The jerky and knotty dynamics of RNA

Methods

Volumn 49, Issue 2, 2009, Pages 189-196

  Isambert, Hervé ^a  

^a INSTITUT CURIE   (France)

Author keywords

Entanglement; Non coding RNA; Pseudoknot; RNA folding dynamics; RNA self assembly; RNA simulation

Indexed keywords

RNA;

ARTICLE; MOLECULAR DYNAMICS; MOTION; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN FOLDING; RNA STABILITY; RNA STRUCTURE; RNA TRANSCRIPTION; SIMULATION;

BACILLUS SUBTILIS; BACTERIOPHAGES; BASE SEQUENCE; BIOPHYSICS; COMPUTER SIMULATION; ESCHERICHIA COLI; KINETICS; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA; RNA, BACTERIAL; RNA, VIRAL; STOCHASTIC PROCESSES; TRANSCRIPTION, GENETIC;

EID: 70349290546     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2009.06.005     Document Type: Article

References (77)

1. Uhlenbeck O.C. RNA 1 (1995) 4-6
2. Morgan S., and Higgs P.J. Chem. Phys. 105 (1996) 7152-7157
3. Craig M.E., Crothers D.M., and Doty P.J. Mol. Biol. 62 (1971) 383-401
4. Pörschke D. Biophys. Chem. 1 (1974) 381-386
5. Viasnoff V., Meller A., and Isambert H. Nano Lett. 6 (2006) 101-104
6. Mironov A.A., Dyakonova L.P., and Kister A.E.J. Biomol. Struct. Dynam. 2 (1985) 953-962
7. Isambert H., and Siggia E.D. Proc. Natl. Acad. Sci. USA 97 (2000) 6515
8. Xayaphoummine A., Bucher T., Thalmann F., and Isambert H. Proc. Natl. Acad. Sci. USA 100 (2003) 15310-15315
9. Xayaphoummine A., Bucher T., and Isambert H. Nucleic Acids Res. 33 (2005) 605-610
10. Gultyaev A.P. Nucleic Acids Res. 19 (1991) 2489-2494
11. Gultyaev A.P., van Batenburg F.H., and Pleij C.W. Nucleic Acids Res. 23 (1995) 3718-3725
12. Gultyaev A.P., van Batenburg F.H., and Pleij C.W.J. Mol. Biol. 276 (1998) 43-55
13. Nagel J.H., Gultyaev A.P., Gerdes K., and Pleij C.W. RNA 5 (1999) 1408-1418
14. Flamm C., Fontana W., Hofacker I.L., and Schuster P. RNA 6 (2000) 325-338
15. Waterman M.S., and Smith T.F. Math. Biosci. 42 (1978) 257-266
16. Nussinov R., Pieczenik G., Griggs J.R., and Kleitman D.J. SIAM J. Appl. Math. 35 (1978) 68-82
17. Nussinov R., and Jacobson A.B. Proc. Natl. Acad. Sci. USA 77 (1980) 7826-7830
18. Zuker M., and Stiegler P. Nucleic Acids Res. 9 (1981) 133-148
19. McCaskill J.S. Biopolymers 29 (1990) 1105-1119
20. Hofacker I.L., Fontana W., Stadler P.F., Bonhoeffer L.S., Tacker M., and Schuster P. Monatsh. Chem. 125 (1994) 167-188
21. Xayaphoummine A., Viasnoff V., Harlepp S., and Isambert H. Nucleic Acids Res. 35 (2007) 614622
22. Boyle J., Robillard G., and Kim S.J. Mol. Biol. 139 (1980) 601-625
23. Kramer F., and Mills D. Nucleic Acids Res. 9 (1981) 5109-5124
24. Nussinov R., and Tinoco Jr. I. J. Mol. Biol. 151 (1981) 519-533
25. Groeneveld H., Thimon K., and van Duin J. RNA 1 (1995) 79-88
26. Poot R.A., Tsareva N.V., Boni I.V., and van Duin J. Proc. Natl. Acad. Sci. USA 94 (1997) 10110-10115
27. Gerdes K., Gultyaev A.P., Franch T., Pedersen K., and Mikkelsen N.D. Annu. Rev. Genet. 31 (1997) 1-31 review
28. Gultyaev A.P., Franch T., and Gerdes K.J. Mol. Biol. 273 (1997) 26-37
29. Franch T., Gultyaev A.P., and Gerdes K.J. Mol. Biol. 273 (1997) 38-51
30. Repsilber D., Wiese S., Rachen M., Schroder A., Riesner D., and Steger G. RNA 5 (1999) 574-584
31. Pan T., Artsimovitch I., Fang X., Landick R., and Sosnick T.R. Proc. Natl. Acad. Sci. USA 96 (1999) 9545-9550
32. Heilman-Miller S.L., and Woodson S.A. RNA 9 (2003) 722-733
33. Koduvayur S.P., and Woodson S.A. RNA 10 (2004) 1526-1532
34. Wickiser J.K., Winkler W.C., Breaker R.R., and Crothers D.M. Mol. Cell 18 (2005) 49-60
35. Mahen E.M., Harger J.W., Calderon E.M., and Fedor M.J. Mol. Cell 19 (2005) 27-37
36. Pan T., and Sosnick T. Annu. Rev. Biophys. Biomol. Struct. 35 (2006) 161-175
37. Chamberlin M., and Ring J. J. Biol. Chem. 248 (1973) 2235-2244
38. Harlepp S., Marchal T., Robert J., Léger J.-F., Xayaphoummine A., Isambert H., and Chatenay D. Eur. Phys. J. E12 (2003) 605-615
39. Abrahams J.P., van den Berg M., van Batenburg E., and Pleij C.W.A. Nucleic Acids Res. 18 (1990) 3035-3044
40. Rivas E., and Eddy S.R. J. Mol. Biol. 285 (1999) 2053-2068
41. Akutsu T. Discrete Appl. Math. 104 (2000) 45-62
42. Lyngsø R., and Pedersen C.J. Comput. Biol. 7 (2000) 409-427
43. Dirks R., and Pierce N.A. J. Comput. Chem. 24 (2003) 1664
44. Ruan J., Stormo G., and Zhang W. Bioinformatics 20 (2004) 58-66
45. Martinez H.M. Methods Enzymol./ 183 (1990) 306-318
46. Mironov A.A., and Lebedev V.F. BioSystems 30 (1993) 4956
47. Gultyaev A.P., van Batenburg E., and Pleij C.W.A. RNA 5 (1999) 60961
48. Aalberts D.P., and Hodos N.O. Nucleic Acids Res. 33 (2005) 2210-2214
49. Cao S., and Chen S.-J. Nucleic Acids Res. 34 (2006) 2634-2652
50. Dawson W.K., Fujiwara K., and Kawai G. PLoS ONE 2 (2007) e905
51. Conway J.H. In: Leech J. (Ed). Computation Problems in Abstract Algebra (1967), Pergamon Press, Oxford 329-358
52. Dawid A., Cayrol B., and Isambert H. RNA synthetic biology inspired from bacteria: construction of transcription attenuators under antisense regulation. Phys. Biol. 6 2 (2009) 25007
53. B. Cayrol, C. Nogues, A. Dawid, I. Sagi, P. Silberzan, H. Isambert, A novel nanostructure made of bacterial non-coding RNA, submitted for publication.
54. Putzer H., Condon C., Brechemier-Baey D., Brito R., and Grunberg-Manago M. Transfer RNA-mediated antitermination in vitro. Nucleic Acids Res. 30 (2002) 3026-3033
55. Grundy F.J., Winkler W.C., and Henkin T.M. Proc. Natl. Acad. Sci. USA 99 (2002) 11121-11126
56. Penchovsky R., and Breaker R.R. Nat. Biotechnol. 23 (2005) 1424-1433
57. Yang X., Wenzler L.A., Qi J., Li X., and Seeman N.C. J. Am. Chem. Soc. 120 (1998) 9779-9786
58. Winfree E., Liu F., Wenzler L.A., and Seeman N.C. Nature 394 (1998) 539-544
59. Mao C., sun W., and Seeman N.C. J. Am. Chem. Soc. 121 (1999) 5437-5443
60. Feng L., Park S.H., Reif J.H., and Yan H. Angew. Chem. Int. Ed. Engl. 42 (2003) 4342-4346
61. Rothemund P.W.K., et al. J. Am. Chem. Soc. 126 (2004) 16344-16352
62. Rothemund P.W.K., Papadakis N., and Winfree E. PLoS Biol. 2 (2004) e424
63. Chelyapov N., et al. J. Am. Chem. Soc. 126 (2004) 13924-13925
64. Ding B., Sha R., and Seeman N.C. J. Am. Chem. Soc. 126 (2004) 10230-10231
65. Shih W.M., Quispe J.D., and Joyce G.F. Nature 427 (2004) 618-621
66. Liu H., Chen Y., He Y., Ribbe A.E., and Mao C. Angew. Chem. Int. Ed. Engl. 45 (2006) 1942-1945
67. Ding B., and Seeman N.C. Science 314 (2006) 1583-1585
68. Schulman R., and Winfree E. Proc. Natl. Acad. Sci. USA 104 (2007) 15236-15241
69. He Y., et al. Nature 452 (2008) 198-201
70. Yin P., Choi H.M.T., Calvert C.R., and Pierce N.A. Nature 451 (2008) 318-322
71. Yin P., et al. Science 321 (2008) 824-826
72. Jaeger L., and Leontis N.B. Angew. Chem. Int. Ed. Engl. 39 (2000) 2521-2524
73. Chworos A., et al. Science 306 (2004) 2068-2072
74. Shu D., Moll W.-D., Deng Z., Mao C., and Guo P. Nano Lett. 4 (2004) 1717-1723
75. Nasalean L., Baudrey S., Leontis N.B., and Jaeger L. Nucleic Acids Res. 34 (2006) 1381-1392
76. Seeman N.C. J. Theor. Biol. 99 (1982) 237-247
77. Dirks R.M., Lin M., Winfree E., and Pierce N.A. Nucleic Acids Res. 32 (2004) 1392-1403