Rapid construction and characterization of synthetic antibody libraries without DNA amplification

Biotechnology and Bioengineering

Volumn 106, Issue 3, 2010, Pages 347-357

  Ge, Xin ^a,b   Mazor, Yariv ^a,b,c   Hunicke Smith, Scott P ^b   Ellington, Andrew D ^b   Georgiou, George ^a,b  

^a The University of Texas at Austin   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c MEDIMMUNE   (United States)

Author keywords

Combinatorial DNA library; Gene assembly; High throughput sequencing; Synthetic antibody; T4 DNA polymerase

Indexed keywords

DNA LIBRARY; DNA POLYMERASE; GENE ASSEMBLY; HIGH-THROUGHPUT; HIGH-THROUGHPUT SEQUENCING;

AMINO ACIDS; AMPLIFICATION; ANTIBODIES; DNA; GENE EXPRESSION; LIBRARIES; NUCLEIC ACIDS; OLIGONUCLEOTIDES; ORGANIC ACIDS; POLYMERS; STEEL BRIDGES; THROUGHPUT;

GENE ENCODING;

AMPICILLIN; BETA LACTAMASE; DNA POLYMERASE; IMMUNOGLOBULIN ANTIBODY; IMMUNOGLOBULIN KAPPA CHAIN; MUTANT PROTEIN; OLIGONUCLEOTIDE; POLYNUCLEOTIDE;

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ANTIBODY LIBRARY; ARTICLE; CLONE; COMBINATORIAL LIBRARY; COMPLEMENTARITY DETERMINING REGION; DNA SEQUENCE; ELECTROPORATION; GENE AMPLIFICATION; GENE EXPRESSION; GENE FUSION; GENE LIBRARY; HIGH THROUGHPUT SCREENING; IMMUNOGLOBULIN HEAVY CHAIN GENE; IMMUNOGLOBULIN VARIABLE REGION; NUCLEOTIDE METABOLISM; OPEN READING FRAME; PROTEIN SYNTHESIS; STOP CODON;

ANTIBODIES; COMBINATORIAL CHEMISTRY TECHNIQUES; GENE LIBRARY; GENETIC VARIATION; MUTANT PROTEINS; POLYNUCLEOTIDES; SELECTION, GENETIC; SINGLE-CHAIN ANTIBODIES; TRANSFORMATION, GENETIC;

EID: 77953592427     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.22712     Document Type: Article

References (44)

