Molecular dynamics studies of trinucleotide repeat dna involved in neurodegenerative disorders

Journal of Biomolecular Structure and Dynamics

Volumn 19, Issue 3, 2001, Pages 479-495

  Jithesh, P V ^a   Singh, Prachi ^b   Joshi, Rajendra R ^a  

^a CENTRE FOR DEVELOPMENT OF ADVANCED COMPUTING   (India)

^b UNIVERSITY OF PUNE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BASE PAIRING; DEGENERATIVE DISEASE; DNA CONFORMATION; DNA SEQUENCE; DNA STRUCTURE; GENE LOCUS; GENE MUTATION; MOLECULAR DYNAMICS; MYOCLONUS EPILEPSY; NUCLEIC ACID BASE SUBSTITUTION; PATHOGENESIS; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; TRINUCLEOTIDE REPEAT;

EID: 0035702197     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2001.10506756     Document Type: Article

References (72)

1. Saenger, W., 1984. Principles of Nucleic Acid Structure New York:Springer-Verlag.
2. Blackburn, G. M., and Gait, M. J., 1990. Nucleic acids in chemistry and biology Oxford:IRL Press.
3. Beveridge, D. L., and McConnell, K. J., 2000. Curr. Opin. Struct. Biol., 10:182–196.
4. Sutherland, G. R., and Richards, R. I., 1995. Proc. Natl. Acad. Sci. USA, 92:3636–3641.
5. Wells, R. D., 1996. J. Biol. Chem., 271:2875–2878.
6. Singer, R. H., 1996. Mol. Med. Today,:65–69.
7. Mitas, M., 1997. Nucleic Acids Res., 25:2245–2253.
8. Pearson, C. E., and Sinden, R. R., 1998. Curr. Opin. Struct. Biol., 8:321–330.
9. McMurray, C. T., 1999. Proc. Natl. Acad. Sci. USA, 96:1823–1825.
10. Sinden, R. R., 1999. Am. J. Hum. Genet., 64:346–353.
11. Cummings, C. J., and Zoghbi, H. Y., 2000. Hum. Mol. Genet., 9:909–916.
12. Smith, G. K., Jie, J., Fox, G. E., and Gao, X., 1995. Nucleic Acids Res., 23:4303–4311.
13. Petruska, J., Arnheim, N., and Goodman, M. F., 1996. Nucleic Acids Res., 24:1992–1998.
14. Zheng, M., Huang, X., Smith, G. K., Yang, X., and Gao, X., 1996. J. Mol. Biol., 264:323–336.
15. Bacolla, A., Gellibolian, R., Shimizu, M., Amirhaeri, S., Kang, S., Ohshima, K., Larson, J. E., Harvey, S., Stollar, B. D., and Wells, R. D., 1997. J. Mol. Biol., 272:16783–16792.
16. Ohshima, K., and Wells, R. D., 1997. J. Biol. Chem., 272:16798–16806.
17. Petruska, J., Hartenstine, M. J., and Goodman, M. F., 1998. J. Biol. Chem., 273:5204–5210.
18. Chastain, P. D., and Sinden, R. R., 1998. J. Mol. Biol., 275:405–411.
19. Kettani, A., Bouaziz, S., Skripkin, E., Majumdar, A., Wang, W., Jones, R. A., and Patel, D. J., 1999. Structure, 7:803–815.
20. Bhattacharyya, D., Kundu, S., Thakur, A. R., and Majumdar, R., 1999. J. Biomol. Struct. Dynam., 17:289–300.
21. Ohshima, K., Kang, S., Larson, J. E., and Wells, R. D., 1996. J. Biol. Chem., 271:16773–16783.
22. Wells, R. D., Parniewski, P., Pluciennik, A., Bacolla, A., Gellibolian, R., and Jaworski, A., 1998. J. Biol. Chem., 273:19532–19541.
23. Iyer, R. R., and Wells, R. D., 1999. J. Biol. Chem., 274:3865–3877.
24. Jakupciak, J. P., and Wells, R. D., 1999. J. Biol. Chem., 274:23468–23479.
25. Moore, H., Greenwell, P. W., Liu, C., Arnheim, N., and Petes, T. D., 1999. Proc. Natl. Acad. Sci. USA, 96:1504–1509.
26. Baldi, P., Brunak, S., Chauvin, Y., and Pedersen, A. G., 1999. Bioinformatics, 15:918–929.
27. Pearson, C. E., Eichler, E. E., Lorenzetti, D., Kramer, S. F., Zoghbi, H. Y., Nelson, D. L., and Sinden, R. R., 1998. Biochemistry, 37:2701–2708.
28. Jeffreys, A. J., 1997. Clin. Sci., 93:383–390.
29. Lalioti, M. D., Buresi, H. S., Rossier, C., Bottani, A., Morris, M. A., Malafosse, A., and Antonarakis, S. E., 1997. Nature, 386:847–851.
30. Lalioti, M. D., Scott, H. S., Genton, P., Grid, D., Ouazzani, R., M'Rabet, A., Ibrahim, S., Gouider, R., Dravet, C., Chkili, T., Bottani, A., Buresi, C., Malafose, A., and Antonarakis, S. E., 1998. Am. J. Hum. Genet., 62:842–847.
31. Feig, M., and Pettitt, B. M., 1998. Biophys. J., 75:134–149.
32. Tieleman, D. P., Sansom, M. S. P., and Berendsen, H. J. C., 1999. Biophys. J., 76:40–49.
33. Dobson, C. M., and Karplus, M., 1999. Curr. Opin. Struct. Biol., 9:92–101.
34. Lu, H., and Schulten, K., 2000. Biophys. J., 79:51–65.
35. Sprous, D., Young, M. A., and Beveridge, D. L., 1999. J. Mol. Biol., 285:1623–1632.
36. Konerding, D. E., Cheatham, T. E., III, Kollman, P. A., and James, T. L., 1999. J. Biomol. NMR, 13:119–131.
37. Chowdhury, S., and Bansal, M., 2000. J. Biomol. Struct. Dynam., 17:11–28.
38. Bevan, D. R., Li, L., Pedersen, L. G., and Darden, T. A., 2000. Biophys. J., 78:668–682.
39. Sherer, E. C., Harris, S. A., Soliva, R., Orozco, M., and Laughton, C. A., 1999. J. Am. Chem. Soc., 121:5981–5991.
40. Barsky, D., Foloppe, N., Ahmadia, S., Wilson, D. M., III and MacKerell, A. D., Jr. 2000. Nucleic Acids Res., 28:2613–2626.
41. Norberto de Souza, O., and Ornstein, R. L., 1998. Biopolymers, 46:403–415.
42. Kolaskar, A. S., and Joshi, R. R., 1998. J. Biomol. Struct. Dynam., 15:1155–1165.
43. Beveridge, D. L., and Ravishanker, G., 1994. Curr. Opin. Struct. Biol., 4:246–255.
44. Darden, T., York, D., and Pedersen, L., 1993. J. Chem. Phys., 98:10089–10092.
45. Darden, T., Perera, L., Li, L., and Pedersen, L., 1999. Structure, 7:R55–R60.
46. Essman, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G., 1995. J. Chem. Phy., 103:8577–8593.
47. Norberto de Souza, O., and Ornstein, R. L., 1997. Biophys. J., 72:2395–2397.
48. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Jr, Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A., 1995. J. Am. Chem. Soc., 117:5179–5197.
49. Cheatham, T. E., III, Cieplak, P., and Kollman, P. A., 1999. J. Biomol. Struct. Dynam., 16:845–862.
50. Foloppe, N., and MacKerell, A. D., Jr. 2000. J. Comput. Chem., 21:86–104.
51. MacKerell, A. D., Jr. and Banavali, N. K., 2000. J. Comput. Chem., 21:105–120.
52. Daura, X., Mark, A. E., and van Gunsteren, W. F., 1998. J. Comput. Chem., 19:535–547.
53. Srinivasan, J., Cheatham, T. E., III, Cieplak, P., Kollman, P. A., and Case, D. A., 1998. J. Am. Chem. Soc., 120:9401–9409.
54. Jayaram, B., Sprous, D., Young, M. A., and Beveridge, D. L., 1998. J. Am. Chem. Soc., 120:10629–10633.
55. Vincent, J. J., and Merz, K. M., Jr. 1995. J. Comp. Chem., 16:1420–1427.
56. Crowley, M. F., Darden, T. A., Cheatham, T. E., III and Deerfield, D. W., II. 1997. J. Supercomp., 11:255–278.
57. Duan, Y., and Kollman, P. A., 1998. Science, 282:740–744.
58. Dagget, V., 2000. Curr. Opin. Struct. Biol., 10:160–164.
59. Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., III, DeBolt, S., Ferguson, D., Seibel, G., and Kollman, P., 1995. Comp. Phys. Commun., 91:1–41.
60. Case, A., Pearlman, D. A., Caldwell, J. W., Cheatham, T. E., III, Ross, W. S., Simmerling, C. L., Darden, T. A., Merz, K. M., Stanton, R. V., Cheng, A. L., Vincent, J. J., Crowley, M., Ferguson, D. M., Radmer, R. J., Seibel, G. L., Singh, U. C., Weiner, P. K., and Kollman, P. A., 1997. AMBER, 5 University of California, San Francisco
61. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L., 1983. J. Chem. Phys., 79:926–936.
62. Cheatham, T. E., III. Tutorial on AMBER web page. available at:http://www.amber.ucsf.edu/amber/tutorial/polyA-polyT/index.html
63. van Gunsteren, W. F., and Berendsen, H. J. C., 1977. Mol. Phys., 34:1311–1327.
64. Laaksonen, L., gOpenMol available at:http://www.csc.fi/~laaksone/gopenmol/gopenmol.html
65. Lavery, R., and Sklenar, H., 1989. J. Biomol. Struct. Dynam., 6:655–667.
66. Lavery, R., and Sklenar, H., 1996. Curves 5.1:Helical analysis of irregular nucleic acids edit. 5.1. Laboratoire de Biochimic Theorique, CNRS URA 77 Paris, France:Institut de Biologie Physico—Chimique.
67. Toh, K., plotMTV available at:ftp://ftp.x.org/contrib/applications
68. Kang, S., Ohshima, K., Shimizu, M., Amirhaeri, S., and Wells, R. D., 1995. J. Biol. Chem., 270:27014–27021.
69. Chastain, P. D., Eichler, E. E., Kang, S., Nelson, D. L., Levene, S. D., and Sinden, R. R., 1995. Biochemistry, 34:16125–16131.
70. Hassan, M. A.E., and Calladine, C. R., 1996. J. Mol. Biol., 259:95–103.
71. Ohshima, K., Kang, S., and Wells, R. D., 1996. J. Biol. Chem., 271:1853–1856.
72. Wang, Y. H., Gellibolian, R., Shimizu, M., Wells, R. D., and Griffith, J. D., 1996. J. Mol. Biol., 263:511–516.