Stacking effects on local structure in RNA: Changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs

Journal of Physical Chemistry B

Volumn 111, Issue 24, 2007, Pages 6718-6727

  Chen, Gang ^a   Kierzek, Ryszard ^c   Yildirim, Ilyas ^a   Krugh, Thomas R ^a   Turner, Douglas H ^a,b   Kennedy, Scott D ^b  

^a UNIVERSITY OF ROCHESTER   (United States)

^b UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

^c INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN BONDS; MOLECULAR INTERACTIONS; MOLECULAR STRUCTURE; NUCLEAR MAGNETIC RESONANCE; THERMODYNAMIC STABILITY;

LOOP STABILITY; RNA SELF COMPLEMENTARY DUPLEXES; TANDEM IMINO;

RNA;

EID: 34547357210     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp068732m     Document Type: Article

References (72)

1. Mathews, D. H.; Sabina, J.; Zuker, M.; Turner, D. H. J. Mol. Biol. 1999, 288, 911.
2. Mathews, D. H.; Disney, M. D.; Childs, J. L.; Schroeder, S. J.; Zuker, M.; Turner, D. H. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 7287.
3. SantaLucia, J., Jr.; Kierzek, R.; Turner, D. H. Biochemistry 1990, 29, 8813.
4. Walter, A. E.; Wu, M.; Turner, D. H. Biochemistry 1994, 33, 11349.
5. Schroeder, S. J.; Turner, D. H. Biochemistry 2001, 40, 11509.
6. Chen, G.; Turner, D. H. Biochemistry 2006, 45, 4025.
7. Yildirim, I.; Turner, D. H. Biochemistry 2005, 44, 13225.
8. SantaLucia, J., Jr.; Turner, D. H. Biochemistry 1993, 32, 12612.
9. Wu, M.; Turner, D. H. Biochemistry 1996, 35, 9677.
10. Wu, M.; SantaLucia. J., Jr.; Turner, D. H. Biochemistry 1997, 36, 4449.
11. Heus, H. A.; Wijmenga, S. S.; Hoppe, H.; Hilbers, C. W. J. Mol. Biol. 1997, 271, 147.
12. Zhang, X. H.; Gaffney, B. L.; Jones, R. A. J. Am. Chem. Soc. 1998, 120, 6625.
13. Chin, K.; Sharp, K. A.; Honig, B.; Pyle, A. M. Nat. Struct. Biol. 1999, 6, 1055.
14. Chen, G.; Znosko, B. M.; Kennedy, S. D.; Krugh, T. R.; Turner, D. H. Biochemistry 2005, 44, 2845.
15. Tolbert, B. S.; Kennedy, S. D.; Schroeder, S. J.; Krugh, T. R.; Turner, D. H. Biochemistry 2007, 46, 1511.
16. Villescas-Diaz, G.; Zächarias, M. Biophys. J. 2003, 85, 416.
17. Disney, M. D.; Turner, D. H. Biochemistry 2002, 41, 8113.
18. Doherty, E. A.; Batey, R. T.; Masquida, B.; Doudna, J. A. Nat. Struct. Biol. 2001, 8, 339.
19. Nissen, P.; Ippolito, J. A.; Ban, N.; Moore, P. B.; Steitz, T. A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 4899.
20. Agris, P. F. Nucleic Acids Res. 2004, 32, 223.
21. Henry, A. A.; Romesberg, F. E. Curr. Opin. Chem. Biol. 2003, 7, 727.
22. Roberts, C.; Bandaru, R.; Switzer, C. J. Am. Chem. Soc. 1997, 119, 4640.
23. Switzer, C.; Moroney, S. E.; Benner, S. A. J. Am. Chem. Soc. 1989, 111, 8322.
24. Switzer, C. Y.; Moroney, S. E.; Benner, S. A. Biochemistry 1993, 32, 10489.
25. Chaput, J. C.; Switzer, C. J. Am. Chem. Soc. 2000, 122, 12866.
26. Roberts, C.; Bandaru, R.; Switzer, C. Tetrahedron Lett. 1995, 36, 3601.
27. Chen, X.; Kierzek, R.; Turner, D. H. J. Am. Chem. Soc. 2001, 123, 1267.
28. Chen, X.; McDowell, J. A.; Kierzek, R.; Krugh, T. R.; Turner, D. H. Biochemistry 2000, 39, 8970.
29. Burkard, M. E.; Turner, D. H. Biochemistry 2000, 39, 11748.
30. Geyer, C. R.; Battersby, T. R.; Benner, S. A. Structure 2003, 11, 1485.
31. Robinson, H.; Gao, Y. G.; Bauer, C.; Roberts, C.; Switzer, C.; Wang, A. H. J. Biochemistry 1998, 37, 10897.
32. Yang, X. L.; Sugiyama, H.; Ikeda, S.; Saito, I.; Wang, A. H. J. Biophys. J. 1998, 75, 1163.
33. Usman, N.; Ogilvie, K. K.; Jiang, M. Y.; Cedergren, R. J. J. Am. Chem. Soc. 1987, 109, 7845.
34. Wincott, F.; Direnzo, A.; Shaffer, C.; Grimm, S.; Tracz, D.; Workman, C.; Sweedler, D.; Gonzalez, C.; Scaringe, S.; Usman, N. Nucleic Acids Res. 1995, 23, 2677.
35. Chen, G.; Znosko, B. M.; Jiao, X. Q.; Turner, D. H. Biochemistry 2004, 43, 12865.
