Site-specific platinum(II) cross-linking in a ribozyme active site

Journal of the American Chemical Society

Volumn 134, Issue 1, 2012, Pages 256-262

  Chapman, Erich G ^a,b   Derose, Victoria J ^a  

^a UNIVERSITY OF OREGON   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; CATALYTIC CORE; DISTANCE CONSTRAINTS; DYNAMIC STRUCTURE; ION CONCENTRATIONS; METAL CENTERS; NUCLEOBASES; PHOSPHOROTHIOATES; RIBOZYMES; RNA STRUCTURES; SCISSILE BOND; SITE-SPECIFIC; STRUCTURAL BIOLOGY; TERTIARY STRUCTURES;

PLATINUM; RNA;

PLATINUM COMPOUNDS;

CATION; CISPLATIN; HAMMERHEAD RIBOZYME; MAGNESIUM ION; NUCLEOPHILE; PHOSPHOROTHIOIC ACID; PLATINUM; RIBOZYME; RNA;

ARTICLE; CATALYSIS; CHEMICAL BOND; CONCENTRATION (PARAMETERS); CROSS LINKING; ENZYME ACTIVE SITE; RNA ISOLATION; RNA STRUCTURE; SUBSTITUTION REACTION;

ANIMALS; BASE SEQUENCE; CATALYTIC DOMAIN; KINETICS; LIGANDS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; ORGANOPLATINUM COMPOUNDS; PHOSPHATES; RNA, CATALYTIC;

EID: 84855655984     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja206455t     Document Type: Article

References (92)

