New information content in RNA base pairing deduced from quantitative analysis of high-resolution structures

Methods

Volumn 47, Issue 3, 2009, Pages 177-186

  Olson, Wilma K ^a   Esguerra, Mauricio ^a   Xin, Yurong ^a   Lu, Xiang Jun ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

Base interactions; Conformational analysis; Double helix; Model building; Non canonical base pairs; RNA structure

Indexed keywords

DOUBLE STRANDED RNA; NUCLEOTIDE; PHOSPHORUS;

ATOM; BASE PAIRING; CANONICAL ANALYSIS; CRYSTAL STRUCTURE; GEOMETRY; HYDROGEN BOND; METHODOLOGY; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVIEW; RNA ANALYSIS; RNA STRUCTURE; STRUCTURE ANALYSIS;

BASE PAIRING; DATABASES, NUCLEIC ACID; HYDROGEN BONDING; MICRORNAS; MODELS, MOLECULAR; RNA, DOUBLE-STRANDED;

EID: 59749092307     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2008.12.003     Document Type: Review

References (43)

1. Ambros V. Cell 107 (2001) 823-826
2. Griffiths-Jones S., Grocock R.J., van Dongen S., Bateman A., and Enright A.J. Nucleic Acids Res. 34 (2006) D140-D144
3. Mazière P., and Enright A.J. Drug Discov. Today 12 (2007) 452-458
4. Grimson A., Srivastava M., Fahey B., Woodcroft B.J., Chiang H.R., King N., Degnan B.M., Rokhsar D.S., and Bartel D.P. Nature 455 (2008) 1193-1197
5. Lewis B.P., Shih I.-H., Jones-Rhoades M.W., Bartel D.P., and Burge C.B. Cell 115 (2003) 787-798
6. Chu C.-Y., and Rana T.M. J. Cell. Physiol. 213 (2007) 412-419
7. Leontis N.B., Stombaugh J., and Westhof E. Nucleic Acids Res. 30 (2002) 3497-3531
8. Das R., and Bake D. Proc. Natl. Acad. Sci. USA 104 (2007) 14664-14669
9. Parisien M., and Major F. Nature 452 (2008) 51-55
10. Tolstorukov M.Y., Colasanti A.V., McCandlish D., Olson W.K., and Zhurkin V.B. J. Mol. Biol. 371 (2007) 725-738
11. Czapla L., Swigon D., and Olson W.K. J. Mol. Biol. 382 (2008) 353-370
12. Mukherjee S., Bansal M., and Bhattacharyya D. J. Comput. Aided Mol. Design 20 (2006) 629-645
13. Crick F.H.C. J. Mol. Biol. 19 (1966) 548-555
14. Saenger W. Principles of Nucleic Acid Structure (1984), Springer-Verlag, New York
15. Lu X.-J., and Olson W.K. Nucleic Acids Res. 31 (2003) 5108-5121
16. Lu X.-J., and Olson W.K. Nature Protocols 3 (2008) 1213-1227
17. Olson W.K., Bansal M., Burley S.K., Dickerson R.E., Gerstein M., Harvey S.C., Heinemann U., Lu X.-J., Neidle S., Shakked Z., Sklenar H., Suzuki M., Tung C.-S., Westhof E., Wolberger C., and Berman H.M. J. Mol. Biol. 313 (2001) 229-237
18. Dickerson R.E., Bansal M., Calladine C.R., Diekmann S., Hunter W.N., Kennard O., von Kitzing E., Lavery R., Nelson H.C.M., Olson W.K., Saenger W., Shakked Z., Sklenar H., Soumpasis D.M., Tung C.-S., Wang A.H.-J., and Zhurkin V.B. J. Mol. Biol. 208 (1989) 787-791
19. Lemieux S., and Major F. Nucleic Acids Res. 30 (2002) 4250-4263
20. Yang H., Jossinet F., Leontis N., Chen L., Westbrook J., Berman H., and Westhof E. Nucleic Acids Res. 31 (2003) 3450-3460
21. Das J., Mukherjee S., Mitra A., and Bhattacharyya D. J. Biomol. Struct. Dyn. 24 (2006) 149-161
22. Lu X.-J., Babcock M.S., and Olson W.K. J. Biomol. Struct. Dyn. 16 (1999) 833-843
23. Leontis N.B., and Westhof E. RNA 7 (2001) 499-512
24. Rose I.A., Hanson K.R., Wilkinson K.D., and Wimmer M.J. Proc. Natl. Acad. Sci. USA 77 (1980) 2439-2441
25. Lavery R., Zakrzewska K., Sun J.S., and Harvey S.C. Nucleic Acids Res. 20 (1992) 5011-5016
26. Hoogsteen K. Acta Crystallogr. 16 (1963) 907-916
27. Lu X.-J., Shakked Z., and Olson W.K. J. Mol. Biol. 300 (2000) 819-840
28. Berman H.M., Olson W.K., Beveridge D.L., Westbrook J., Gelbin A., Demeny T., Hsieh S.-H., Srinivasan A.R., and Schneider B. Biophys. J. 63 (1992) 751-759
29. Xin Y., and Olson W.K. Nucleic Acids Res. 37 (2009) D83-D88
30. Harms J., Schluenzen F., Zarivach R., Bashan A., Gat S., Agmon I., Bartels H., Franceschi F., and Yonath A. Cell 107 (2001) 679-688
31. Schmeing T.M., Huang K.S., Kitchen D.E., Strobel S.A., and Steitz T.A. Mol. Cell 20 (2005) 437-448
32. Schuwirth B.S., Day J.M., Hau C.W., Janssen G.R., Dahlberg A.E., Cate J.H.D., and Vila-Sanjurjo A. Nat. Struct. Mol. Biol. 13 (2006) 879-886
33. Selmer M., Dunham C.M., Murphy IV F.V., Weixlbaumer A., Petry S., Kelley A.C., Weir J.R., and Ramakrishnan V. Science 313 (2006) 1935-1942
34. Olson W.K., Gorin A.A., Lu X.-J., Hock L.M., and Zhurkin V.B. Proc. Natl. Acad. Sci. USA 95 (1998) 11163-11168
35. Watson J.D., and Crick F.H.C. Nature 171 (1953) 737-738
36. Lee J.C., and Gutell R.R. J. Mol. Biol. 344 (2004) 1225-1249
37. Turner D.H., Sugimoto N., and Freier S.M. Ann. Rev. Biophys. Biophys. Chem. 17 (1988) 167-192
38. Gorin A.A., Zhurkin V.B., and Olson W.K. J. Mol. Biol. 247 (1995) 34-48
39. Babcock M.S., and Olson W.K. J. Mol. Biol. 237 (1994) 98-124
40. McDowell J.A., and Turner D.H. Biochemistry 35 (1996) 14077-14089
41. Deng J., and Sundaralingam M. Nucleic Acids Res. 28 (2000) 4376-4381
42. Xu D., Landon T., Greenbaum N.L., and Fenley M.O. Nucleic Acids Res. 35 (2007) 3836-3847
43. François B., Russell R.J.M., Murray J.B., Aboul-ela F., Masquida B., Vicens Q., and Westhof E. Nucleic Acids Res. 33 (2005) 5677-5690