Nucleic acid evolution and minimization by nonhomologous random recombination

Nature Biotechnology

Volumn 20, Issue 10, 2002, Pages 1024-1029

  Bittker, Joshua A ^a   Le, Brian V ^a   Liu, David R ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLONING; DNA;

LIGANDS;

NUCLEIC ACID SEQUENCES;

APTAMER; NUCLEIC ACID; STREPTAVIDIN;

ARTICLE; MOLECULAR CLONING; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; STRUCTURE ACTIVITY RELATION;

BASE SEQUENCE; CLONING, MOLECULAR; DIRECTED MOLECULAR EVOLUTION; DNA; DNA PRIMERS; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID AMPLIFICATION TECHNIQUES; POLYMERASE CHAIN REACTION; RANDOM AMPLIFIED POLYMORPHIC DNA TECHNIQUE; RECOMBINATION, GENETIC; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; STREPTAVIDIN;

EID: 0036788537     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt736     Document Type: Article

References (33)

1. Wilson, D.S. & Szostak, J,W. In vitro selection of functional nucleic acids. Annu. Rev. Biochem. 68, 611-647 (1999).
2. Bittker, J,A., Phillips, K.J. & Liu, D.R. Recent advances in the in vitro evolution of nucleic acids. Curr. Opin. Chem. Biol. 6, 367-374 (2002).
3. Kopylov, A.M. & Spiridonova, V.A. Combinatorial chemistry of nucleic acids: SELEX. Mol. Biol. 34, 940-954 (2000).
4. Tuerk, C. & Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 RNA polymerase. Science 249, 505-510 (1990).
5. Cadwell, R.C. & Joyce, G.F. Mutagenic PCR. PCR Methods Appl. 3, S136-S140 (1994).
6. Vartanian, J.P., Henry, M. & Wain-Hobson, S. Hypermutagenic PCR involving all four transitions and a sizeable proportion of transversions. Nucleic Acids Res. 24, 2627-2631 (1996).
7. Piganeau, N., Jenne, A., Thuillier, V. & Famulok, M. An allosteric ribozyme regulated by doxycyline. Angew. Chem. Int. Ed. 39, 4369-4373 (2000).
8. Santoro, S.W., Joyce, G.F., Sakthivel, K., Gramatikova, S. & Barbas, C.F. RNA cleavage by a DNA enzyme with extended chemical functionality. J. Am. Chem. Soc. 122, 2433-2439 (2000).
9. Tsang, J. & Joyce, G.F. Specialization of the DNA-cleaving activity of a group I ribozyme through in vitro evolution. J. Mol. Biol. 262, 31-42 (1996).
10. McGinness, K.E., Wright, M.C. & Joyce, G.F. Continuous in vitro evolution of a ribozyme that catalyzes three successive nucleotidyl addition reactions. Chem. Biol. 9, 585-596 (2002).
11. Rao, J., Lahiri, J., Isaacs, L., Weis, R.M. & Whitesides, G.M. A trivalent system from vancomycin.D-ala-D-Ala with higher affinity than avidin.biotin. Science 280, 708-711 (1998).
12. Meyerhans, A., Vartanian, J.P. & Wain-Hobson, S. DNA recombination during PCR. Nucleic Acids Res. 18, 1687-1691 (1990).
13. Paabo, S., Irwin, D.M. & Wilson, A.C. DNA damage promotes jumping between templates during enzymatic amplification. J. Biol. Chem, 265, 4718-4721 (1990).
14. DeStefano, J.J. Kinetic analysis of the catalysis of strand transfer from internal regions of heteropolymeric RNA templates by human immunodeficiency virus reverse transcriptase. J. Mol. Biol. 243, 558-567 (1994).
15. Ness, J.E., Del Cardayre, S.B., Minshull, J. & Stemmer, W.P.C. in Advances in Protein Chemistry, Vol. 55 (ed. Arnold, F.H.) 261-292 (Academic Press, San Diego, CA, 2001).
16. Stemmer, W.R Rapid evolution of a protein in vitro by DNA shuffling. Nature 370, 389-391 (1994).
17. Volkov, A.A. & Arnold, F.H. Methods for in vitro DNA recombination and random chimeragenesis. Methods Enzymol. 328, 447-456 (2000).
18. Zhao, H., Giver, L., Shao, Z., Affholter, J.A. & Arnold, F.H. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat. Biotechnol. 16, 258-261 (1998).
19. Sieber, V., Martinez, C.A. & Arnold, F.H. Libraries of hybrid proteins from distantly related sequences. Nat. Biotechnol. 19, 456-460 (2001).
20. Kolkman, J.A. & Stemmer, W.P. Directed evolution of proteins by exon shuffling. Nat. Biotechnol. 19, 423-428 (2001).
21. Lutz, S., Ostermeier, M., Moore, G.L., Maranas, C.D. & Benkovic, S.J. Creating multiple-crossover DNA libraries independent of sequence identity. Proc. Natl. Acad. Sci. USA 98, 11248-11253 (2001).
22. Tsuji, T., Onimaru, M. & Yanagawa, H. Random multi-recombinant PCR for the construction of combinatorial protein libraries. Nucleic Acids Res. 29, E97 (2001).
23. Ostermeier, M., Shim, J.H. & Benkovic, S.J. A combinatorial approach to hybrid enzymes independent of DNA homology. Nat. Biotechnol. 17, 1205-1209 (1999).
24. Wedel, A.B. Fishing the best pool for novel ribozymes. Trends Biotechnol. 14, 459-465 (1996).
25. Upcroft, P. & Healey, A. Rapid and efficient method for cloning of blunt-ended DNA fragments. Gene 51, 69-75 (1987).
26. Engler, M.J. & Richardson, C.C. in The Enzymes, Vol. 15 (ed. Boyer, P.D.) 1-29 (Academic Press, New York, 1982).
27. SantaLucia, J. Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA 95, 1460-1465 (1998).
28. Pagratis, N.C. et al. Potent 2′-amino-, and 2′-fluoro-2′-deoxyribonucleotide RNA inhibitors of keratinocyte growth factor. Nat. Biotechnol. 15, 68-73 (1997).
29. Ekland, E.H., Szostak, J.W. & Bartel, D.P. Structurally complex and highly active RNA ligases derived from random RNA sequences, Science 269, 364-370 (1995).
30. Kuwabara, T., Warashina, M. & Taira, K. Allosterically controllable ribozymes with biosensor functions. Curr. Opin. Chem. Biol. 4, 669-677 (2000).
31. Soukup, G.A. & Breaker, R.R. Nucleic acid molecular switches. Trends Biotechnol. 17, 469-476 (1999).
32. Bogarad, L.D. & Deem, M.W. A hierarchical approach to protein molecular evolution. Proc. Natl. Acad. Sci. USA 96, 2591-2595 (1999).
33. Schuler, G.D.,ltschul, S.R. & Lipman, D.J. A workbench for multiple alignment construction and analysis. Proteins 9, 180-190 (1991).