Kinetic isotope effects for RNA cleavage by 2′-O- transphosphorylation: Nucleophilic activation by specific base

Journal of the American Chemical Society

Volumn 132, Issue 33, 2010, Pages 11613-11621

  Harris, Michael E ^a   Dai, Qing ^b   Gu, Hong ^a   Kellerman, Daniel L ^b   Piccirilli, Joseph A ^b,c   Anderson, Vernon E ^a,b  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

^c NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BASE CATALYSIS; BOND FORMATION; BREAKPOINT; COMBINED EFFECT; DEUTERIUM ISOTOPE EFFECT; DINUCLEOTIDES; DIRECT ANALYSIS; GENERAL BASE; HYDROXIDE IONS; ISOTOPE EFFECT; KINETIC ISOTOPE EFFECTS; LEAVING GROUPS; NUCLEOPHILIC ACTIVATION; NUCLEOPHILIC ADDITIONS; OXYGEN BONDS; PH DEPENDENCE; PH INDEPENDENT; PHOSPHODIESTERS; RATE PROFILES; REACTION CATALYZED; RNA CLEAVAGE; TRANSITION STATE;

ADDITION REACTIONS; CARRIER MOBILITY; CATALYSIS; DEUTERIUM; ESTERS; NUCLEOPHILES; OXYGEN; PHOSPHORUS; RNA; SOLVENTS;

PH EFFECTS;

DEUTERIUM; HYDROXIDE; ISOTOPE; NUCLEIC ACID BASE; NUCLEOPHILE; OXYGEN; PHOSPHORUS;

ARTICLE; CATALYSIS; CATALYST; CHEMICAL BOND; CHEMICAL REACTION; CONFORMATIONAL TRANSITION; KINETICS; NUCLEOPHILICITY; PH; PHOSPHORYLATION; PROTON TRANSPORT; RNA CLEAVAGE;

HYDROGEN-ION CONCENTRATION; HYDROXIDES; KINETICS; OXYGEN ISOTOPES; PHOSPHORYLATION; RNA;

EID: 77955815606     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja103550e     Document Type: Article

References (71)