1. Briggs AW, Stenzel U, Johnson PLF, Green RE, Kelso J, Prufer K, Meyer M, Krause J, Ronan MT, Lachmann M, Paabo S. 2007. Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci USA 104(37):14616-14621.
2. Clark M. 2000. Antibody humanization: A case of the 'Emperor's new clothes'? Immunol Today 21(8):397-402.
3. Cline J, Braman JC, Hogrefe HH. 1996. PCR fidelity of Pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res 24(18): 3546-3551. (Pubitemid 26315766)
4. Cobaugh CW, Almagro JC, Pogson M, Iverson B, Georgiou G. 2008. Synthetic antibody libraries focused towards peptide ligands. J Mol Biol 378(3):622-633.
5. Diehl F, Li M, He YP, Kinzler KW, Vogelstein B, Dressman D. 2006. BEAMing: Single-molecule PCR on microparticles in water-in-oil emulsions. Nat Methods 3(7):551-559. (Pubitemid 43941774)
6. Ewert S, Huber T, Honegger A, Pluckthun A. 2003. Biophysical properties of human antibody variable domains. J Mol Biol 325(3):531-553.
7. Feldhaus MJ, Siegel RW, Opresko LK, Coleman JR, Feldhaus JMW, Yeung YA, Cochran JR, Heinzelman P, Colby D, Swers J, et al. 2003. Flowcytometric isolation of human antibodies from a nonimmune Saccharomyces cerevisiae surface display library. Nat Biotechnol 21(2):163-170.
8. Fellouse FA, Esaki K, Birtalan S, Raptis D, Cancasci VJ, Koide A, Jhurani P, Vasser M, Wiesmann C, Kossiakoff AA, Koide S, Sidhu SS. 2007. High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries. J Mol Biol 373(4):924-940.
9. Glanville J, Zhai WW, Berka J, Telman D, Huerta G, Mehta GR, Ni I, Mei L, Sundar PD, Day GMR, Cox D, Rajap A, Pons J. 2009. Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire. Proc Natl Acad Sci USA 106(48): 20216-20221.
10. Hartley JL, Temple GF, Brasch MA. 2000. DNA cloning using in vitro sitespecific recombination. Genome Res 10(11):1788-1795.
11. Hayashi N, Welschof M, Zewe M, Braunagel M, Dubel S, Breitling F, Little M. 1994. Simultaneous mutagenesis of antibody CDR regions by overlap extension and PCR. Biotechniques 17(2):310.
12. Hayhurst A, Happe S, Mabry R, Koch Z, Iverson BL, Georgiou G. 2003. Isolation and expression of recombinant antibody fragments to the biological warfare pathogen Brucella melitensis. J Immunol Methods 276(1-2):185-196. (Pubitemid 36513849)
13. Hecker KH, Rill RL. 1998. Error analysis of chemically synthesized polynucleotides. Biotechniques 24(2):256-260.
14. Hoet RM, Cohen EH, Kent RB, Rookey K, Schoonbroodt S, Hogan S, Rem L, Frans N, Daukandt M, Pieters H, van Hegelsom R, Neer NC, Nastri HG, Rondon IJ, Leeds JA, Hufton SE, Huang L, Kashin I, Devlin M, Kuang G, Steukers M, Viswanathan M, Nixon AE, Sexton DJ, Hoogenboom HR, Ladner RC. 2005. Generation of high-affinity human antibodies by combining donor-derived and synthetic complementarity- determining-region diversity. Nat Biotechnol 23(3):344-348.
15. Hoogenboom HR. 2005. Selecting and screening recombinant antibody libraries. Nat Biotechnol 23(9):1105-1116.
16. Huse SM, Huber JA, Morrison HG, Sogin ML, Mark Welch D. 2007. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8(7):9.
17. Kanagawa T. 2003. Bias and artifacts in multitemplate polymerase chain reactions (PCR). J Biosci Bioeng 96(4):317-323. (Pubitemid 37500201)
18. Knappik A, Ge LM, Honegger A, Pack P, Fischer M, Wellnhofer G, Hoess A, Wolle J, Pluckthun A, Virnekas B. 2000. Fully synthetic human combinatorial antibody libraries (HuCAL) based on modular consensus frameworks and CDRs randomized with trinucleotides. J Mol Biol 296(1):57-86.
19. Kunkel TA, Loeb LA, Goodman MF. 1984. On the fidelity of DNA replication. The accuracy of T4 DNA polymerases in copying phi X174 DNA in vitro. J Biol Chem 259(3):1539-1545.
20. Lee CV, Liang WC, Dennis MS, Eigenbrot C, Sidhu SS, Fuh G. 2004. High-affinity human antibodies from phage-displayed synthetic fab libraries with a single framework scaffold. JMol Biol 340(5):1073-1093. (Pubitemid 38976491)
21. Liang WC, Dennis MS, Stawicki S, Chanthery Y, Pan Q, Chen YM, Eigenbrot C, Yin JP, Koch AW, Wu XM, Ferrara N, Bagri A, Tessier-Lavigne M, Watts RJ, Wu Y. 2007. Function blocking antibodies to neuropilin-1 generated from a designed human synthetic antibody phage library. J Mol Biol 366(3):815-829.
22. Lueders T, Friedrich MW. 2003. Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl Environ Microbiol 69(1):320-326. (Pubitemid 36077491)
