The essential role of stacking adenines in a two-base-pair RNA kissing complex

Journal of the American Chemical Society

Volumn 135, Issue 15, 2013, Pages 5602-5611

  Stephenson, William ^a   Asare Okai, Papa Nii ^a   Chen, Alan A ^b   Keller, Sean ^a   Santiago, Rachel ^a   Tenenbaum, Scott A ^a   Garcia, Angel E ^a,b   Fabris, Daniele ^a   Li, Pan T X ^a  

^a STATE UNIVERSITY OF NEW YORK   (United States)

^b RENSSELAER POLYTECHNIC INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BASE PAIRING; BASE PAIRS; ELECTROSPRAY IONIZATION MASS SPECTROMETRY; MOLECULAR DYNAMICS SIMULATIONS; RNA MOLECULES; STABILIZING EFFECTS; TERTIARY INTERACTIONS; TETRALOOPS;

DIMERS; FUNCTIONAL GROUPS; MASS SPECTROMETRY; MOLECULAR DYNAMICS; OPTICAL TWEEZERS;

RNA;

ADENINE DERIVATIVE; HETERODIMER; HOMODIMER;

ARTICLE; BASE PAIRING; DIMERIZATION; DISSOCIATION; DYNAMICS; ELECTROSPRAY MASS SPECTROMETRY; HYDROGEN BOND; HYDROPHOBICITY; INTERACTIONS WITH RNA; IONIC STRENGTH; OPTICAL TWEEZERS; RNA CONFORMATION; STATIC ELECTRICITY; THERMODYNAMICS;

ADENINE; BASE PAIRING; BASE SEQUENCE; KINETICS; MOLECULAR DYNAMICS SIMULATION; NUCLEOTIDES; OPTICAL TWEEZERS; RNA; THERMODYNAMICS;

EID: 84876466060     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja310820h     Document Type: Article

References (57)

