Molecular dynamics simulations of xDNA

Biopolymers

Volumn 91, Issue 5, 2009, Pages 351-360

  Varghese, Mathew K ^a   Thomas, Renjith ^b   Unnikrishnan, N V ^a   Sudarsanakumar, C ^a  

^a MAHATMA GANDHI UNIVERSITY   (India)

^b ST BERCHMANS COLLEGE   (India)

Author keywords

Expanded bases; MD; Modified DNA; Stability; xDNA

Indexed keywords

AMBER FORCE-FIELD; BASE-PAIRING; DOUBLE-HELICAL STRUCTURES; EXPANDED BASES; EXPLICIT SOLVENTS; GROOVE WIDTH; HELICAL PARAMETERS; IDEAL GEOMETRY; MD; MINOR GROOVES; MODIFIED DNA; MOLECULAR DYNAMICS SIMULATIONS; NATURAL BASIS; NMR STRUCTURES; REDUCED MINORS; STACKING INTERACTION; SUGAR PUCKER; TORSION ANGLE; XDNA;

BENZENE; DNA; DYNAMICS; MOLECULAR DYNAMICS; NUCLEIC ACIDS; STRUCTURAL DYNAMICS; SUGAR (SUCROSE); SUGARS; GENES;

GENES; NUCLEIC ACIDS;

DNA; ALANINE; DNA A; DNA B; GLYCINE; THREONINE; UNCLASSIFIED DRUG; XDNA;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; DNA HELIX; DNA MODIFICATION; DNA STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR MODEL; CONFORMATIONAL TRANSITION; DNA BASE COMPOSITION; DNA CONFORMATION; DNA DETERMINATION; DNA SEQUENCE; GEOMETRY; HYDRATION; HYDROGEN BOND; INTERACTIONS WITH DNA; MOLECULAR INTERACTION; MOLECULAR STABILITY; NUCLEAR MAGNETIC RESONANCE; SIMULATION; STRUCTURE ANALYSIS;

BASE SEQUENCE; CARBOHYDRATES; DNA; HYDROGEN BONDING; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; WATER;

EID: 67749137255     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.21137     Document Type: Article

References (48)

1. Benner, S. A. Nature 2003, 421, 118-118.
2. Rawls, R. Chem Eng News 2000, 78, 49-53.
3. Brabec, V.; Vrana, O.; Kiseleva, V. I.; Poverenny, A. M. Eur J Biochem 1991, 201, 723-730.
4. Milligan, J. F.; Matteucci, M. D.; Martin, J. C. J Med Chem 1993, 36, 1923-1937.
5. Elgi, M.; Pallan, P. S. Ann Rev Biophys Biomol Struct 2007, 36, 281-305.
6. Dallas, A.; Vlassov, A. V. Med Sci Monit 2006, 12, RA67-RA74.
7. Stauffiger, A.; Leumann, C. J. Nuclios Nucleot Nucleic Acids 2007, 26, 615-619.
8. McLaugin, L. W.; Wilson, M.; Ha, S. B. Comprehensive Natural Products Chemistry; Kool, E. T., Ed.; Elsevier press: Oxford, UK, 1999; Vol. VII, Chapter 8.
9. Earnshaw, D. J.; Gait, M. J. Biopolymers 1998, 48, 39-55.
10. Teplova, M.; Wilds, C. J.; Wawrzak, Z.; Tereshko, V.; Du, Q.; Carrasco, N.; Huang, Z.; Egli, M. Biochimie 2002, 84, 849-858.
11. Endres, R. G.; Cox, D. L.; Singh, R. R. P. Rev Mod Phys 2004, 76, 195-214.
12. Seeman, N. C. Biochemistry 2003, 42, 7259-7269.
13. Fuentes-Cabrera, M.; Zhao, X.; Kent, P. H. C.; Sumpter, B. G. J Phys Chem B 2007, 111, 9057-9061.
14. Lynch, S. R.; Liu, H.; Gao, J.; Kool E. T. J Am Chem Soc 2006, 128, 14704-14711.
15. Liu, H.; Lynch, S. R.; Kool, E. T. J Am Chem Soc 2004, 126, 6900-6905.
16. Lee, A. H. F.; Kool, E. T. J Org Chem 2005, 70, 132-140.
17. Kruger, A. T.; Lu, H.; Lee, A. H.; Kool, E. T. Acc Chem Res 2007, 40, 141-150.
18. McConnel, T. L.; Wetmore, S. D. J Phys Chem B 2007, 111, 2999-3009.
19. Fauntes-Cabrera, M.; Sumpter, B. G.; Wells, J. C. J Phys Chem B 2005, 109, 21135-21139.
20. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Wang, B.; Pearlman, D. A.; Crowley, M.; Brozell, S.; Tsui, V.; Gohlke, H.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Schafmeister, C.; Caldwell, J. W.; Ross, W. S.; Kollman, P. A. AMBER 8; University of California: San Francisco, 2004.
21. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. R., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1995, 117, 5179-5197.
22. Wang, J.; Cieplak, P.; Kollman, P. A. J Comp Chem 2000, 21, 1049-1074.
23. Aduri, R.; Psciuk, B. T.; Saro, P.; Taniga, H.; Schlegel, H. B.; SantaLucia, J., Jr. J Chem Theory Comput 2007, 3, 1464-1475.
24. Bernstein, F. C.; Koetzle, T. F.; Williams, G. J. B.; Meyer, E. F., Jr.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. J Mol Biol 1977, 112, 535-542.
25. Bayley, C. I.; Cieplak, P.; Cornell, W.; Kollman, P. A. J Phys Chem 1993, 97, 10269-10280.
26. