NO: 88)), 6-19.1 (441, sequence: GYSSGWY (SEQ ID NO: 218)), 6-13.1 (399, sequence: GYSSSWY (SEQ ID NO: 215)), and 4-17.2 (392, sequence: DYGDY (SEQ ID NO: 760)). Of the Ds containing paired Cys residues, 2-15.2 (sequence: GYCSGGSCYS (SEQ ID NO: 136)) was the most used; there were 139 examples which is 0.6% of the collection.
When V or V::D is joined to J, there is often editing of the 3′ end of V or V::D and the 5′ end of J. Inspection of many CDR3-FR4 sequences shows that there is often a portion of JH making up part of CDR3. Often there are mutations in the CDR3 residues corresponding to JH residues 1-9. Herein the portion of CDR3 that is thought to derive from JH is called the “J stump”. The JH used in a heavy chain is determined by comparing each of the residues of the six JH chains from position 6 to 20 to fusion of the last four amino acids of CDR3 to FR4. The JH that has the fewest mismatches is selected. The CDR3 sequence is examined for a J stump by working backward in the selected JH from position 9 toward the first position of the selected JH comparing to CDR3 until the search is terminated by a) the end of JH, b) the end of CDR3, or c) two consecutive mismatches. If one of the chains ends and the last compared position is a match, then it is included in J stump. If not, it is not. Table 1070 shows several examples. The CDR is written above, the JH is below, and the J stump is underlined. In 1070 A, we start at 9, V matches V, and we continue to position 6 with matches. The search stops at 4 because of the double mismatch. GMDV (SEQ ID NO: 974) goes into the J stump pile and GL goes into the “Leadin” pile. In 1070 B, the search ends with the end of JH6. The underscored residues go into the J stump pile and EPIWG (SEQ ID NO: 975) goes into the Leadin pile. In 1070 E, the search terminates because of the end of JH4, but the final residue tested (D in the CDR vs Y in JH4) is a mismatch and so the J stump is FDS and DSGVVAAAD (SEQ ID NO: 976) goes into the Leadin pile.
Table 1015 shows the amino-acid distribution of CDR3s that have no D segments from which the J stump has been removed. Note that the frequency of Tyr is much lower than when the whole CDR3s were compiled. This indicates that Tyr comes into CDR3s to a large extent through incorporation of D segments and J stumps. These Tyrs are not randomly inserted, but occur in a sequence that has been selected throughout mammalian evolution. It is a feature of the present invention that high levels (more than 20%) of Tyr should be inserted into libraries through the incorporation of Ds and J stumps that contain Tyr. At leadin or DJ filler positions, Tyr is allowed, but at no more than 20%.

TABLE 1070

Examples of assignment of J stump

A)

6	GLGMDV (SEQ ID NO: 977)
JH6	YYYYYGMDVWGQGTTVTVSS (SEQ ID NO: 3)
	123456789

B)
13	EPIWGYYYYGMDV (SEQ ID NO: 978)
JH6	YYYYYGMDVWGQGTTVTVSS (SEQ ID NO: 3)

C)
9	DFFTSYFDY (SEQ ID NO: 979)
JH4	-----YFDYWGQGTLVTVSS (SEQ ID NO: 1)

D)
12	DRGVSLLGAFDI (SEQ ID NO: 980)
JH3	-----AFDIWGQGTMVTVSS (SEQ ID NO: 2)