23. Lutz S, Fast W, Benkovic SJ. 2002. A universal, vector-based system for nucleic acid reading-frame selection. Protein Eng 15(12):1025-1030. (Pubitemid 36331374)
24. Marks JD, Hoogenboom HR, Bonnert TP, McCafferty J, Griffiths AD, Winter G. 1991. By-passing immunization. Human antibodies from V-gene libraries displayed on phage. J Mol Biol 222(3):581-597.
25. Martin ACR. 1996. Accessing the Kabat antibody sequence database by computer. Proteins Struct Funct Genet 25(1):130-133.
26. Mazor Y, Van Blarcom T, Iverson BL, Georgiou G. 2008. E-clonal antibodies: Selection of full-length IgG antibodies using bacterial periplasmic display. Nat Protoc 3(11):1766-1777.
27. Mazor Y, Van Blarcom T, Mabry R, Iverson BL, Georgiou G. 2007. Isolation of engineered, full-length antibodies from libraries expressed in Escherichia coli. Nat Biotechnol 25(5):563-565. (Pubitemid 46834839)
28. Orlandi R, Gussow DH, Jones PT, Winter G. 1989. Cloning immunoglobulin variable domains for expression by the polymerase chain reaction. Proc Natl Acad Sci USA 86(10):3833-3837. (Pubitemid 19141839)
29. Pienaar E, Theron M, Nelson M, Viljoen HJ. 2006. A quantitative model of error accumulation during PCR amplification. Computat Biol Chem 30(2):102-111.
30. Polz MF, Cavanaugh CM. 1998. Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64(10):3724-3730.
31. Puigbo P, Guzman E, Romeu A, Garcia-Vallve S. 2007. OPTIMIZER: A web server for optimizing the codon usage of DNA sequences. Nucleic Acids Res 35:W126-W131.
32. Rajpal A, Beyaz N, Haber L, Cappuccilli G, Yee H, Bhatt RR, Takeuchi T, Lerner RA, Crea R. 2005. A general method for greatly improving the affinity of antibodies by using combinatorial libraries. Proc Natl Acad Sci USA 102(24):8466-8471.
33. Rehakrantz LJ, Stocki S, Nonay RL, Dimayuga E, Goodrich LD, Konigsberg WH, Spicer EK. 1991. DNA polymerization in the absence of exonucleolytic proofreading: In vivo and in vitro studies. Proc Natl Acad Sci USA 88(6):2417-2421.
34. Rothe C, Urlinger S, Lohning C, Prassler J, Stark Y, Jager U, Hubner B, Bardroff M, Pradel I, Boss M, Bittlingmaier R, Bataa T, Frisch C, Brocks B, Honegger A, Urban M. 2008. The human combinatorial antibody library HuCAL GOLD combines diversification of all six CDRs according to the natural immune system with a novel display method for efficient selection of high-affinity antibodies. J Mol Biol 376(4):1182-1200.
35. Seehaus T, Breitling F, Dubel S, Klewinghaus I, Little M. 1992. A vector for the removal of deletion mutants from antibody libraries. Gene 114(2): 235-237.
36. Sidhu SS, Fellouse FA. 2006. Synthetic therapeutic antibodies. Nat Chem Biol 2(12):682-688.
37. Sidhu SS, Li B, Chen Y, Fellouse FA, Eigenbrot C, Fuh G. 2004. Phage-displayed antibody libraries of synthetic heavy chain complementarity determining regions. J Mol Biol 338(2):299-310.
38. Silacci M, Brack S, Schirru G, Marlind J, Ettorre A, Merlo A, Viti F, Neri D. 2005. Design, construction, and characterization of a large synthetic human antibody phage display library. Proteomics 5(9):2340-2350.
39. Sipos R, Szekely AJ, Palatinszky M, Revesz S, Marialigeti K, Nikolausz M. 2007. Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis. FEMS Microbiol Ecol 60(2):341-350.
40. Soderlind E, Strandberg L, Jirholt P, Kobayashi N, Alexeiva V, Aberg AM, Nilsson A, Jansson B, Ohlin M, Wingren C, Danielsson L, Carlsson R, Borrebaeck CA. 2000. Recombining germline-derived CDR sequences for creating diverse single-framework antibody libraries. Nat Biotechnol 18(8):852-856.
41. Gomez-Alvarez V, Teal TK, Schmidt TM. 2009. Systematic artifacts in metagenomes from complex microbial communities. ISME J 3(11): 1314-1317.
42. Weinstein JA, Jiang N, White RA, Fisher DS, Quake SR. 2009. High-throughput sequencing of the zebrafish antibody repertoire. Science 324(5928):807-810.
43. Yin CC, Ren LL, Zhu LL, Wang XB, Zhang Z, Huang HL, Yan XY. 2008. Construction of a fully synthetic human scFv antibody library with CDR3 regions randomized by a split-mix-split method and its application. J Biochem 144(5):591-598.
44. Zemlin M, Klinger M, Link J, Zemlin C, Bauer K, Engler JA, Schroeder Jr HW, Kirkham PM. 2003. Expressed murine and human CDR-H3 intervals of equal length exhibit distinct repertoires that differ in their amino acid composition and predicted range of structures. J Mol Biol 334(4):773-749.