A novel RNA motif based on the structure of unusually stable 2′,5′-linked r(UUCG) loops

Journal of the American Chemical Society

Volumn 125, Issue 38, 2003, Pages 11525-11531

  Denisov, Alexei Yu ^a   Hannoush, Rami N ^a,b   Gehring, Kalle ^a   Damha, Masad J ^a  

^a MCGILL UNIVERSITY   (Canada)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPOSITION; DNA; THERMODYNAMIC STABILITY;

NUCLEOTIDES;

RNA;

APTAMER; CARBOHYDRATE; COMPLEMENTARY RNA; CYTOSINE; DNA; GUANINE; NUCLEOTIDE; RIBOZYME; RNA; SOLVENT; URACIL;

ARTICLE; BASE PAIRING; CHEMICAL BOND; MOLECULAR INTERACTION; RNA CONFORMATION; RNA SEQUENCE; RNA STABILITY; RNA STRUCTURE; THERMODYNAMICS;

BASE SEQUENCE; CARBOHYDRATE CONFORMATION; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; RNA;

EID: 0141757449     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja036207k     Document Type: Article

References (39)

1. Varani, G. Annu. Rev. Biophys. Biomol. Struct. 1995, 24, 379-404.
2. Tinoco, I., Jr.; Puglisi, J. D.; Wyatt, J. R. Nucleic Acids Mol. Biol. 1990, 4, 206-226.
3. Heaphy, S.; Dingwall, C.; Ernberg, I.; Gait, M. J.; Green, S. M.; Karn, J.; Lowe, A. D.; Singh, M.; Skinner, M. A. Cell 1990, 60, 685-693.
4. Leulliot, N.; Varani, G. Biochemistry 2001, 40, 7947-7956.
5. Perez-Ruiz, M.; Sievers, D.; Garcia-Lopez, P. A.; Berzal-Herranz, A. Antisense Nucleic Acid Drug Dev. 1999, 9, 33-42.
6. Lee, A. J.; Crothers, D. M. Structure 1998, 6, 993-1005.
7. Tuerk, C.; Gauss, P.; Thermes, C.; Groebe, D. R.; Gayle, M.; Guild, N.; Stormo, G.; d'Aubenton-Carafa, Y.; Uhlenbeck, O. C.; Tinoco, I., Jr.; Brody, E. N.; Gold, L. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 1364-1368.
8. Adams, C. C.; Stern, D. B. Nucleic Acids Res. 1990, 18, 6003-6010.
9. Khan, I. M.; Coulson, J. M. Nucleic Acids Res. 1993, 21, 2957-2958.
10. Woese, C. R.; Winker, S.; Gutell, R. R. Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 8467-8471.
11. Antao, V. P.; Lai, S. Y.; Tinoco, I., Jr. Nucleic Acids Res. 1991, 19, 5901-5905.
12. Antao, V. P.; Tinoco, I., Jr. Nucleic Acids Res. 1992, 20, 819-824.
13. Serra, M. J.; Lyttle, M. H.; Axenson, T. J.; Schadt, C. A.; Turner, D. H. Nucleic Acids Res. 1993, 21, 3845-3849.
14. Cheong, C.; Varani, G.; Tinoco, I., Jr. Nature 1990, 346, 680-682.
15. Varani, G.; Cheong, C.; Tinoco, I., Jr. Biochemistry 1991, 30, 3280-3289.
16. Allain, F. H. T.; Varani, G. J. Mol. Biol. 1995, 250, 333-353.
17. Comolli, L. R.; Ulyanov, N. B.; Soto, A. M.; Marky, L. A.; James, T. L.; Gmeiner, W. H. Nucleic Acids Res. 2002, 30, 4371-4379.
18. Hannoush, R. N.; Damha, M. J. J. Am. Chem. Soc. 2001, 123, 12368-12374.
19. Hannoush, R. N.; Damha, M. J. Nucleosides Nucleotides 2001, 20, 1201-1204.
20. Premraj, B. J.; Patel, P. K.; Kandimalla, E. R.; Agrawal, S.; Hosur, R. V.; Yathindra, N. Biochem. Biophys. Res. Commun. 2001, 283, 537-543.
21. Wasner, M.; Arion, D.; Borkow, G.; Noronha, A.; Uddin, A. H.; Parniak, M. A.; Damha, M. J. Biochemistry 1998, 37, 7478-7486.
22. Kierzek, R.; He, L.; Turner, D. H. Nucleic Acids Res. 1992, 20, 1685-1690.
23. Giannaris, P. A.; Damha, M. J. Nucleic Acids Res. 1993, 21, 4742-4749.
24. Vargeese, C.; Carter, J.; Yegge, J.; Krivjansky, S.; Settle, A.; Kropp, E.; Peterson, K.; Pieken, W. Nucleic Acids Res. 1998, 26, 1046-1050.
25. Gasparutto, D.; Livache, T.; Bazin, H.; Duplaa, A. M.; Guy, A.; Khorlin, A.; Molko, D.; Roget, A.; Teoule, R. Nucleic Acids Res. 1992, 20, 5159-5166.
26. Damha, M. J.; Ogilvie, K. K. Methods Mol. Biol. 1993, 20, 81-114.
27. Trempe, J. F.; Wilds, C. J.; Denisov, A. Y.; Pon, R. T.; Damha, M. J.; Gehring, K. J. Am. Chem. Soc. 2001, 123, 4896-4903.
28. Denisov, A. Y.; Noronha, A. M.; Wilds, C. J.; Trempe, J. F.; Pon, R. T.; Gehring, K.; Damha, M. J. Nucleic Acids Res. 2001, 29, 4284-4293.
29. Brünger, A. T. X-PLOR 3.1, A system for X-ray crystallography and NMR; Yale University Press: New Haven, CT, 1992.
30. James, J. K.; Tinoco, I., Jr. Nucleic Acids. Res. 1993, 21, 3287-3293.
31. Lavery, R.; Sklenar, H. CURVES 5.2, Helical analysis of irregular nucleic acids; Laboratory de Biochimie Theorique, CNRS URA 77: Paris, 1997.
32. Wüthrich, K. NMR of protein and nucleic acids; John Wiley & Sons: New York, 1986.
33. de Leeuw, F. A. A. M.; Altona, C. Quantum chemistry program exchange, No.463: PSEUROT 3B; Indiana University: Bloomington, IN, 1983.
34. Saenger, W. Principles of nucleic acids structure; Springer-Verlag: New York, 1984.
35. Kim, S. G.; Lin, L. J.; Reid, B. R. Biochemistry 1992, 31, 3564-3574.
36. van Wijk, J.; Huckriede, B. D.; Ippel, J. H.; Altona, C. Methods Enzymol. 1992, 211, 286-306.
37. Rinkel, L. J.; Altona, C. J. Biomol. Struct. Dyn. 1987, 4, 621-649.
38. Heus, H. A.; Pardi, A. Science 1991, 253, 191-194.
39. Premraj, B. J.; Yathindra, N. J. Biomol. Struct. Dyn. 1998, 16, 313-328.