E)
12	DSGVVAAADFDS (SEQ ID NO: 981)
JH4	-----YFDYWGQGTLVTVSS (SEQ ID NO: 1)
	6789

Table 1082 shows the distribution of amino-acid usage in the J stumps of each JH. Since the most common JHs are JH3, JH4, and JH6, these are the preferred JHs on which to build libraries. Table 1082 shows that most examples of JH3 retain the tetrapeptide sequence AFDI (SEQ ID NO: 986) in CDR3. With JH4, a majority retain DY and a large fraction retain the sequence FDY in CDR3. With JH6, a large majority retain the sequence DV, a majority retain the sequence MDV, and a substantial fraction retain the sequence GMDV (SEQ ID NO: 974). A non-negligible fraction retain the sequence YGMDV (SEQ ID NO: 982), YYGMDV (SEQ ID NO: 983), or YYYGMDV (SEQ ID NO: 984).
Included in libraries of the present invention are libraries such as 5.001 (Table 1097). Library 5.001 contains LC and HC CDR1-2 as described elsewhere in the present application. The library contains a HC VH (such as 3-23) followed by 6, 7, or 8 amino acids allowing [GSRDLY] in proportion shown in Table 1097. In the J stump, the parental amino acid is present at 3, 4, 5, 6, 7, 8, 10 times as likely as “other” amino-acid types. The “other” amino-acid types comprise Y, S, D, R, G. Thus at A6, we allow 7/12 A, plus 1/12 each of Y, S, D, R, and G. At F7, we allow 7/12 F plus 1/12 each of Y, S, D, R, and G. At D8, we allow 7/11 D plus 1/11 of Y, S, R, and G. At 19, we allow 7/12 I plus 1/12 Y, S, R, D, G. The parental amino acid could be 5, 6, 7, 8, 10 time more likely than the other amino-acid types.
Included in the libraries of the present invention is library 5.002 in Table 1097. This library comprises CDR3 of length 13, 14, and 15 and no D segment. There are 6, 7, or 8 leadin residues allowing G, S, R, D, L, or Y in the ratios 1:0.57:0.46:0.42:0.36:0.35 or reasonable approximation thereto. The CDR3 is completed with a portion of JH6: YYYGMDV (SEQ ID NO: 984). The DNA that encodes the parental sequence YYYGMDV (SEQ ID NO: 984) is synthesized with the parental amino acid at 5, 6, 7, 8, or 10 times more likely than the others.
Included in the library of the present invention is library 5.003 in Table 1097. FR3 is followed by 4, 5, or 6 leadin residues allowing G, S, R, D, L, Y in the ratio 1.0:0.57:0.46:0.42:0.36:0.35. Next comes D segment 3-3.2; the DNA that encodes this region favors the parental amino acid by 5-fold and allows as other amino acids Y, G, D, R, S. There is no DJ filler and the final four amino acids come from the J stump of JH3. The DNA encoding the J stump are synthesized with the parental amino acid 5-fold more likely than the others: YSGRD.
Library 5.004 in Table 1097 is a part of the present invention. There are 2, 3, or 4 leadin residues allowing GSRDLY in the ratios shown. The DNA encoding the sequence GYSSGWY (SEQ ID NO: 218) is synthesized so that the parental amino acid is 6-X as likely as the others, two DJ-filler residues are allowed with GSRDLY allowed in the ratios 1.0:0.57:0.46:0.42:0.36:0.35. The DNA to encode AFDI (SEQ ID NO: 986) is synthesized with the parental amino acid 6-x as likely as the others.
Library 5.005 is part of the present invention. Library 5.005 comprises members with CDR3 lengths 11-14. After FR3, there are 0, 1, or 2 leadin residues allowing GSRDLY in the ratios shown followed by DNA that encodes the parental sequence GYSSGWY (SEQ ID NO: 218) with variability that allows YGSRD such that the parental amino acid is 6-X as likely as the other allowed types. Following the D region there is zero or one DJ filler residues allowing GSRDLY in the ratios shown. Finally is JH3 with variability in the J stump (sequence: YFDY (SEQ ID NO: 985)) which allows YGSRD with the parental amino acid 6-X as likely as the other allowed types.
Library 5.006 in Table 1097 is part of the present invention. The CDR3 may be of length 19-25. There are zero to three leadin residues allowing GSRDLY in the ratios shown. Following the leadin is the D region 2-2.2. The DNA encoding 2-2.2 is synthesized so that the parental amino acid is 6-X as likely as the others (viz. YGSRD) except that the two Cys residues are fixed. Following 2-2.2 are zero to three DJ filler residues allowing GSRDLY in the ratios shown. The DNA that encodes the first nine residues of JH6 allows the parental amino acid plus YSGDR with the parental type being 6× more likely than the others.

TABLE 1001

Utilization of JHs

			11111111112	SEQ ID
JH	Number	%	12345678901234567890	NO:

JH1	1356	6.15	---AEYFQHWGQGTLVTVSS	66

JH2	1720	7.80	---YWYFDLWGRGTLVTVSS	67

JH3	5601	25.39	-----AFDIWGQGTMVTVSS	2

JH4	7658	34.71	-----YFDYWGQGTLVTVSS	1

JH5	1062	4.81	----NWFDPWGQGTLVTVSS	68

JH6	4666	21.15	YYYYYGMDVWGQGTTVTVSS	3
Total	22063

TABLE 1010

Utilization of Amino acids in HC CDR3

			Rel	Rel
AA	Number	%	up	dwn

Y	42863	15.47	35.87	1.00
G	37512	13.54	31.39	0.88
D	34051	12.29	28.49	0.79
S	23068	8.33	19.30	0.54
F	17813	6.43	14.91	0.42
A	15150	5.47	12.68	0.35
R	14090	5.09	11.79	0.33
V	13834	4.99	11.58	0.32
L	12351	4.46	10.34	0.29
I	10014	3.61	8.38	0.23
P	9514	3.43	7.96	0.22
W	9340	3.37	7.82	0.22
T	7544	2.72	6.31	0.18
M	6093	2.20	5.10	0.14
E	6042	2.18	5.06	0.14
N	5901	2.13	4.94	0.14
H	4403	1.59	3.68	0.10
K	3147	1.14	2.63	0.07
Q	3097	1.12	2.59	0.07
C	1195	0.43	1.00	0.03
	277022

TABLE 1015

Frequency of amino acids
in Leadin of CDR3s lacking D regions

AA	Number	percent	rel up	rel dn

G	23134	18.24	46.45	1.000
S	13555	10.69	27.22	0.586
R	10562	8.33	21.21	0.457
D	9704	7.65	19.49	0.419
L	8255	6.51	16.58	0.357
Y	8099	6.39	16.26	0.350
A	7188	5.67	14.43	0.311
V	6599	5.20	13.25	0.285
P	5768	4.55	11.58	0.249
W	4804	3.79	9.65	0.208
T	4769	3.76	9.58	0.206
E	4497	3.55	9.03	0.194
N	3733	2.94	7.50	0.161
F	3616	2.85	7.26	0.156
I	3464	2.73	6.96	0.150
H	2787	2.20	5.60	0.120
K	2460	1.94	4.94	0.106
Q	2124	1.67	4.27	0.092
M	1225	0.97	2.46	0.053
C	498	0.39	1.00	0.022
	126841

TABLE 1020

Lengths of HC CDR3s

Length	Number	%

1	0	0.00
2	6	0.03
3	36	0.16
4	153	0.69
5	121	0.55
6	669	3.03
7	756	3.43
8	1066	4.83
9	2227	10.09
10	2701	12.24
11	2240	10.15
12	2071	9.39
13	2006	9.09
14	1594	7.22
15	1396	6.33
16	1254	5.68
17	1102	4.99
18	783	3.55
19	588	2.67
20	474	2.15
21	285	1.29
22	237	1.07
23	133	0.60
24	81	0.37
25	32	0.15
26	25	0.11
27	11	0.05
28	6	0.03
29	2	0.01
30	3	0.01
31	2	0.01
32	1	0.00
33	1	0.00
34	0	0.00
35	0	0.00
36	1	0.00
	22063

TABLE 1030

Utilization of D segments.

