Enhanced functional potential of nucleic acid aptamer libraries patterned to increase secondary structure

Journal of the American Chemical Society

Volumn 132, Issue 27, 2010, Pages 9453-9464

  Ruff, Karen M ^a   Snyder, Thomas M ^a   Liu, David R ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMERS; BINDING MOTIF; COMMONLY USED; FUNCTIONAL MOLECULES; FUNCTIONAL PROPERTIES; IN-VITRO; NUCLEIC ACID APTAMERS; POTENTIAL ACTIVITIES; PROTEIN BINDING; PROTEIN TARGETS; SECONDARY STRUCTURES; SPECIFIC SEQUENCES; STEM-LOOP STRUCTURES; STRUCTURAL REQUIREMENTS;

BINDING ENERGY; BIOCHEMISTRY; CATALYSTS; LIBRARIES; NUCLEIC ACIDS; PROTEINS; RNA;

BIOMOLECULES;

APTAMER; NUCLEIC ACID; PROTEIN BINDING;

ARTICLE; DNA SEQUENCE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; POLYMERASE CHAIN REACTION; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; PROTEIN TARGETING; CHEMISTRY; CONFORMATION; GENE LIBRARY;

APTAMERS, NUCLEOTIDE; GENE LIBRARY; NUCLEIC ACID CONFORMATION; PROTEIN BINDING;

EID: 77955791967     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja103023m     Document Type: Article

References (42)

1. Strobel, S. A.; Cochrane, J. C. Curr. Opin. Chem. Biol. 2007, 11, 636-643.
2. Joyce, G. F. Annu. Rev. Biochem. 2004, 73, 791-836.
3. Seelig, B.; Keiper, S.; Stuhlmann, F.; Jaschke, A. Angew. Chem., Int. Ed. Engl. 2000, 39, 4576-4579.
4. Fusz, S.; Eisenfuhr, A.; Srivatsan, S. G.; Heckel, A.; Famulok, M. Chem. Biol. 2005, 12, 941-950.
5. Tsukiji, S.; Pattnaik, S. B.; Suga, H. J. Am. Chem. Soc. 2004, 126, 5044-5045.
6. Tucker, B. J.; Breaker, R. R. Curr. Opin. Struct. Biol. 2005, 15, 342-348.
7. The Aptamer Handbook: Functional Oligonucleotides and Their Applications; Klussmann, S., Ed.; WILEY-VCH Verlag GmbH & Co: Weinheim, 2006.
8. Dausse, E.; Da Rocha Gomes, S.; Toulme, J. J. Curr. Opin. Pharmacol. 2009, 9, 602-607.
9. Sen, D.; Geyer, C. R. Curr. Opin. Chem. Biol. 1998, 2, 680-687.
10. Baum, D. A.; Silverman, S. K. Cell. Mol. Life Sci. 2008, 65, 2156-2174.
11. Ellington, A. D.; Szostak, J. W. Nature 1992, 355, 850-852.
12. Wilson, C.; Szostak, J. W. Chem. Biol. 1998, 5, 609-617.
13. Bock, L. C.; Griffin, L. C.; Latham, J. A.; Vermaas, E. H.; Toole, J. J. Nature 1992, 355, 564-566.
14. Hicke, B. J.; Watson, S. R.; Koenig, A.; Lynott, C. K.; Bargatze, R. F.; Chang, Y. F.; Ringquist, S.; Moon-McDermott, L.; Jennings, S.; Fitzwater, T.; Han, H. L.; Varki, N.; Albinana, I.; Willis, M. C.; Varki, A.; Parma, D. J. Clin. Invest. 1996, 98, 2688-2692.
15. O'Connell, D.; Koenig, A.; Jennings, S.; Hicke, B.; Han, H. L.; Fitzwater, T.; Chang, Y. F.; Varki, N.; Parma, D.; Varki, A. Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 5883-5887.
16. Wlotzka, B.; Leva, S.; Eschgfaller, B.; Burmeister, J.; Kleinjung, F.; Kaduk, C.; Muhn, P.; Hess-Stumpp, H.; Klussmann, S. Proc Natl Acad Sci U S A 2002, 99, 8898-902.
17. Chandra, M.; Silverman, S. K. J. Am. Chem. Soc. 2008, 130, 2936-2937.
18. Chinnapen, D. J.; Sen, D. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 65-69.
19. Thorne, R. E.; Chinnapen, D. J.; Sekhon, G. S.; Sen, D. J. Mol. Biol. 2009, 388, 21-29.
20. Mayer, G. Angew. Chem., Int. Ed. 2009, 48, 2672-2689.
21. Eaton, B. E.; Gold, L.; Zichi, D. A. Chem. Biol. 1995, 2, 633-638.
22. Noller, H. F. Science 2005, 309, 1508-1514.
23. Gagnon, M. G.; Steinberg, S. V. RNA 2010, 16, 375-381.
24. Carothers, J. M.; Oestreich, S. C.; Davis, J. H.; Szostak, J. W. J. Am. Chem. Soc. 2004, 126, 5130-5137.
25. Carothers, J. M.; Oestreich, S. C.; Szostak, J. W. J. Am. Chem. Soc. 2006, 128, 7929-7937.
26. Kim, N.; Gan, H. H.; Schlick, T. RNA 2007, 13, 478-492.
27. Chushak, Y.; Stone, M. O. Nucleic Acids Res. 2009, 37, e87.
28. Davis, J. H.; Szostak, J. W. Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 11616-11621.
29. Xiong, H.; Buckwalter, B. L.; Shieh, H. M.; Hecht, M. H. Proc. Natl. Acad. Sci. U. S. A. 1995, 92, 6349-6353.
30. Legiewicz, M.; Lozupone, C.; Knight, R.; Yarus, M. RNA 2005, 11, 1701-1709.
31. Ward, B.; Juehne, T. Nucleic Acids Res. 1998, 26, 879-886.
32. Chapple, K. E.; Bartel, D. P.; Unrau, P. J. RNA 2003, 9, 1208-1220.
33. Bing, T.; Yang, X.; Mei, H.; Cao, Z.; Shangguan, D. Bioorg. Med. Chem. 2010, 18, 1798-1805.
34. Bittker, J. A.; Le, B. V.; Liu, D. R. Nat. Biotechnol. 2002, 20, 1024-1029.
35. Mosing, R. K.; Bowser, M. T. Methods Mol. Biol. 2009, 535, 33-43.
36. Ekland, E. H.; Bartel, D. P. Nucleic Acids Res. 1995, 23, 3231-3238.
37. Knight, R.; Yarus, M. Nucleic Acids Res. 2003, 31, e30.
38. Wiegand, T. W.; Williams, P. B.; Dreskin, S. C.; Jouvin, M. H.; Kinet, J. P.; Tasset, D. J. Immunol. 1996, 157, 221-230.
39. Katilius, E.; Flores, C.; Woodbury, N. W. Nucleic Acids Res. 2007, 35, 7626-7635.
40. Van Guilder, H. D.; Vrana, K. E.; Freeman, W. M. BioTechniques 2008, 44, 619-626.
41. Jellinek, D.; Green, L. S.; Bell, C.; Janjic, N. Biochemistry 1994, 33, 10450-10456.
42. Wong, I.; Lohman, T. M. Proc. Natl. Acad. Sci. U. S. A. 1993, 90, 5428-5432.