1. Mildvan, A. S. Proteins 1997, 29, 401-416
2. Wolfenden, R. Biophys. Chem. 2003, 105, 559-572
3. Westheimer, F. H. Acc. Chem. Res. 1968, 1, 70-78
4. Kirby, A. J. and Jencks, W. P. J. Am. Chem. Soc. 1965, 87, 3209-3216
5. Oivanen, M., Kuusela, S., and Lonnberg, H. Chem. Rev. 1998, 98, 961-990
6. Cleland, W. W. and Hengge, A. C. Chem. Rev. 2006, 106, 3252-3278
7. Rosta, E., Kamerlin, S. C., and Warshel, A. Biochemistry 2008, 47, 3725-3735
8. Harris, M. E. and Cassano, A. G. Curr. Opin. Chem. Biol. 2008, 12, 626-639
9. Cleland, W. W. and Hengge, A. C. FASEB J. 1995, 9, 1585-1594
10. Hengge, A. C., Aleksandra, T. E., and Cleland, W. W. J. Am. Chem. Soc. 1995, 117, 5919-5926
11. Hengge, A. C. Acc. Chem. Res. 2002, 35, 105-112
12. Kirby, A. J. and Younas, M. J. Chem. Soc. B 1970, 1165-1172
13. Lonnberg, H., Stromberg, R., and Williams, A. Org. Biomol. Chem. 2004, 2, 2165-2167
14. Rawlings, J., Cleland, W. W., and Hengge, A. C. J. Am. Chem. Soc. 2006, 128, 17120-17125
15. Humphry, T., Forconi, M., Williams, N. H., and Hengge, A. C. J. Am. Chem. Soc. 2004, 126, 11864-11869
16. Grzyska, P. K., Czyryca, P. G., Purcell, J., and Hengge, A. C. J. Am. Chem. Soc. 2003, 125, 13106-13111
17. Humphry, T., Forconi, M., Williams, N. H., and Hengge, A. C. J. Am. Chem. Soc. 2002, 124, 14860-14861
18. Davis, A. M., Hall, A. D., and Williams, A. J. Am. Chem. Soc. 1988, 110, 5105-5108
19. Li, Y. and Breaker, R. R. J. Am. Chem. Soc. 1999, 121, 5364-5372
20. Jarvinen, P., Oivanen, M., and Lonnberg, H. J. Org. Chem. 1991, 56, 5396-5401
21. Koike, T. and Inoue, Y. Chem. Lett. 1972, 7, 569-572
22. Lipkin, D., Talbert, P. T., and Cohn, M. J. Am. Chem. Soc. 1954, 76, 2871-2872
23. Breslow, R. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 1208-1211
24. Fedor, M. J. Annu. Rev. Biophys. 2009, 38, 271-299
25. Hamilton, C. S., Spedaliere, C. J., Ginter, J. M., Johnston, M. V., and Mueller, E. G. Arch. Biochem. Biophys. 2005, 433, 322-334
26. Polgar, L. Cell. Mol. Life Sci. 2005, 62, 2161-2172
27. Richard, J. P. Biochemistry 1998, 37, 4305-4309
28. Schowen, K. B., Limbach, H. H., Denisov, G. S., and Schowen, R. L. Biochim. Biophys. Acta 2000, 1458, 43-62
29. Seibert, C. M. and Raushel, F. M. Biochemistry 2005, 44, 6383-6391
30. Oivanen, M., Ora, M., Almer, H., Stromberg, R., and Lonnberg, H. J. Org. Chem. 1995, 60, 5620-5627
31. Emilsson, G. M., Nakamura, S., Roth, A., and Breaker, R. R. RNA 2003, 9, 907-918
32. Lopez, C. S., Faza, O. N., Gregersen, B. A., Lopez, X., de Lera, A. R., and York, D. M. ChemPhysChem. 2004, 5, 1045-1049
33. Cook, R. M., Turley, P. C., Deibert, C. E., Fierman, A. H., and Haake, P. J. Am. Chem. Soc. 1972, 94, 9260-9261
34. Perreault, D. M. and Anslyn, E. V. Angew. Chem. 1997, 109, 470-490
35. Lim, C. and Karplus, M. J. Am. Chem. Soc. 1990, 112, 5872-5873
36. Davies, J. E., Doltsinis, N. L., Kirby, A. J., Roussev, C. D., and Sprik, M. J. Am. Chem. Soc. 2002, 124, 6594-6599
37. Lopez, X., Schaefer, M., Dejaegere, A., and Karplus, M. J. Am. Chem. Soc. 2002, 124, 5010-5018
38. Lui, X. and Reese, C. B.. Tetrahedron Lett. 1995, 3413-3416
39. Acharya, S., Foldesi, A., and Chattopadhyaya, J. J. Org. Chem. 2003, 68, 1906-1910
40. Hengge, A. C. FEBS Lett. 2001, 501, 99-102
41. Cleland, W. W. and Cook, P. F. Enzyme Kinetics and Mechanism; Garland Publishers: London and New York, 2007.
42. Buddenbaum, W. E. and Shiner, V. J. Computation of Isotope Effects on Equilibria and Rates. In Isotope Effects on Enzyme-Catalyzed Reactions; Cleland, W. W., OLeary, M. H., and Northrop, D. B., Eds.; University Park Press: London, 1977; pp 1 - 36.
43. Bigeleisen, J. Pure Appl. Chem. 1964, 8, 217-223
44. Kolmodin, K., Luzhkov, V. B., and Aqvist, J. J. Am. Chem. Soc. 2002, 124, 10130-51013
45. Humphry, T., Iyer, S., Iranzo, O., Morrow, J. R., Richard, J. P., Paneth, P., and Hengge, A. C. J. Am. Chem. Soc. 2008, 130, 17858-17866
46. Hengge, A. C., Bruzik, K. S., Tobin, A. E., Cleland, W. W., and Tsai, M. D. Bioorg. Chem. 2000, 28, 119-133
47. Feng, G., Tanifum, E. A., Adams, H., Hengge, A. C., and Williams, N. H. J. Am. Chem. Soc. 2009, 131, 12771-12779
48. Cleland, W. W. CRC Crit. Rev. Biochem. 1982, 13, 385-428
49. Rishavy, M. A., Hengge, A. C., and Cleland, W. W. Bioorg. Chem. 2000, 28, 283-292
50. Dai, Q., Frederiksen, J. K., Anderson, V. E., Harris, M. E., and Piccirilli, J. A. J. Org. Chem. 2008, 73, 309-311
51. Cassano, A. G., Wang, B., Anderson, D. R., Previs, S., Harris, M. E., and Anderson, V. E. Anal. Biochem. 2007, 367, 28-39
52. Cook, P. F. and Cleland, W. W. Isotope effects as a probe of mechanism. In Enzyme Kinetics and Mechanism; Garland Science: New York, 2007; pp 253 - 324.
53. Breaker, R. R., Emilsson, G. M., Lazarev, D., Nakamura, S., Puskarz, I. J., Roth, A., and Sudarsan, N. RNA 2003, 9, 949-957
54. Nakano, S. and Bevilacqua, P. C. J. Am. Chem. Soc. 2001, 123, 11333-11334
55. Cassano, A. G., Anderson, V. E., and Harris, M. E. J. Am. Chem. Soc. 2002, 124, 10964-10965
56. Yang, M. Y., Iranzo, O., Richard, J. P., and Morrow, J. R. J. Am. Chem. Soc. 2005, 127, 1064-1065
57. Rishavy, M. A. and Cleland, W. W. Can. J. Chem. 1999, 77, 967-977
58. Hengge, A. C. and Hess, R. A. J. Am. Chem. Soc. 1994, 116, 11256-11263
59. Knight, W. B., Weiss, P. M., and Cleland, W. W. J. Am. Chem. Soc. 1986, 108, 2759-2761
60. Green, M. and Taube, H. J. Phys. Chem. 1963, 67, 1565-6156
61. Iyer, S. and Hengge, A. C. J. Org. Chem. 2008, 73, 4819-4829
62. Virtanen, A., Polari, L., Valila, M., and Mikkola, S. J. Phys. Org. Chem. 2005, 18, 385-397
63. Bonfa, L., Gatos, F., Mancin, F., Tecilla, P., and Tonellato, U. Inorg. Chem. 2003, 42, 3943-3949
64. Usher, D. A., Richardson, D. I., Jr., and Oakenfull, D. G. J. Am. Chem. Soc. 1970, 92, 4699-4712
65. Bruice, T. C., Blasko, A., Arasasingham, R. D., and Kim, J.-S. J. Am. Chem. Soc. 1995, 117, 12070-12077
66. Melander, L. and Saunders, W. H. Reaction Rates of Isotopic Molecules; Wiley Interscience: New York, 1987.
67. Lewars, E. Computaional Chemistry: Introduction to the Theory and Application of Molecular and Quantum Mechanics; Kluwer Academic Publishers: Norwell, MA, 2003.
68. Cassano, A. G., Anderson, V. E., and Harris, M. E. Biochemistry 2004, 43, 10547-10559
69. Gerratana, B., Sowa, G. A., and Cleland, W. W. J. Am. Chem. Soc. 2000, 122, 12615-12621
70. Hammond, G. S. J. Am. Chem. Soc. 1955, 77, 334-338
71. Leffler, J. E. Science 1953, 117, 340-341