Id	Number	Sequence	SEQ ID NO:

1-1.1	29	GTTGT	156

1-1.2	6	VQLER	157

1-1.3	151	YNWND	158

1-7.1	34	GITGT	159

1-7.2	0	V*LEL	160

1-7.3	65	YNWNY	161

1-20.1	0	GITGT	268

1-20.2	0	V*LER	162

1-20.3	0	YNWND	163

1-26.1	48	GIVGAT	164

1-26.2	3	V*WELL	165

1-26.3	220	YSGSYY	166

2-2.1	0	RIL**YQLLY	177 & 167

2-2.2	102	GYCSSTSCYT	70

2-2.3	37	DIVVVPAAI	168

2-8.1	0	RILY@WCMLY	169 & 392

2-8.2	23	GYCTNGVCYT	115

2-8.3	1	DIVLMVYAI	170

2-15.1	0	RILWWLLL	171

2-15.2	139	GYCSGGSCYS	136

2-15.3	12	DIVVVVAAT	172

2-21.1	0	SILWW$LLF	173

2-21.2	24	AYCGGDCYS	174

2-21.3	6	HIVVVTAI	175

3-3.1	28	VLRFLEWLLY	176

3-3.2	743	YYDFWSGYYT	177

3-3.3	15	ITIFGVVII	178

3-9.1	41	VLRYFDWLL@	179

3-9.2	8	YYDILTGYYN	180

3-9.3	0	ITIF*LVII	181 & 579

3-10.1	26	VLLWFGELL@	182

3-10.2	136	YYYGSGSYYN	81

3-10.2	32	ITMVRGVII	183

3-16.1	0	VL$LRLGELSLY	184

3-16.2	109	YYDYVWGSYRYT	104

3-16.2	8	IMITFGGVIVI	185

3-22.1	0	VLL***WLLL	186

3-22.2	617	YYYDSSGYYY	187

3-22.3	2	ITMIVVVIT	188

4-4.1	0	$LQ@L	189

4-4.2	75	DYSNY	192

4-4.3	165	TTVT	190

4-11.1	0	$LQ@L	191

4-11.2	0	DYSNY	192

4-11.3	0	TTVT	193

4-17.1	0	$LR@L	194

4-17.2	392	DYGDY	195

4-17.3	0	TTVT	196

4-23.1	0	$LRW@L	197

4-23.2	60	DYGGNS	198

4-23.3	16	TTVVT	199

5-5.1	25	VDTAMV	200

5-5.2	29	WIQLWL	201

5-5.3	292	GYSYGY	202

5-12.1	13	VDIVATI	203

5-12.2	0	WI*WLRL	204

5-12.3	200	GYSGYDY	205

5-18.1	0	VDTAMV	206

5-18.2	0	WIQLWL	207

5-18.3	0	GYSYGY	208

5-24.1	9	VEMATI	209

5-24.2	21	*RWLQL	210

5-24.3	44	RDGYNY	211

6-6.1	87	EYSSSS	212

6-6.2	122	SIAAR	213

6-6.3	1	V*QLV	214

6-13.1	399	GYSSSWY	215

6-13.2	170	GIAAAG	216

6-13.3	0	V*QQLV	217

6-19.1	441	GYSSGWY	218

6-19.2	104	GIAVAG	219

6-19.3	3	V*QWLV	220

7-27.1	257	LTG	221

7-27.2	0	@LG	222

7-27.3	64	NWG	223
none	16409

TABLE 1040

JH vs Length

	Length	JH1	JH2	JH3	JH4	JH5	JH6

1	0	0	0	0	0	0
2	1	4	0	1	0	0
3	20	2	3	9	0	2
4	75	3	10	45	8	12
5	47	6	10	38	8	12
6	273	14	43	280	26	33
7	88	27	194	337	30	80
8	134	43	243	503	41	102
9	121	70	855	886	61	234
10	116	693	623	979	68	222
11	105	81	675	1003	84	292
12	107	84	552	905	121	302
13	87	274	538	672	113	322
14	48	81	480	532	105	348
15	50	83	372	421	80	390
16	28	54	316	322	87	447
17	27	49	239	334	69	384
18	11	64	174	140	49	345
19	8	28	104	99	41	308
20	4	23	59	56	20	312
21	0	13	40	30	24	178
22	3	14	31	30	13	146
23	1	3	22	12	7	88
24	0	5	9	12	4	51
25	1	0	1	3	1	26
26	0	0	5	5	0	15
27	0	1	2	1	1	6
28	1	0	0	2	0	3
29	0	0	0	0	0	2
30	0	0	0	0	0	3
31	0	0	1	0	0	1
32	0	1	0	0	0	0
33	0	0	0	1	0	0
34	0	0	0	0	0	0
35	0	0	0	0	0	0
36	0	0	0	0	1	0