1. Sharp, P. A. Cell 2009, 136, 577-580
2. RNA Worlds. In Cold Spring Harbor Perspectives in Biology; Atkins, J. F.; Gestetland, R. F.; Cech, T. R., Eds.; Cold Springs Harbor Laboratory Press: Cold Springs Harbor, NY, 2011.
3. Mattick, J. S. Nat. Rev. Genetics 2004, 5, 316-323
4. Darnell, R. B. Wiley Int. Rev. RNA 1 2010, 266-286
5. Hogan, D. J.; Riordan, D. P.; Gerber, A. P.; Herschlag, D.; Brown, P. O. PLoS Biol. 2008, 6, e255
6. Cruz, J. A.; Westhof, E. Cell 2009, 136, 604-609
7. Schroeder, S. J. Virol. 2009, 83, 6326-6334
8. Jossinet, F.; Ludwig, T. E.; Westhof, E. Curr. Op. Microbio. 2007, 10, 279-285.
9. Shapiro, B. A.; Yingling, Y. G.; Kasprzak, W.; Bindewald, E. Curr. Opin. Struct. Biol. 2007, 17, 157-165
10. Westhof, E.; Masquida, B.; Jossinet, F. Cold Spring Harbor Perspectives in Biology 2010.
11. Das, R.; Karanicolas, J.; Baker, D. Nat. Meth. 2010, 7, 291-294
12. Flores, S. C.; Altman, R. B. RNA 2010, 16, 1769-1778
13. Reues, F. E.; Garst, A. D.; Batey, R. T. Methods Ezymol. 2009, 469, 119-139
14. Moers, B. H. M. Methods 2009, 47, 168-176
15. Holbrook, S. R.; Kim, S. H. Biopolymers 1997, 44, 3-21
16. Mitra, K.; Frank, J. Annu. Rev. Biophys. Biomol. Struct. 2006, 35, 299-317
17. Baird, N. J.; Ludtke, S. J.; Khan, H.; Chiu, W.; Pan, t.; Sosnik, T. R. J. Am. Chem. Soc. 2010, 132, 16352-16353
18. Jurica, M. S. Curr. Opin. Struct. Biol. 2008, 18, 315-320
19. Wang, Y. X.; Zuo, X. B.; Wang, J. B.; Yu, P.; Butcher, S. E. Methods 2010, 52, 180-191
20. Biophysical, Chemical and Functional Probes of RNA Structure, Interactions and Folding: Part A; Herschlag, D., Ed.; Academic Press: London, 2009; Methods in Enzymology 468.
21. Weeks, K. M. Curr. Opin. Struct. Biol. 2010, 20, 1-10
22. Das, R.; Kudaravalli, M.; Jonikas, M.; Laederach, A.; Fong, R.; Schwans, J. P.; Baker, D.; Piccirilli, J. A.; Altman, R. B.; Herschlag, D. Proc. Natl. Acad. Sci. U.S.A. 2008, 205, 4144-4149
23. Efimov, V. A.; Fedyunin, S. V.; Chakhmakhcheva, O. G. Russ. J. Bioorg. Chem. 2010, 36, 49-72
24. Harris, M. E.; Christian, E. L. In Handbook of RNA Biochemistry; Hartmann, R. K.; Bindereif, A.; Schon, A.; Westhof, E., Eds.; Wiley: New York, 2008; pp 374-384.
25. Juzumiene, D.; Shapakina, T.; Kirillov, S.; Wollenzein, P. Methods 2001, 25, 333-343
26. Lambert, D.; Heckman, J. E.; Burke, J. M. Biochemistry 2006, 45, 7140-7147
27. Hummel, C. F.; Pincus, M. R.; Brandt-Rauf, P. W.; Frei, G. M.; Carty, R. P. Biochemistry 1987, 26, 135-146
28. Thomas, J. M.; Perrin, D. M. J. Am. Chem. Soc. 2008, 46, 15467-15475
29. Sigurdsson, S. T.; Tuschl, T.; Eckstein, F. RNA 1995, 1, 575-583
30. Cohen, S. B.; Cech, T. R. J. Am. Chem. Soc. 1997, 119, 6259-6268
31. Stage-Zimmerman, T. K.; Uhlenbeck, O. C. Nat. Struct. Biol. 2001, 8, 863-867
32. Brimacombe, R.; Stiege, W.; Kyriatsoulis, A.; Maly, P. Methods Enzymol. 1988, 164, 287-309
33. Chapman, E. G.; Hostetter, A.; Osborn, M.; Miller, A.; DeRose, V. J. In Metal Ions In Life Sciences: Structural and Catalytic Roles of Metal Ions in RNA; Sigel, A.; Sigel, H.; Sigel, R. K. O., Eds.; Royal Society of Chemistry: Cambridge, UK, 2011.
34. Lippert, B. Prog. Inorg. Chem. 1989, 37, 1-97
35. Kelland, L. Nat. Rev. Cancer 2007, 7, 573-583
36. Wang, D.; Lippard, S. J. Nat. Rev. Drug Disc. 2005, 4, 307-320
37. Escaffre, M.; Chottard, J.-C.; Bombard, S. Nucleic Acids Res. 2002, 30, 5222-5228
38. Redon, S.; Bombard, S.; Elizondo-Riojas, M.-A.; Chottard, J.-C. Nucleic Acids Res. 2003, 31, 1605-1613
39. Bombard, S.; Kozelka, J.; Favre, A.; Chottard, J. C. Eur. J. Biochem. 1998, 252, 25-35
40. Hostetter, A. A.; Chapman, E. G.; DeRose, V. J. J. Am. Chem. Soc. 2009, 131, 9250-9257
41. Tukalo, M. H.; Kubler, M. D.; Kern, D.; Mougel, M.; Ehresmann, C.; Ebel, J.-P.; Ehresmann, B.; Giegé, R. Biochemistry 1987, 26, 5200-5208
42. Moine, H.; Bienaimé, C.; Mougel, M.; Reinbolt, J.; Ebel, J. P.; Ehresmann, C.; Ehresmann, B. FEBS Lett. 1988, 228, 1-6
43. Metz-Boutigue, M.-H.; Reinbolt, J.; Ebel, J.-P.; Ehresmann, C.; Ehresmann, B. FEBS Lett. 1989, 245, 194-200