36. Borer, P. N. Optical properties of nucleic acids, absorption and circular dichroism spectra. In Handbook of Biochemistry and Molecular Biology: Nucleic Acids, 3rd ed.; Fasman, G. D., Ed.; CRC Press: Cleveland, OH, 1975; Vol. I; p 589.
37. Richards, E. G. Use of tables in calculation of absorption, optical rotatory dispersion and circular dichroism of polyribonucleotides. In Handbook of Biochemistry and Molecular Biology: Nucleic Acids, 3rd ed.; Fasman, G. D., Ed.; CRC Press: Cleveland, OH, 1975; Vol. 1; pp 596.
38. McDowell, J. A.; Turner, D. H. Biochemistry 1996, 35, 14077.
39. Petersheim, M.; Turner, D. H. Biochemistry 1983, 22, 256.
40. Xia, T.; SantaLucia, J., Jr.; Burkard, M. E.; Kierzek, R.; Schroeder, S. J.; Jiao, X.; Cox, C.; Turner, D. H. Biochemistry 1998, 37, 14719.
41. Borer, P. N.; Dengler, B.; Tinoco, I., Jr.; Uhlenbeck, O. C. J. Mol. Biol. 1974, 86, 843.
42. Znosko, B. M.; Burkard, M. E.; Schroeder, S. J.; Krugh, T. R.; Turner, D. H. Biochemistry 2002, 41, 14969.
43. Lukavsky, P. J.; Puglisi, J. D. Methods 2001, 25, 316.
44. Varani, G.; Aboulela, F.; Allain, F. H. T. Prog. Nucl. Magn. Reson. Spectrosc. 1996, 29, 51.
45. Varani, G.; Tinoco, I., Jr. Q. Rev. Biophys. 1991, 24, 479.
46. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179.
47. Ding, H. Q.; Karasawa, N.; Goddard, W. A. J. Chem. Phys. 1992, 97, 4309.
48. DeLano, W. L. The PyMOL User's Manual; DeLano Scientific: San Carlos, CA, 2002.
49. Gralla, J.; Crothers, D. M. J. Mol. Biol. 1973, 78, 301.
50. Turner, D. H.; Sugimoto, N.; Freier, S. M. Annu. Rev. Biophys. Biophys. Chem. 1988, 17, 167.
51. Turner, D. H. Conformational Changes. In Nucleic Acids: Structures, Properties, and Functions; Bloomfield, V. A., Crothers, D. M., Tinoco, I., Jr., Eds.; University Science Books: Sausalito, CA, 2000; p 259.
52. Kerwood, D. J.; Cavaluzzi, M. J.; Borer, P. N. Biochemistry 2001, 40, 14518.
53. Mueller, L.; Legault, P.; Pardi, A. J. Am. Chem. Soc. 1995, 117, 11043.
54. Schroeder, K. T.; Skalicky, J. J.; Greenbaum, N. L. RNA 2005, 11, 1012.
55. Hennig, M.; Fohrer, J.; Carlomagno, T. J. Am. Chem. Soc. 2005, 127, 2028.
56. Du, Z. H.; Yu, J. H.; Ulyanov, N. B.; Andino, R.; James, T. L. Biochemistry 2004, 43, 11959.
57. Gutowsky, H. S.; Holm, C. H. J. Chem. Phys. 1956, 23, 1228.
58. Legault, P.; Pardi, A. J. Am. Chem. Soc. 1997, 119, 6621.
59. Sponer, J.; Mokdad, A.; Sponer, J. E.; Spackova, N.; Leszczynski, J.; Leontis, N. B. J. Mol. Biol. 2003, 330, 967.
60. Michiels, P. J. A.; Schouten, C. H. J.; Hilbers, C. W.; Heus, H. A. RNA 2000, 6, 1821.
61. Jucker, F. M.; Heus, H. A.; Yip, P. F.; Moors, E. H. M.; Pardi, A. J. Mol. Biol. 1996, 264, 968.
62. Jang, S. B.; Baeyens, K.; Jeong, M. S.; SantaLucia, J., Jr.; Turner, D. H.; Holbrook, S. R. Acta Crystallogr. D 2004, 60, 829.
63. Jeffrey, G. A. An Introduction to Hydrogen Bonding; Oxford University Press, Inc.: New York, 1997, p12.
64. Chen, G.; Kennedy, S. D.; Qiao, J.; Krugh, T. R.; Turner, D. H. Biochemistry 2006, 45, 6889.
65. Strobel, S. A.; Ortoleva-Donnelly, L.; Ryder, S. P.; Cate, J. H.; Moncoeur, E. Nat. Struct. Biol. 1998, 5, 60-66.
66. Masquida, B.; Westhof, E. A modular and hierarchical approach for all-atom RNA modeling. In The RNA World, 3rd ed.; Gesteland, R. F., Cech, T. R., Atkins, J. F., Eds.; Cold Spring Harbor Laboratory Press: Woodbury, NY, 2005; p 659.
67. Nicholls, A.; Sharp, K. A.; Honig, B. Proteins 1991, 11, 281-296.
68. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollman, P. A. J. Am. Chem. Soc. 1993, 115, 9620-9631.
69. Lu, X. J.; Olson, W. K. Nucleic Acids. Res. 2003, 31, 5108-5121.
70. Schneider, C.; Suhnel, J. Biopolymers 1999, 50, 287.
71. Su, L.; Chen, L.; Egli, M.; Berger, J. M.; Rich, A. Nat. Stuct. Biol. 1999, 6, 285.
72. Burkard, M. E.; Kierzek, R.; Turner, D. H. J. Mol. Biol. 1999, 290, 967.