TABLE 1050

Utilization of amino acids in Leadin with no D segment

			Rel	Rel
AA	Number	%	up	dn

G	23134	18.24	46.45	1.00
S	13555	10.69	27.22	0.59
R	10562	8.33	21.21	0.46
D	9704	7.65	19.49	0.42
L	8255	6.51	16.58	0.36
Y	8099	6.39	16.26	0.35
A	7188	5.67	14.43	0.31
V	6599	5.20	13.25	0.29
P	5768	4.55	11.58	0.25
W	4804	3.79	9.65	0.21
T	4769	3.76	9.58	0.21
E	4497	3.55	9.03	0.19
N	3733	2.94	7.50	0.16
F	3616	2.85	7.26	0.16
I	3464	2.73	6.96	0.15
H	2787	2.20	5.60	0.12
K	2460	1.94	4.94	0.11
Q	2124	1.67	4.27	0.09
M	1225	0.97	2.46	0.05
C	498	0.39	1.00	0.02
	126841

TABLE 1080

Dipepides in HC CDR3s, part 1

YY	13565	FG	1073	PL	591	TV	397
FD	11637	RS	1072	TT	589	TP	390
DY	8337	SW	1014	ID	588	NA	389
SG	5979	DW	1003	DD	583	NS	388
GY	5805	LR	990	AS	570	ER	387
YG	5461	DG	989	KG	566	HG	386
DI	5448	PG	976	VD	556	VW	381
AF	4975	LL	974	VP	551	QL	378
DV	4968	AY	962	LT	540	RI	374
GG	4575	DR	923	LF	539	WN	365
SS	4491	VR	882	VL	539	YT	365
MD	4436	YM	877	FY	534	CS	360
GS	4047	AR	872	PD	533	DH	359
GM	3501	VV	869	RV	531	EA	359
YF	3438	YR	865	RF	525	WD	353
YD	3430	VA	857	AL	521	ES	350
RG	3118	RA	844	PS	510	FR	349
SY	2770	SP	820	EY	508	YC	343
GA	2611	GN	812	LW	508	PT	337
YS	2576	HY	809	PA	505	TL	326
DA	2285	SD	805	LP	500	KR	325
DS	2087	GI	804	VS	497	VF	324
WY	2079	NW	785	IR	493	MG	314
GD	2017	LS	760	YV	493	PN	313
GR	1985	LY	757	VY	478	RE	312
GL	1800	TY	749	IG	476	IV	311
DL	1777	PR	742	VT	475	KS	310
DF	1763	GE	737	TR	472	SC	310
GW	1725	SA	736	DN	471	FL	309
WS	1675	SF	728	SI	469	FF	306
AA	1671	PF	725	AD	462	CY	303
LD	1651	ND	693	LA	459	SH	302
EG	1610	ST	684	PP	451	LK	300
AG	1606	GH	683	RT	451	IT	298
RY	1558	YP	676	DT	448	LE	298
DP	1547	WL	675	RW	447	FS	296
GV	1500	SN	667	GQ	446	ED	294
RR	1498	TS	652	QG	446	RK	294
LG	1387	RD	648	TD	446	HF	292
GF	1386	YA	648	TA	437	VI	290
VG	1366	SL	644	TF	426	RH	287
GP	1339	RP	643	GK	422	MV	285
WF	1282	YL	638	YW	421	KY	284
FW	1277	IA	634	HD	420	Al	282
NY	1271	RL	627	IL	417	HS	281
PY	1209	EL	622	LV	406	YH	281
GT	1194	YN	607	IS	402	LN	278
WG	1177	AV	605	NG	398	PV	276
SR	1162	AP	600	RN	398	QY	276
TG	1142	AT	592	SV	397	WA	271

Dipeptides in HC CDR3s, part 2

QH	267	KD	176	II	102	NQ	53
FQ	264	SK	176	HI	101	CF	51
LI	257	YK	176	KP	101	MP	50
EV	255	EF	174	MY	100	CP	49
AM	253	FN	174	RM	99	RC	47
DQ	250	HN	171	AQ	98	HE	46
HR	250	FH	165	EQ	96	VC	46
PH	248	YQ	165	QT	96	QI	45
AN	242	KN	164	LM	95	MN	44
WR	242	MA	163	HV	94	MF	43
NF	240	NN	160	IK	93	HQ	41
PI	239	KA	159	PM	93	CD	38
TN	239	SQ	157	QN	93	CL	38
TI	238	PE	156	CG	91	NC	38
PW	229	WV	154	QF	91	HM	37
IP	228	EI	153	FI	90	FM	36
QR	227	TH	153	HW	90	ME	36
EW	225	FV	152	WH	90	MK	35
YI	221	AK	151	QV	89	QM	35
FE	220	TK	151	WI	89	NM	34
IY	220	WT	151	KH	88	KM	32
EP	219	PK	150	MI	88	TC	31
NR	217	KK	148	MS	87	CR	29
DM	214	IW	145	TQ	86	CV	25
FA	212	VH	145	NV	85	HC	25
AE	210	VE	141	EM	84	WM	25
IF	210	EE	138	HK	84	AC	24
QW	208	DE	136	IN	83	FC	24
YE	208	KL	136	NH	82	CA	23
FP	201	PQ	136	NI	82	CH	21
TM	201	QP	135	HT	81	CN	21
WE	201	SM	134	WK	79	MW	21
WP	201	QD	133	KF	77	PC	19
AH	199	QS	131	VM	73	LC	17
NP	198	VQ	130	MT	71	IC	16
VN	198	QQ	129	IH	69	MM	16
HA	196	WW	129	EH	68	MH	15
LH	196	NT	128	IE	67	WC	15
AW	193	DC	118	QK	65	EC	12
HP	192	KT	118	WQ	65	CK	10
HL	191	QA	118	GC	64	CW	10
RQ	191	NK	113	KE	61	MQ	10
TW	186	KW	112	KI	61	CI	9
EN	185	EK	109	CT	58	CC	8
LQ	182	FT	108	FK	58	CM	8
SE	180	KV	108	IM	57	CQ	6
VK	180	MR	105	KQ	57	QC	6
ET	178	TE	104	ML	55	CE	5
DK	177	HH	103	QE	55	KC	5
NL	177	IQ	103	NE	53	MC	3

