The effect of salt concentration on DNA conformation transition: A molecular-dynamics study

Journal of Molecular Modeling

Volumn 12, Issue 3, 2006, Pages 249-254

  Song, Chen ^a   Xia, Yueyuan ^a   Zhao, Mingwen ^a   Liu, Xiangdong ^a   Li, Feng ^a   Ji, Yanju ^a   Huang, Boda ^a   Yin, Yanyan ^a  

^a SHANDONG UNIVERSITY   (China)

Author keywords

DNA conformation transition; Minor groove width; Molecular dynamics simulation; Salt concentration; Sugar pucker

Indexed keywords

DNA A; DNA B; SODIUM CHLORIDE;

ARTICLE; COMPUTER PROGRAM; CONCENTRATION RESPONSE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DNA CONFORMATION; DNA STRUCTURE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; SIMULATION; STRUCTURE ANALYSIS;

CARBOHYDRATES; DNA; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; SODIUM CHLORIDE;

EID: 33644750628     PISSN: 16102940     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00894-005-0023-9     Document Type: Article

References (24)

1. Kubinec MG, Wemmer DE (1992) J Am Chem Soc 114:8739-8740
2. Rau DC, Parsegian A (1992) Biophys J 61:246-259
3. Urabe H, Kato M, Tominaga Y (1990) J Chem Phys 92:768-774
4. Forester TR, McDonald IR (1991) Mol Phys 72:643-660
5. Feig M, Pettitt BM (1999) Biophys J 77:1769-1781
6. Nishimura Y, Torigoe C, Tsuboi M (1986) Nucleic Acids Res 14:2737-2748
7. Misra VK, Sharp KA, Friedman RA, Honig BJ (1994) J Mol Biol 238:245-263
8. Wang Y, Thomas GA, Peticolas WL (1989) J Biomol Struct Dyn 6:1177-1187
9. Rinkel LJ, Sanderson MR, van der Marel GA, Altona C (1986) Eur J Biochem 159:85-93
10. Wolk S, Thurmes WN, Ross WS, Hardin CC, Tinoco I (1989) Biochemistry 28:2452-2459
11. Cheatham TE III, Kollman PA (1996) J Mol Biol 259:434-444
12. Mazur AK (2003) J Am Chem Soc 125:7849-7859
13. Tsui V, Case DA (2000) J Am Chem Soc 122:2489-2498
14. Real AN, Greenall RJ (2000) J Mol Model 6:654-658
15. Hud NV, Polak M (2001) Curr Opin Struc Biol 11:293-301
16. McConnell KJ, Beveridge DL (2000) J Mol Biol 304:803-820
17. Young MA, Jayaram B, Beveridge DL (1997) J Am Chem Soc 119:59-69
18. Lavery R, Sklenar HJ (1989) J Biomol Struct Dynam 6:63-91
19. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz Jr KM, Ferguson DM, Spelleyer DC, Fox T, Caldwell JW, Kollman PA (1996) J Am Chem Soc 117:5179-5197
20. Feig M, Pettitt BM (1997) J Phys Chem B 101:7361-7363
21. Feig M, Pettitt BM (1998) Biophys J 75:134-149
22. Cheatham TE III, Crowley MF, Fox T, Kollman PA (1997) Proc Natl Acad Sci USA 94:9626-9630
23. Cheatham TE III, Kollman PA (1997) Structure 5:1297-1311
24. Cheatham TE III, Young MA (2001) Biopolymers 56:232-256