1. Butcher, S. E.; Pyle, A. M. Acc. Chem. Res. 2011, 44, 1302
2. Westhof, E.; Masquida, B.; Jossinet, F. Cold Spring Harb. Perspect. Biol. 2011, 3, a003632
3. Borer, P. N.; Dengler, B.; Tinoco, I. J.; Uhlenbeck, O. C. J. Mol. Biol. 1974, 86, 843
4. Brahms, J.; Aubertin, A. M.; Dirheimer, G.; Grunberg-Manago, M. Biochemistry 1969, 8, 3269
5. Jaskunas, S. R.; Cantor, C. R.; Tinoco, I. J. Biochemistry 1968, 7, 3164
6. Alkema, D.; Bell, R. A.; Hader, P. A.; Neilson, T. J. Am. Chem. Soc. 1981, 103, 2866
7. Kim, C.; Tinoco, I. J. Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 9396
8. Li, P. T. X.; Bustamante, C.; Tinoco, I., Jr. Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 15847
9. Liu, J. D.; Zhao, L.; Xia, T. Biochemistry 2008, 47, 5962
10. Isaksson, J.; Chattopadhyaya Biochemistry 2005, 44, 5390
11. Turner, D. H.; Sugimoto, N.; Freier, S. M. Annu. Rev. Biophys. Biophys. Chem. 1988, 17, 16
12. Serra, M. J.; Turner, D. H. Methods Enzymol. 1995, 259, 242
13. Turner, D. H.; Mathews, D. H. Nucleic Acids Res. 2009, 38, D280
14. Chen, A. A.; Garcia, A. E. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 1530
15. D'Souza, V.; Melamed, J.; Habib, D.; Pullen, K.; Wallace, K.; Summers, M. F. J. Mol. Biol. 2001, 314, 217
16. Yamashita, M.; Fenn, J. B. J. Phys. Chem. 1984, 88, 4671
17. Fabris, D. Anal. Chem. 2011, 83 (15) 5810
18. Smith, S. B.; Cui, Y.; Bustamante, C. Methods Enzymol. 2003, 361, 134
19. Hofstadler, S. A.; Griffey, R. H. Chem. Rev. 2001, 101, 377
20. Daniel, J. M.; Friess, S. D.; Rajagopalan, S.; Wendt, S.; Zenobi, R. Int. J. Mass Spectrom. Ion Proc. 2002, 216, 1
21. Turner, K. B.; Kohlway, A. S.; Hagan, N. A.; Fabris, D. Biopolymers 2009, 91, 283
22. Brinson, R. G.; Turner, K. B.; Yi-Brunozzi, H. Y.; Le Grice, S. F.; Fabris, D.; Marino, J. P. Biochemistry 2009, 48 (29) 6988
23. Hagan, N. A.; Fabris, D. Biochemistry 2003, 42, 10736
24. Turner, K. B.; Hagan, N. A.; Fabris, D. Nucleic Acids Res. 2006, 34, 1305
25. Li, P. T.; Tinoco, I., Jr. J. Mol. Biol. 2009, 386, 1343
26. Tinoco, I.; Jr, Li, P. T. X.; Bustamante, C. Q. Rev. Biophys. 2006, 39, 325
27. Woodside, M. T.; Garcia-Garcia, C.; Block, S. M. Curr. Opin. Chem. Biol. 2008, 12, 640
28. Ganem, B.; Li, Y.-T.; Henion, J. D. Tetrahedron Lett. 1993, 34, 1445
29. Light-Wahl, K. J.; Springer, D. L.; Winger, B. E.; Edmonds, C. G.; Camp, D. G.; Thrall, B. D.; Smith, R. D. J. Am. Chem. Soc. 1993, 115, 803
30. Turner, K. B.; Brinson, R. G.; Yi-Brunozzi, Y. H.; Rausch, J. W.; Milletr, J. T.; Le Grice, S. F.; Marino, J. P.; Fabris, D. Nucleic Acids Res. 2008, 36, 2799
31. Hagan, N. A.; Fabris, D. J. Mol. Biol. 2007, 365, 396
32. Turner, K. B.; Hagan, N. A.; Fabris, D. J. Mol. Biol. 2007, 369, 812
33. Liphardt, J.; Onoa, B.; Smith, S. B.; Tinoco, I., Jr.; Bustamante, C. Science 2001, 292, 733
34. Li, P. T. X. submitted.
35. Li, P. T. X. Soft Matter 2013, 9, 3246-3254
36. Woodside, M. T.; Anthony, P. C.; Behnke-Parks, W. M.; Larizadeh, K.; Block, S. M. Science 2006, 314, 1001
37. Li, P. T. X.; Collin, D.; Smith, S. B.; Bustamante, C.; Tinoco, I., Jr. Biophys. J. 2006, 90, 250
38. Guckian, K. M.; Schweitzer, B. A.; Ren, R. X.; Sheils, C. J.; Tahmassebi, D. C.; Kool, E. T. J. Am. Chem. Soc. 2000, 122, 2213
39. Vanquelef, E.; Simon, S.; Marquant, G.; Garcia, E.; Klimerak, G.; Delepine, J. C.; Cieplak, P.; Dupradeau, F. Y. Nucleic Acids Res. 2011, 39, W511
40. Bayly, C. I.; Cieplak, P.; Cornell, W.; Kollman, P. A. J. Phys. Chem. 1993, 97, 10269
41. Dunkle, J. A.; Cate, J. H. Annu. Rev. Biophys. 2010, 39, 227
42. Schuwirth, B. S.; Borovinskaya, M. A.; Hau, C. W.; Zhang, W.; Vila-Sanjurjo, A.; Holton, J. M.; Cate, J. H. Science 2005, 310, 827
43. Steitz, T. A. Nat. Rev. Mol. Cell Biol. 2008, 9, 242
44. Yusupov, M. M.; Yusupova, G. Z.; Baucom, A.; Lieberman, K.; Earnest, T. N.; Cate, J. H.; Noller, H. F. Science 2001, 292, 883
45. Hess, B.; Kutzner, C.; Van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435
46. Wang, J.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049
47. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926
48. Äqvist, J. J. Phys. Chem. 1990, 94, 8021
49. Chen, A. A.; Pappu, R. V. J. Phys. Chem. 2007, 111, 11884
50. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684
51. Hockney, R. W.; Goel, S. P.; Eastwood, J. J. Comput. Chem. 1974, 14, 148
52. Miyamoto, S.; Kollman, P. A. J. Comput. Chem. 1992, 13, 952
53. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089
54. Shirts, M. R.; Pande, V. S. J. Chem. Phys. 2005, 122, 134508
55. Chodera, J. D.; Mobley, D. L.; Shirts, M. R.; Dixon, R. W.; Branson, K.; Pande, V. S. J. Chem. Phys. 2011, 134, 244107
56. Shirts, M. R.; Pande, V. S. J. Chem. Phys. 2008, 129, 124105
57. Bennett, C. H. J. Comput. Phys. 1976, 22, 245