TABLE 1060a

Lengths of HC CDR3s vs which D segments occur (if any) for lengths 3-17

SEQ ID

Length

Name	Sequence	NO:	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17

1-1.1	GTTGT	156	0	0	0	0	0	0	2	2	3	6	2	3	3	4	0
1-1.2	VQLER	157	0	0	0	0	0	0	0	0	1	0	1	0	1	2	1
1-1.3	YNWND	158	0	0	0	0	0	2	6	14	16	19	16	14	17	16	9
1-7.1	GITGT	159	0	0	0	0	0	0	0	1	2	7	6	4	4	0	4
1-7.3	YNWNY	161	0	0	0	0	1	0	2	5	7	8	8	6	5	9	4
1-26.1	GIVGAT	164	0	0	0	1	0	0	2	4	10	4	6	9	3	2	2
1-26.2	V*WELL	165	0	0	0	0	0	0	0	0	1	0	1	0	0	0	1
1-26.3	YSGSYY	166	0	0	0	0	1	0	2	10	14	24	24	27	21	26	13
2-2.2	GYCSSTSCYT	70	0	0	0	0	0	0	0	0	0	2	2	9	15	15	11
2-2.3	DIVVVPAAI	168	0	0	0	0	0	0	0	0	0	0	1	3	2	5	5
2-8.2	GYCTNGVCYT	115	0	0	0	0	0	0	0	0	0	1	0	2	4	3	4
2-8.3	DIVLMVYAI	170	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
2-15.2	GYCSGGSCYS	136	0	0	0	0	0	0	0	0	1	3	5	12	10	25	22
2-15.3	DIVVVVAAT	172	0	0	0	0	0	0	0	0	0	0	1	1	2	3	1
2-21.2	AYCGGDCYS	174	0	0	0	0	0	0	0	0	0	1	1	3	5	2	5
2-21.3	HIVVVTAI	175	0	0	0	0	0	0	0	0	0	1	2	0	2	0	1
3-3.1	VLRFLEWLLY	176	0	0	0	0	0	0	0	0	0	0	1	2	2	2	3
3-3.2	YYDFWSGYYT	177	0	0	0	0	0	0	0	1	5	8	22	38	44	72	69
3-3.3	ITIFGVVII	178	0	0	0	0	0	0	0	0	0	0	0	1	0	2	5
3-9.1	VLRYFDWLL@	179	0	0	0	0	0	0	0	0	1	0	0	4	5	5	5
3-9.2	YYDILTGYYN	180	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1
3-10.1	VLLWFGELL@	182	0	0	0	0	0	0	0	0	2	1	2	4	2	3	5
3-10.2	YYYGSGSYYN	81	0	0	0	0	0	0	0	2	4	7	10	13	15	18	14
3-10.2	ITMVRGVII	183	0	0	0	0	0	0	0	0	0	3	1	2	7	5	2
3-16.2	YYDYVWGSYRYT	104	0	0	0	0	0	0	0	0	0	0	0	1	7	7	7
3-16.2	IMITFGGVIVI	185	0	0	0	0	0	0	0	0	0	0	0	0	1	0	2
3-22.2	YYYDSSGYYY	187	0	0	0	0	0	0	0	0	6	30	45	56	59	108	101
3-22.3	ITMIVVVIT	188	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
4-4.2	DYSNY	192	0	0	0	0	0	3	3	4	6	14	4	7	4	10	6
4-4.3	TTVT	190	0	0	0	0	2	4	11	19	23	19	25	19	10	11	9
4-17.2	DYGDY	195	0	0	2	6	12	8	38	40	48	47	50	40	29	21	10
4-23.2	DYGGNS	198	0	0	0	0	0	2	7	4	5	17	4	8	5	1	1
4-23.3	TTVVT	199	0	0	0	0	0	0	2	0	1	1	2	1	2	0	0
5-5.1	VDTAMV	200	0	0	0	0	0	0	0	1	4	8	1	3	2	0	1
5-5.2	WIQLWL	201	0	0	0	0	0	0	0	3	2	0	3	1	4	3	3
5-5.3	GYSYGY	202	0	0	0	0	1	6	9	20	43	29	27	22	32	26	27
5-12.1	VDIVATI	203	0	0	0	0	0	0	0	2	0	1	2	4	0	2	1
5-12.3	GYSGYDY	205	0	0	0	0	4	10	13	15	19	15	22	27	16	15	9
5-24.1	VEMATI	209	0	0	0	0	0	0	1	1	0	0	6	0	0	0	0
5-24.2	*RWLQL	210	0	0	0	0	1	0	3	1	3	2	2	1	2	2	2
5-24.3	RDGYNY	211	0	0	0	0	0	0	0	1	8	12	6	7	3	2	1
6-6.1	EYSSSS	212	0	0	0	0	0	0	0	9	7	16	19	13	2	4	2
6-6.2	SIAAR	213	0	0	0	1	1	0	17	8	7	13	17	6	16	16	7
6-6.3	V*QLV	214	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
6-13.1	GYSSSWY	215	0	0	0	0	0	1	6	11	35	40	56	44	50	42	35
6-13.2	GIAAAG	216	0	0	0	0	1	2	18	14	15	20	20	15	16	14	11
6-19.1	GYSSGWY	218	0	0	0	0	1	1	4	27	57	58	48	52	45	35	30
6-19.2	GIAVAG	219	0	0	0	0	1	1	0	7	8	20	8	13	16	8	10
6-19.3	V*QWLV	220	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0
7-27.1	LTG	221	0	0	1	0	2	8	12	7	14	11	17	17	24	24	31
7-27.3	NWG	223	0	0	0	1	2	11	6	5	10	6	7	5	7	1	0
none			36	153	118	660	726	1007	2063	2463	1851	1596	1502	1075	874	681	609

