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(12) United States Patent (10) Patent No.: US 7.058,515 B1 Selifonov Et Al

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(12) United States Patent (10) Patent No.: US 7.058,515 B1 Selifonov Et Al US007058515B1 (12) United States Patent (10) Patent No.: US 7.058,515 B1 Selifonov et al. (45) Date of Patent: *Jun. 6, 2006 (54) METHODS FOR MAKING CHARACTER (56) References Cited STRINGS, POLYNUCLEOTIDES AND POLYPEPTIDES HAVING DESRED CHARACTERISTICS U.S. PATENT DOCUMENTS 4.959,312 A 9, 1990 Sirokin (75) Inventors: Sergey A. Selifonov, Los Altos, CA 4,994,379 A 2/1991 Chang (US); Willem P. C. Stemmer, Los 5,023,171 A 6, 1991 Ho et al. ....................... 435/6 Gatos, CA (US); Claes Gustafsson, 5,043,272 A 8/1991 Hartly et al. Belmont, CA (US); Matthew Tobin, 5,066,584 A 11/1991 Gyllensten et al. San Jose, CA (US); Stephen del 5,264,563 A 11/1993 Huse Cardayre, Belmont, CA (US); Phillip SE A Rhen A. Patten, Menlo Park, CA (US); 3.) A 96 MTS al. Jeremy Minshull, Menlo Park, CA 5.512.463 A 4/1996 Stemmer ................... 435,912 (US); Lorraine J. 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No. 6,368,861, and a con tinuation-in-part of application No. PCT/US00/ (Continued) 01203, filed on Jan. 18, 2000, and a continuation-in part of application No. PCT/US00/01138, filed on FOREIGN PATENT DOCUMENTS Jan. 18, 2000, which is a continuation-in-part of EP 0911396 A2 4f1999 application No. 09/416,375, filed on Oct. 12, 1999, now abandoned, which is a continuation-in-part of (Continued) application No. 09/416,837, filed on Oct. 12, 1999, now abandoned, which is a continuation-in-part of OTHER PUBLICATIONS application No. 09/408,392, filed on Sep. 28, 1999, Venkatasubramanian et al. J. Chem. Inf. Comput. Sci. 1995, now Pat. No. 6,376,246. 33. 188-195.* (60) Provisional application No. 60/141,049, filed on Jun. 24, 1999, provisional application No. 60/118,813, (Continued) filed on Feb. 5, 1999, provisional application No. 60/118,854, filed on Feb. 5, 1999, provisional appli- Primary Examiner John Brusca cation No. 60/116,447, filed on Jan. 19, 1999. Assistant Examiner Shubo (Joe) Zhou (74) Attorney, Agent, or Firm Jeffrey K. Weaver; Sharon (51) Int. Cl. M. Fujita; Norman J. Kruse GOIN 33/48 (2006.01) CI2P 19/34 (2006.01) (57) ABSTRACT C7H 2L/02 (2006.01) (52) U.S. Cl. ......................... 702/19; 702/20: 435/91.1; - 0 435/91.2:536/23.1 “In silico” nucleic acid recombination methods, related (58) Field of Classification Search .................... 456 integrated systems utilizing genetic operators and libraries 435/4, 91.2, 15, 91.1 : 536/23.1, 24.1; 325/4. made by in silico shuffling methods are provided. 702/19, 20 See application file for complete search history. 43 Claims, 22 Drawing Sheets US 7,058,515 B1 Page 2 U.S. PATENT DOCUMENTS WO WO99/414O2 8, 1999 WO WO 99.45154 9, 1999 5,925,749 A 7, 1999 Mathur et al. ............. 536,231 WO WO 99,57128 11, 1999 5,928.905 A 7, 1999 Stemmer et al. 435,911 WO WO 99,65927 12/1999 5,939,250 A 8/1999 Short ............................ 435/4 WO WOOOOO632 1, 2000 5,939,300 A 8, 1999 Robertson et al. .......... 435.192 WO WOOO, 23564 A2 4/2000 5,942,430 A 8, 1999 Robertson et al. .......... 435/197 WO WOOOf 37684 6, 2000 5.948,666 A 9, 1999 Callen et al. ... ... 435,194 WO WOOOf 42559 T 2000 5,958,672 A 9/1999 Short ............................ 435/4 WO WOOOf 42560 T 2000 5,958,751 A 9/1999 Murphy et al. ............. 435,208 WO WOOOf 42561 T 2000 5,962,258 A 10, 1999 Mathur et al. ............. 435/69.1 WO WOOOf 47612 8, 2000 5,962.283 A 10, 1999 Warren et al. .. ... 