Review: Recent advances in DNA catalysis

Biopolymers

Volumn 87, Issue 5-6, 2007, Pages 279-292

  Höbartner, Claudia ^a   Silverman, Scott K ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Cleavage; Deoxyribozyme; DNA enzyme; DNAzyme; Ligation

Indexed keywords

CATALYST ACTIVITY; ENZYME ACTIVITY; RNA; SUBSTRATES;

DEOXYRIBOZYME; LIGATION;

DNA;

AZOBENZENE; DEOXYRIBODIPYRIMIDINE PHOTOLYASE; DEOXYRIBOZYME; DNA; OLIGONUCLEOTIDE; PEROXIDASE; PURINE; PYROPHOSPHATE; RNA; RNA LIGASE; THYMINE;

CATALYSIS; DNA CLEAVAGE; DNA SEQUENCE; GENE AMPLIFICATION; PHOTOCHEMISTRY; REVIEW; RNA CLEAVAGE; RNA SPLICING; CHEMICAL STRUCTURE; CHEMISTRY; RADIATION EXPOSURE; SYNTHESIS; ULTRAVIOLET RADIATION;

CATALYSIS; DNA, CATALYTIC; MOLECULAR STRUCTURE; RNA; ULTRAVIOLET RAYS;

EID: 37549019376     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.20813     Document Type: Review

References (63)

