Focused libraries of genetic packages
Focused libraries of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of antibody peptides, polypeptides or proteins and collectively display, display and express, or comprise at least a portion of the focused diversity of the family. The libraries have length and sequence diversities that mimic that found in native human antibodies.
1. An antibody library comprising a first set of variegated DNA molecules encoding a first collection of antibody light chains (LC), wherein each light chain comprises an LC CDR1 region, an LC CDR2 region, and an LC CDR3 region, and wherein:
(a) the first collection of antibody light chains are kappa light chains, which comprise a plurality of LC κ CDR3 regions selected from the group consisting of:
(1) QQ<3><1><1><1>P<1>T (SEQ ID NO:16), wherein <1> is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y; and <3> is a mixture of amino acid residues Y, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, and W;
(2) QQ<3><3><1><1><1>P (SEQ ID NO:103), wherein <1> and <3> are as defined in (1) above;
(3) QQ<3><2><1><1>PP<1>T (SEQ ID NO:17), wherein <1> and <3> are as defined in (1) above and <2> is a mixture of amino acid residues S, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, and Y; and
(4) a mixture of any of (1) to (3) set forth above; or
(b) the first collection of antibody light chains are lambda light chains, which comprise a plurality of LC λ CDR3 regions selected from the group consisting of:
(1) <4><5><4><2><4>S<4><4><4><4>V (SEQ ID NO:106), wherein <2> is a mixture of amino acid residues D, N, A, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, and Y; <4> is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, and W; and <5> is a mixture of amino acid residues S, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, and Y;
(2) <5>SY<1><5>S<5><1><4>V (SEQ ID NO:19), wherein <1> is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; and <4> and <5> are as defined in (1) above; and
(3) a mixture of (1) and (2) set forth above.
2. The library of claim 1 , wherein the first collection of antibody light chains are kappa light chains, which further comprises:
(A) a plurality of LC κ CDR1 regions selected from the group consisting of:
(1) RASQ<1>V<2><2><3>LA (SEQ ID NO:14), wherein <1> is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; <2> is a mixture of amino acid residues S, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, Y; and <3> is a mixture of amino acid residues Y, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W and S; and
(2) RASQ<1>V<2><2><2><3>LA (SEQ ID NO:15); wherein <1>, <2>, and <3> are as defined in (1) above; and
(3) a mixture of (1) and (2) set forth above;
(B) a plurality of LC κ CDR2 regions <1>AS<2>R<4><1> (SEQ ID NO:102), wherein <1> is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; <2> is a mixture of amino acid residues S, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, and Y; and <4> is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; or
both (A) and (B).
3. The library of claim 1 , wherein the LC κ CDR3s (1), (2) and (3) are present in the library in a ratio of 0.65:0.1:0.25.
4. The library of claim 2 , wherein the LC κ CDR1s (1) and (2) are present in the library in a ratio of 0.68:0.32.
5. The library of claim 4 , wherein the first collection of antibody light chains are kappa light chains, and wherein the library further comprises a second set of variegated DNA molecules encoding a second collection of antibody light chains, which are lambda light chains comprising a plurality of LC λ CDR3 regions selected from the group consisting of:
(1) <4><5><4><2><4>S<4><4><4><4>V (SEQ ID NO:106), wherein <2> is a mixture of amino acid residues D, N, A, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, and Y; <4> is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, and W; and <5> is a mixture of amino acid residues S, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, and Y;
(2) <5>SY<1><5>S<5><1><4>V (SEQ ID NO:19), wherein <1> is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; and <4> and <5> are as defined in (1) above; and
(3) a mixture of (1) and (2) set forth above.
6. The library of claim 5 , wherein the second collection of antibody light chains further comprises:
(A) a plurality of LC λ CDR1 regions selected from the group consisting of:
(1) TG<1>SS<2>VG<1><3><2><3>VS (SEQ ID NO:18), wherein <1> is a mixture of amino acid residues T, G, A, D, E, F, H, I, K, L, M, N, P, Q, R, S, V, W, and Y, <2> is a mixture of amino acid residues D, N, A, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, and Y, and <3> is a mixture of amino acid residues Y, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, and W;
(2) G<2><4>L<4><4><4><3><4><4>(SEQ ID NO:104), wherein <2> is as defined in (1) above, <3> is a mixture of amino acid residues Y, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and <4> is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; and
(3) a mixture of (1) and (2) set forth above;
(B) a plurality of LCλ CDR2 regions <4><4><4><2>RPS (SEQ ID NO:105), wherein <2> is a mixture of amino acid residues D, N, A, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, and Y, and <4> is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, and W; or
both (A) and (B).
7. The library of claim 6 , wherein the LC λ CDR3s (1) and (2) are present in the library in an equimolar mixture.
8. The library of claim 6 , wherein the LC λ CDR1s (1) and (2) are present in the library in a ratio of 0.67:0.33.
9. The library of claim 1 , wherein the first collection of antibody light chains are lambda chains, which further comprise
(A) a plurality of LC λ CDR1 regions selected from the group consisting of:
(1) TG<1>SS<2>VG<1><3><2><3>VS (SEQ ID NO:18), wherein <1> is a mixture of amino acid residues T, G, A, D, E, F, H, I, K, L, M, N, P, Q, R, S, V, W, and Y, <2> is a mixture of amino acid residues D, N and, A, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, and Y, and <3> is a mixture of amino acid residues Y, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, and W;
(2) G<2><4>L<4><4><4><3><4><4>(SEQ ID NO:104), wherein <2> is as defined in (1) above, <3> is a mixture of amino acid residues Y, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and <4> is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; and
(3) a mixture of (1) and (2) set forth above;
(B) a plurality of LC λ CDR2 regions <4><4><4><2>RPS (SEQ ID NO:105), wherein <2> is a mixture of amino acid residues D, N, A, E, F, G, H, I, K, L, M, P, Q, R, S, T, V, W, and Y and <4> is a mixture of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, and W; or
both (A) and (B).
10. The library of claim 9 , wherein the LC λ CDR3s (1) and (2) are present in the library in an equimolar mixture.
11. The library of claim 9 , wherein the LC λ CDR1s (1) and (2) are present in the library in a ratio of 0.67:0.33.
12. The library of claim 1 , wherein the library is a library of vectors.
13. The library of claim 12 , wherein the vectors are yeast vectors or phagemids.
14. The library of claim 1 , wherein the library is a library of genetic packages.
15. The library of claim 14 , wherein the genetic packages are cells, spores, or viral particles.
16. The library of claim 15 , wherein the genetic packages are phage particles or yeast cells, which display the collection of antibody light chains encoded by the variegated DNA molecules in the library.