44. Rasmussen, N.-J.; Wikman, F. P.; Clark, B. F. C. Nucleic Acids Res. 1990, 18, 4883-4889
45. Yusupova, G.; Reinbolt, J.; Wakao, H.; Laalami, S.; Grunberg-Manago, M.; Romboy, P.; Ehresmann, B.; Ehresmann, C. Biochemistry 1996, 352987-2984
46. Rijal, K.; Chow, C. S. Chem. Commun. 2009, 107-109
47. Hostetter, A. A.; Osborn, M. F.; DeRose, V. J. ACS Chem. Biol. DOI: 10.1021/cb200279p.
48. Strothkamp, K. G.; Lippard, S. J. Proc. Natl. Acad. Sci. U.S.A. 1976, 73, 2536-2540
49. Elmroth, S. K. C.; Lippard, S. J. J. Am. Chem. Soc. 1994, 116, 3633-3634
50. Elmroth, S. K. C.; Lippard, S. J. Inorg. Chem. 1995, 34, 5234-5243
51. Kjellström, J.; Elmroth, S. K. C. Inorg. Chem. 1999, 38, 6193-6199
52. Chu, B. C. F.; Orgel, L. E. Nucleic Acids Res. 1989, 17, 4783-4798
53. Chu, B. F.; Orgel, L. E. Nucleic Acids Res. 1990, 18, 5163-5171
54. Chu, B. F.; Orgel, L. E. DNA Cell Biol. 1990, 9, 71-76
55. Gruff, E.; Orgel, L. E. Nucleic Acids Res. 1991, 19, 6849-6854
56. Hutchins, C. J.; Rathjen, P. D.; Forster, A. C.; Symons, R. H. Nucleic Acids Res. 1986, 14, 3627-3640
57. Uhlenbeck, O. C. Nature 1987, 328, 596-600
58. Blount, K. F.; Uhlenbeck, O. C. Annu. Rev. Biophys. Biomol. Struct. 2005, 34, 415-440
59. de la Peña, M.; García Robles RNA 2010, 16, 1943-1950
60. Seehafer, C.; Kalweit, A.; Steger, G.; Gräf, S.; Hammann, C. RNA 2011, 17, 21-28
61. de la Peña, M.; García Robles, I. EMBO Rep. 2010, 11, 711-716
62. Rios, A. C.; Tor, Y Curr. Opin. Chem. Biol. 2009, 13, 660-668
63. Osborne, E. M.; Schaak, J. E.; DeRose, V. J. RNA 2005, 11, 187-196
64. Ward, L. W.; DeRose, V. J. RNA, in press.
65. Martick, M.; Lee, T.-S.; York, D. M.; Scott, W. G. Chem. Biol. 2008, 15, 332-342
66. Martick, M.; Scott, W. G Cell 2006, 126, 309-320
67. Nelson, J. A.; Uhlenbeck, O. RNA 2008, 14, 605-615
68. Leclerc, F. Molecules 2010, 15, 5389-5407
69. Wang, S.; Karbenstein, K.; Peracchi, A.; Beigelman, L.; Herschlag, D. Biochemistry 1999, 38, 14363-14378
70. Kim, N.-K.; Murali, A.; DeRose, V. J. J. Am. Chem. Soc. 2005, 127, 14134-14135
71. Boots, J. L.; Canny, M. D.; Azimi, E.; Pardi, A. RNA 2008, 14, 2212-2122
72. Huggins, W.; Shapkina, T.; Wollenzien, P. RNA 2007, 13, 2000-2011
73. Behlen, L. S.; Sampson, J. R.; Uhlenbeck, O. C. Nucleic Acids Res. 1992, 20, 4055-4059
74. Butcher, S. E.; Burke, J. M. Biochemistry 1994, 33, 992-999
75. Crabtree, R. H. The Organometallic Chemistry of the Transition Metals, 3 rd ed.; Wiley: New York, 2001.
76. Al-Hashimi, H. H.; Walter, N. G. Curr. Opin. Struct. Biol. 2008, 18, 321-329
77. Hindmarsh, K.; House, D. A.; Turnbull, M. M. Inorg. Chim. Acta 1997, 257, 11-18
78. Kim, H. D.; Nienhaus, G. U.; Ha, T.; Orr, J. W.; Williamson, J. R.; Chu, S. Proc. Natl. Acad. Sci. U.S.A. 2002, 96, 9077-9082
79. Mohanty, U.; Spasic, Al; Kim, H. D.; Chu, S. J. Phys. Chem. B 2005, 109, 21369-21374
80. Kim, N.-K., Bowman, M. K., and DeRose, V. J. J. Am. Chem. Soc. 2010, 132, 8882-8884
81. Osborne, E. M.; Ward, W. L.; Ruehle, M. Z.; DeRose, V. J. Biochemistry 2009, 48, 10654-10664
82. Kratochwil, N. A.; Parkinson, J. A.; Sacht, C.; Murdoch, P. S.; Brown, T.; Sadler, P. J. Eur. J. Inorg. Chem. 2001, 2743-2746
83. Chapman, E. G.; DeRose, V. J. J. Am. Chem. Soc. 2010, 132, 1946-1952
84. Klein, D. J.; Moore, P. B.; Steitz, T. A. RNA 2004, 10, 1366-1379
85. Pyle, A. M. J. Biol. Inorg, Chem. 2002, 7, 679-690
86. DeRose, V. J.; Burns, S.; Kim, N. K.; Vogt, M. In Comprehensive Coordination Chemistry I; Elsevier, St. Louis, MO, 2003; pp 787-813.
87. Shi, H.; Moore, P. B. RNA 2000, 6, 1091-1105
88. Lee, T.-S.; Giambaşu, G. M.; Sosa, C. P.; Martick, M.; Scott, W. G.; York, D. M. J. Mol. Biol. 2009, 388, 195-206
89. Nelson, J. A.; Uhlenbeck, O. C. RNA 2008, 14, 43-54
90. Lee, T. S.; York, D. M. J. Am. Chem. Soc. 2010, 132, 13505-13518
91. Frederiksen, J. K.; Piccirilli, J. Methods Enzymol. 2009, 468, 289-309
92. Suydam, I. T.; Strobel, S. A. Methods Enzymol. 2009, 468, 4-30