TABLE1060b

Lengths of HC CDR3s vs which D segments occur (if any) for lengths 18-32

SEQ ID

Length

Name	Sequence	NO:	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32

1-1.1	GTTGT	156	0	1	0	0	1	1	1	0	0	0	0	0	0	0	0
1-1.2	VQLER	157	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
1-1.3	YNWND	158	6	5	3	4	1	1	1	0	0	1	0	0	0	0	0
1-7.1	GITGT	159	2	2	1	0	0	0	1	0	0	0	0	0	0	0	0
1-7.3	YNWNY	161	5	2	1	1	0	0	0	0	0	0	0	1	0	0	0
1-26.1	GIVGAT	164	0	0	3	0	1	0	0	1	0	0	0	0	0	0	0
1-26.2	V*WELL	165	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
1-26.3	YSGSYY	166	14	11	9	8	6	3	3	0	3	1	0	0	0	0	0
2-2.2	GYCSSTSCYT	70	11	7	2	10	11	4	2	0	0	0	1	0	0	0	0
2-2.3	DIVVVPAAI	168	2	6	3	4	3	2	1	0	0	0	0	0	0	0	0
2-8.2	GYCTNGVCYT	115	3	0	1	1	3	1	0	0	0	0	0	0	0	0	0
2-8.3	DIVLMVYAI	170	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
2-15.2	GYCSGGSCYS	136	20	10	7	4	8	9	3	0	0	0	0	0	0	0	0
2-15.3	DIVVVVAAT	172	0	1	1	1	0	0	0	0	1	0	0	0	0	0	0
2-21.2	AYCGGDCYS	174	1	3	1	1	1	0	0	0	0	0	0	0	0	0	0
2-21.3	HIVVVTAI	175	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
3-3.1	VLRFLEWLLY	176	6	2	4	3	2	0	0	0	1	0	0	0	0	0	0
3-3.2	YYDFWSGYYT	177	82	97	104	67	61	32	23	7	3	4	0	0	2	1	0
3-3.3	ITIFGVVII	178	3	2	0	0	2	0	0	0	0	0	0	0	0	0	0
3-9.1	VLRYFDWLL@	179	7	2	2	6	1	2	1	0	0	0	0	0	0	0	0
3-9.2	YYDILTGYYN	180	3	2	0	0	0	0	0	0	0	0	0	0	0	0	0
3-10.1	VLLWFGELL@	182	3	4	0	0	0	0	0	0	0	0	0	0	0	0	0
3-10.2	YYYGSGSYYN	81	15	10	8	7	6	3	2	1	1	0	0	0	0	0	0
3-10.2	ITMVRGVII	183	3	3	6	0	0	0	0	0	0	0	0	0	0	0	0
3-16.2	YYDYVWGSYRYT	104	11	11	14	10	18	13	5	2	2	0	0	0	1	0	0
3-16.2	IMITFGGVIVI	185	1	3	1	0	0	0	0	0	0	0	0	0	0	0	0
3-22.2	YYYDSSGYYY	187	77	54	28	22	18	8	1	2	1	1	0	0	0	0	0
3-22.3	ITMIVVVIT	188	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0
4-4.2	DYSNY	192	7	2	2	1	1	0	1	0	0	0	0	0	0	0	0
4-4.3	TTVT	190	4	2	2	1	3	0	0	0	0	0	1	0	0	0	0
4-17.2	DYGDY	195	17	7	8	3	2	1	1	0	1	0	1	0	0	0	0
4-23.2	DYGGNS	198	3	1	0	2	0	0	0	0	0	0	0	0	0	0	0
4-23.3	TTVVT	199	2	2	1	1	1	0	0	0	0	0	0	0	0	0	0
5-5.1	VDTAMV	200	0	1	1	2	1	0	0	0	0	0	0	0	0	0	0
5-5.2	WIQLWL	201	3	3	1	0	1	0	0	0	0	1	0	0	0	1	0
5-5.3	GYSYGY	202	13	18	7	2	2	6	0	0	2	0	0	0	0	0	0
5-12.1	VDIVATI	203	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
5-12.3	GYSGYDY	205	11	10	6	6	0	2	0	0	0	0	0	0	0	0	0
5-24.1	VEMATI	209	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
5-24.2	*RWLQL	210	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0
5-24.3	RDGYNY	211	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0
6-6.1	EYSSSS	212	9	3	1	1	0	0	0	1	0	0	0	0	0	0	0
6-6.2	SIAAR	213	2	3	2	6	0	0	0	0	0	0	0	0	0	0	0
6-6.3	V*QLV	214	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
6-13.1	GYSSSWY	215	24	22	17	4	5	1	3	2	0	0	1	0	0	0	0
6-13.2	GIAAAG	216	10	4	2	5	2	1	0	0	0	0	0	0	0	0	0
6-19.1	GYSSGWY	218	23	25	13	7	7	3	0	2	1	0	1	0	0	0	0
6-19.2	GIAVAG	219	6	2	2	0	0	0	2	0	0	0	0	0	0	0	0
6-19.3	V*QWLV	220	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
7-27.1	LTG	221	29	23	12	9	7	4	3	1	0	1	0	0	0	0	0
7-27.3	NWG	223	1	0	0	0	2	0	0	0	0	0	0	0	0	0	0
none			339	217	198	85	60	36	27	13	9	2	1	1	0	0	1