1. Breaker, R. R.; Joyce, G. F. Chem Biol 1994, 1, 223-229.
2. Silverman, S. K. Nucleic Acids Res 2005, 33, 6151-6163.
3. Santoro, S. W.; Joyce, G. F. Proc Natl Acad Sci USA 1997, 94, 4262-4266.
4. Pyle, A. M.; Chu, V. T.; Jankowsky, E.; Boudvillain, M. Methods Enzymol 2000, 317, 140-146.
5. Cruz, R. P. G.; Withers, J. B.; Li, Y. Chem Biol 2004, 11, 57-67.
6. Silverman, S. K. Chem Biol 2004, 11, 7-8.
7. Nawrot, B.; Widera, K.; Wojcik, M.; Rebowska, B.; Nowak, G.; Stec, W. J. FEBS J 2007, 274, 1062-1072.
8. Leung, E. K.; Sen, D. Chem Biol 2007, 14, 41-51.
9. Liu, J.; Lu, Y. J Am Chem Soc 2002, 124, 15208-15216.
10. Kim, H. K.; Liu, J.; Li, J.; Nagraj, N.; Li, M.; Pavot, C. M.; Lu, Y. J Am Chem Soc 2007, 129, 6896-6902.
11. Ting, R.; Lermer, L.; Perrin, D. M. J Am Chem Soc 2004, 126, 12720-12721.
12. Lusic, H.; Young, D. D.; Lively, M. O.; Deiters, A. Org Lett 2007, 9, 1903-1906.
13. Liu, Y.; Sen, D. J Mol Biol 2004, 341, 887-892.
14. Asanuma, H.; Hayashi, H.; Zhao, J.; Liang, X.; Yamazawa, A.; Kuramochi, T.; Matsunaga, D.; Aiba, Y.; Kashida, H.; Komiyama, M. Chem Commun 2006, 5062-5064.
15. Keiper, S.; Vyle, J. S. Angew Chem Int Ed 2006, 45, 3306-3309.
16. Li, J.; Zheng, W.; Kwon, A. H.; Lu, Y. J Am Chem Soc 2000, 122, 10466-10467.
17. Lu, Y. Chem Eur J 2002, 8, 4589-4596.
18. Liu, J.; Brown, A. K.; Meng, X.; Cropek, D. M.; Istok, J. D.; Watson, D. B.; Lu, Y. Proc Natl Acad Sci USA 2007, 104, 2056-2061.
19. Liu, J.; Lu, Y. Anal Chem 2003, 75, 6666-6672.
20. Shen, Y.; Mackey, G.; Rupcich, N.; Gloster, D.; Chiuman, W.; Li, Y.; Brennan, J. D. Anal Chem 2007, 79, 3494-3503.
21. Yim, T. J.; Liu, J.; Lu, Y.; Kane, R. S.; Dordick, J. S. J Am Chem Soc 2005, 127, 12200-12201.
22. Xiao, Y.; Rowe, A. A.; Plaxco, K. W. J Am Chem Soc 2007, 129, 262-263.
23. Buchhaupt, M.; Peifer, C.; Entian, K. D. Anal Biochem 2007, 361, 102-108.
24. Flynn-Charlebois, A.; Wang, Y.; Prior, T. K.; Rashid, I.; Hoadley, K. A.; Coppins, R. L.; Wolf, A. C.; Silverman, S. K. J Am Chem Soc 2003, 125, 2444-2454.
25. Semlow, D. R.; Silverman, S. K. J Mol Evol 2005, 61, 207-215.
26. Coppins, R. L.; Silverman, S. K. J Am Chem Soc 2004, 126, 16426-16432.
27. Wang, Y.; Silverman, S. K. Biochemistry 2005, 44, 3017-3023.
28. Purtha, W. E.; Coppins, R. L.; Smalley, M. K.; Silverman, S. K. J Am Chem Soc 2005, 127, 13124-13125.
29. Wang, Y.; Silverman, S. K. J Am Chem Soc 2003, 125, 6880-6881.
30. Wang, Y.; Silverman, S. K. Biochemistry 2003, 42, 15252-15263.
31. Wang, Y.; Silverman, S. K. Angew Chem Int Ed 2005, 44, 5863-5866.
32. Coppins, R. L.; Silverman, S. K. Nat Struct Mol Biol 2004, 11, 270-274.
33. Coppins, R. L.; Silverman, S. K. J Am Chem Soc 2005, 127, 2900-2907.
34. Coppins, R. L.; Silverman, S. K. Biochemistry 2005, 44, 13439-13446.
35. Zelin, E.; Wang, Y.; Silverman, S. K. Biochemistry 2006, 45, 2767-2771.
36. Baum, D. A.; Silverman, S. K. Angew Chem Int Ed 2007, 46, 3502-3504.
37. Wang, Y.; Silverman, S. K. ACS Chem Biol 2006, 1, 316-324.
38. Pratico, E. D.; Wang, Y.; Silverman, S. K. Nucleic Acids Res 2005, 33, 3503-3512.
39. Pratico, E. D.; Silverman, S. K. RNA 2007, 13, in press. DOI 10.1261/rna.629607.
40. Lauhon, C. T.; Szostak, J. W. J Am Chem Soc 1995, 117, 1246-1257.
41. Travascio, P.; Bennet, A. J.; Wang, D. Y.; Sen, D. Chem Biol 1999, 6, 779-787.
42. Paul, N.; Springsteen, G.; Joyce, G. F. Chem Biol 2006, 13, 329-338.
43. Li, Y.; Liu, Y.; Breaker, R. R. Biochemistry 2000, 39, 3106-3114.
44. Wang, W.; Billen, L. P.; Li, Y. Chem Biol 2002, 9, 507-517.
45. Achenbach, J. C.; Jeffries, G. A.; McManus, S. A.; Billen, L. P.; Li, Y. Biochemistry 2005, 44, 3765-3774.
46. McManus, S. A.; Li, Y. Biochemistry 2007, 46, 2198-2204.
47. Salehi-Ashtiani, K.; Szostak, J. W. Nature 2001, 414, 82-84.
48. Chinnapen, D. J.; Sen, D. Proc Natl Acad Sci USA 2004, 101, 65-69.
49. Chinnapen, D. J.; Sen, D. J Mol Biol 2007, 365, 1326-1336.
50. Cheglakov, Z.; Weizmann, Y.; Beissenhirtz, M. K.; Willner, I. Chem Commun 2006, 3205-3207.
51. Cheglakov, Z.; Weizmann, Y.; Basnar, B.; Willner, I. Org Biomol Chem 2007, 5, 223-225.
52. Tian, Y.; He, Y.; Mao, C. ChemBioChem 2006, 7, 1862-1864.
53. Xiao, Y.; Pavlov, V.; Gill, R.; Bourenko, T.; Willner, I. ChemBioChem 2004, 5, 374-379.
54. Pavlov, V.; Xiao, Y.; Gill, R.; Dishon, A.; Kotler, M.; Willner, I. Anal Chem 2004, 76, 2152-2156.
55. Li, D.; Shlyahovsky, B.; Elbaz, J.; Willner, I. J Am Chem Soc 2007, 129, 5804-5805.
56. Liu, J.; Lu, Y. Angew Chem Int Ed 2006, 45, 90-94.
57. Hansen, J. A.; Wang, J.; Kawde, A. N.; Xiang, Y.; Gothelf, K. V.; Collins, G. J Am Chem Soc 2006, 128, 2228-2229.
58. Höbartner, C.; Pradeepkumar, P. I.; Silverman, S. K. Chem Commun 2007, 2255-2257.
59. Höbartner, C.; Silverman, S. K. Angew Chem Int Ed 2007, 46, in press. DOI 10.1002/anie.200702217.
60. Tarasow, T. M.; Tarasow, S. L.; Eaton, B. E. Nature 1997, 389, 54-57.
61. Seelig, B.; Jäschke, A. Chem Biol 1999, 6, 167-176.
62. Serganov, A.; Keiper, S.; Malinina, L.; Tereshko, V.; Skripkin, E.; Höbartner, C.; Polonskaia, A.; Phan, A. T.; Wombacher, R.; Micura, R.; Dauter, Z.; Jäschke, A.; Patel, D. J. Nat Struct Mol Biol 2005, 12, 218-224.
63. Nowakowski, J.; Shim, P. J.; Prasad, G. S.; Stout, C. D.; Joyce, G. F. Nat Struct Biol 1999, 6, 151-156.