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

Abstract

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

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 1×10 9  members. 
     
     
         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.