TABLE 1082

Tally of J stumps

---AEYFQHWGQGTLVTSS 6.15%

(SEQ ID NO:66)

JH1	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y

4	41	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	605
5	1	0	1	64	0	6	0	1	0	0	0	0	0	1	2	1	1	0	0	0	568
6	0	0	0	0	0	1	1	0	0	3	0	2	1	0	1	1	0	0	0	211	425
7	1	0	1	0	363	3	1	0	0	8	0	0	1	0	1	6	0	3	0	6	252
8	8	0	59	23	4	17	11	3	5	19	0	8	3	221	11	6	8	5	0	4	231
9	2	1	13	2	13	3	447	19	2	6	3	20	1	2	0	20	3	5	4	9	71

---YWYFDLWGRGTLVTVSS 7.80%

(SEQ ID NO:67)

JH2	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y

4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	159	1519
5	0	0	2	0	2	11	0	0	0	1	0	1	0	0	7	1	1	1	929	21	701
6	3	2	9	0	40	5	7	4	1	9	0	7	1	0	1	11	2	0	1	1083	492
7	1	6	1	0	1209	2	6	23	0	89	30	1	2	1	1	12	0	11	1	42	240
8	31	2	1241	90	4	38	30	3	1	0	1	29	3	4	2	2	3	19	0	15	160
9	3	1	9	3	34	2	26	17	5	1064	36	17	30	38	33	20	8	83	1	177	71

-----AFDIWGQGTMVTVSS 25.4%

(SEQ ID NO:2)

JH3	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y

6	4374	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1074
7	1	4	0	1	4612	2	0	8	0	56	3	2	1	1	0	29	2	15	12	74	625
8	23	0	4765	51	0	28	14	0	3	0	0	15	2	1	1	2	2	6	0	4	531
9	7	5	5	0	73	2	1	4439	4	64	64	43	2	1	11	54	49	113	2	18	491

-----YFDYWGQGTLVTVSS 34.7%

(SEQ ID NO:1)

JH4	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y

6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1975	5683
7	9	1	10	7	3950	31	6	26	0	109	4	5	24	4	5	35	7	28	16	59	3322
8	26	0	5991	32	5	91	19	2	1	6	1	21	7	0	8	13	3	6	2	14	1410
9	5	18	17	0	119	2	0	0	14	0	2	64	15	16	10	216	11	3	6	6317	823

----NWFDPWGQGTLVTVSS 4.8%

(SEQ ID NO:68)

JH5	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y

5	0	0	0	0	0	0	0	0	0	0	0	274	0	0	0	0	0	0	0	0	764
6	2	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	644	0	390
7	1	1	0	0	768	2	1	1	0	13	0	0	0	0	0	1	0	2	0	4	244
8	2	0	810	3	0	1	0	0	0	0	0	1	0	0	0	0	1	1	0	1	218
9	3	0	3	0	3	0	3	0	0	4	0	4	814	1	0	14	2	0	0	0	187

YYYYYGMDVWGQGTTVTVSS 21.1%

(SEQ ID NO:3)

JH6	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y

1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	690	3967
2	4	0	15	0	16	31	12	2	1	4	0	8	7	4	14	18	7	4	1	1694	2815
3	3	0	19	3	14	23	16	1	5	9	0	16	9	5	12	20	4	1	4	2440	2053
4	4	0	14	2	31	16	25	3	2	10	0	13	6	5	15	35	5	5	4	2815	1647
5	2	1	9	1	23	19	21	1	1	3	1	15	3	1	7	26	3	0	1	3350	1169
6	69	5	14	1	4	3057	8	1	0	0	0	8	7	5	4	15	3	7	0	657	792
7	3	0	1	0	4	5	0	18	2	108	3866	0	2	2	3	1	7	18	3	1	613
8	7	0	4064	5	1	17	4	1	0	2	0	11	2	0	0	3	2	3	2	6	527
9	9	0	1	0	6	1	1	19	0	7	2	1	1	0	1	4	0	4092	0	1	511

TABLE1097

HC CDR3 libraries

	CDR3		D region	DJ fill	J stump
Library	Length	Leadin	sequence	sequence	sequence	FR4 sequence