435/128 WO WOOO,53744 9, 2000 5,965,408 A 10, 1999 Short ........................ 435,911 WO WOOO,585.17 10, 2000 5,985,646 A 11/1999 Murphy et al. .......... 435/252.3 WO WOO1,61344 8, 2001 6,001,574 A 12, 1999 Short et al. .................... 435/6 WO WOO 1/75767 10, 2001 6,004,788 A 12/1999 Short ...... 435/183 6,030,779 A 2/2000 Short ... ... 435/6 OTHER PUBLICATIONS 6,054,267 A 4/2000 Short ............................ 435/6 6,096,548 A 8, 2000 Stemmer Darnell et al., Molecular Cell Biology, Scientific American 6,117,679 A 9, 2000 Stemmer Books, 1986, p. 237.* 6,125,331 A 9, 2000 Toh Stemmer et al., Single-step assembly of a gene and entire 6,132,970 A 10/2000 Stemmer plasmid for large numbers of oligodeoxyribonucleotides 85.k --- A 23 SeaOrrebaecket al. DahiyatGene 164 et (1995)al., “Automated 49-53. design of the Surface positions of 6.269,3126,188,965 B1 7/20012/2001 Mayo et al. proteintein heliceshelices’ Protein ScienceSci (1997),1997) 6:1333-1337.6:1333-1337 6,403,312 B1 6, 2002 Bassil et al. Dahiyat and Mayo “De Novo Protein Design: Fully Auto 6,537,776 B1 3/2003 Short ........................ 435/69.1 mated Sequence Selection Science (1997) vol. 278 pp. 6,605.449 B1 8/2003 Short ........................ 435/69.1 82-87. Dahiyat et al., “De Novo Protein Design: Towards Fully FOREIGN PATENT DOCUMENTS Automated Sequence Selection' J. Mol. Biol. (1997) EP O911396 A3 5, 1999 273:789-796. EP 0934999 A1 8, 1999 Dahiyat and Mayo “Probing the role of packing specificity WO WO 91 06643 A1 5, 1991 in protein design” Proc. Matl. Acad. Sci. U.S.A., 1997, vol. WO WO 92,06176 4f1992 94 pp. 10172-10177. WO WO96, 16073 A2 5, 1996 WO WO96, 16073 A3 5, 1996 Gordon and Mayo “Branch-and-Terminate: a combinatorial WO WO 97/O7205 2, 1997 optimization algorithm for protein design' Structure (1999) WO WO 97/20078 6, 1997 7:1089-1098. WO WO 97.25410 7/1997 Gordon et al., “Energy functions for protein design Current WO WO 9733957 9, 1997 Opinion in Structural Biology (1999) 9:509-513. WO WO 97.35957 10, 1997 Gordon and Mayo “Radical Performance Enhancements for WO WO 97/35966 10, 1997 Combinatorial Optimization Algorithms Based on the Dead WO WO 97/44361 11, 1997 End Elimination Theorem” Journal of Computational WO WO 97/48416 12/1997 Chemistry, 1998 vol. 19. No. 13. 1505-1514. WO WO 97/48717 12/1997 Haney et al., “Structural Basis for Thermostability and WO WO 97/48794 12/1997 Identification of Potential Active Site Residues for WO WO 98.00.526 1, 1998 WO WO 98/O1581 1, 1998 Adenylate Kinases From the Archaeal Genus Methanococ WO WO 98.13485 4f1998 cus' Proteins (1997) 28:117-130. WO WO 98.13487 4f1998 Malakauskas and Mayo “Design, structure and stability of a WO WO 98.24799 6, 1998 hyperthermophilic protein variant Nature Structural Biol WO WO 98.27 230 6, 1998 ogy (1998) vol. 5, No. 6, 470-475. WO WO 98.28416 7, 1998 Pollock et al., “Coevolving Protein Residues: Maximum WO WO 98,31837 7, 1998 Likelihood Identification and Relationship to Structure” J. WO WO 98.3608O 8, 1998 WO WO 98/41622 9, 1998 Mol. Biol. (1999) 287: 187-198. WO WO 98/41623 9, 1998 Street and Mayo “Computational protein design' Structure WO WO 98/41653 9, 1998 (1999) 7:R105-R109. WO WO 98.42832 10, 1998 Street and Mayo “Intrinsic B-sheet propensities result from WO WO 98.48O34 10, 1998 van der Waals interactions between side chains and local WO WO 98.58O85 12/1998 backbone' Proc. Natl. Acad. Sci. U.S.A. (1999) vol. 96 pp. WO WO 99/O7837 2, 1999 9074-9076. WO WO 99,08539 2, 1999 Street and Mayo “Pairwise calculation of protein solvent WO WO 99/10472 3, 1999 accessible surface areas” Folding & Design (1998) 3:253 WO WO 99/10539 3, 1999 258.
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