5.001	10, 11, 12	6, 7, or 8	none	none	AFDI	WGQGTMVTVSS
		X			(diversity	(JH4) (SEQ
		X = (1.0G,			in text)	IDNO:987)
		.57S,			(SEQ ID
		.46R,			NO: 986)
		.42D,
		.36L,
		.35Y)
5.002	13, 14, 15	6, 7, 8 X	none	none	YYYGMDV	WGQGTTVTVSS
		X = (1.0G,			(diversity	(jh6) (SEQ
		.57S,			in text)	ID NO: 988)
		.46R,			(SEQ ID
		.42D,			NO: 984)
		.36L,
		.35Y)
5.003	18, 19, 20	4, 5, 6 X =	YYDFWSGYYT	none	YFDY	WGQGTLVTVSS
		(1.0G,	(3-3.2)		(SEQ ID	(JH3) (SEQ
		.57S,	(SEQ ID		NO: 985)	ID NO: 989)
		.46R,	NO: 177)
		.42D,
		.36L,
		.35Y)
5.004	15, 16, 17	2, 3, 4 X =	GYSSGWY	2 X, X =	AFDI	WGQGTMVTVSS
		(1.0G,	(6-19.1)	(1.0G,	(SEQ ID	(JH4) (SEQ
		.57S,	(SEQ ID	.57S,	NO: 986)	ID NO: 987)
		.46R,	NO: 218)	.46R,
		.42D,		.42D,
		.36L,		.36L,
		.35Y)		.35Y)
5.005	11-14	0, 1, 2 X =	GYSSGWY	0, 1 X =	YFDY	WGQGTLVTVSS
		(1.0G,	(6-19.1)	(1.0G,	(SEQ ID	(JH3) (SEQ
		.57S,	(SEQ ID	.57S,	NO: 985)	ID NO: 989)
		.46R,	NO: 218)	.46R,
		.42D,		.42D,
		.36L,		.36L,
		.35Y)		.35Y)
5.006	19-25	0, 1, 2, 3 X	GYCSGGSCYS	0, 1, 2, 3	YYYYYGMDV	WGQGTTVTVSS
		X = (1.0G,	(2-2.2)	X = (1.0G,	(parent AA	(jh6) (SEQ
		.57S,	(Cys	.57S,	8X others)	ID NO: 988)
		.46R,	residues	.46R,	(SEQ ID
		.42D,	constant)	.42D,	NO: 990)
		.36L,	(SEQ ID	.36L,
		.35Y)	NO: 136)	.35Y)

REFERENCES

The contents of all cited references including literature references, issued patents, published or non-published patent applications cited throughout this application as well as those listed below are hereby expressly incorporated by reference in their entireties. In case of conflict, the present application, including any definitions herein, will control.

U.S. Published Application 2005-0119455 Å1
Sidhu et al., J Mol Biol. 2004 338:299-310.

EQUIVALENTS

A number of embodiments of the invention have been described. Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, other embodiments are within the scope of the following claims.

Claims

1.-28. (canceled)

29. A library of vectors or genetic packages, wherein the vectors or genetic packages comprise variegated DNA sequences, each encoding a heavy chain (HC) variable region, which comprises three complementarity determining regions (CDRs) 1-3 and framework regions (FRs) 1-4, arranged from the amino-terminus to the carboxy-terminus in an order of FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4, wherein the HC CDR3 region contains 3-35 amino acid residues, and wherein less than about 20% of the HC CDR3 sequence consists of Tyr residues.

30. The library of claim 29, wherein leadin or DJ filler positions of the HC CDR3 consist of less than about 20% of Tyr residues.

31. The library of claim 29, wherein the library is a library of genetic packages.

32. The library of claim 31, wherein the genetic packages are bacteriophages.

33. The library of claim 32, wherein the library is a phage display library.

34. The library of claim 29, wherein the library is a library of vectors.

35. The library of claim 34, wherein the vectors are phage vectors or phagemid vectors.

36. The library of claim 29, wherein a leadin region of the HC CDR3 comprises at least 1, 2, 3, 4, 5, 6, 7, or 8 amino acids.

37. The library of claim 36, wherein the amino acids of the leadin region vary among G, S, R, D, L, Y in a 1.0:0.57:0.46:0.42:0.36:0.35 ratio, respectively.

38. The library of claim 29, wherein the HC CDR3 does not comprise a leadin region.

39. The library of claim 29, wherein a DJ filler region of the HC CDR3 comprises at least 1, 2, or 3 amino acids.

40. The library of claim 39, wherein the amino acids of the DJ filler region vary among G, S, R, D, L, Y in a 1.0:0.57:0.46:0.42:0.36:0.35 ratio, respectively.

41. The library of claim 29, wherein the HC CDR3 does not comprise a DJ filler region.

42. The library of claim 29, wherein the HC CDR3 comprises a D region selected from the group consisting of 3-3.2 (SEQ ID NO: 177), 3-22.2 (SEQ ID NO: 88), 6-19.1 (SEQ ID NO: 218), 6-13.1 (SEQ ID NO: 215) and 4-17.2 (SEQ ID NO: 760).

43. The library of claim 29, wherein the HC CDR3 comprises a J stump selected from the libraries consisting of 5.002 (SEQ ID NO: 984), 5.003 (SEQ ID NO: 985), 5.005 (SEQ ID NO: 985) and 5.006 (SEQ ID NO: 990).

44. The library of claim 29, wherein the library comprises at least 1×10⁹members.

45. A method of preparing a library, comprising mutagenizing the library, wherein the library is a library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, wherein the vectors or genetic packages comprise variegated DNA sequences that encode a heavy chain (HC) CDR3, wherein 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 of the positions in the HC CDR3 of the family are varied among Tyr, Gly, Asp, Ser, and Arg residues.

46. The method of claim 45, wherein the mutagenizing comprises error-prone PCR, wobbling or dobbling.

47. The method of claim 46, wherein the mutagenizing introduces on average about 1 to about 10 mutations (e.g., about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10 mutations; e.g., base changes) per HC CDR3.

48. The method of claim 45, wherein about 50% of all the positions of the HC CDR3 are Tyr, Gly, Asp, Ser, or Arg.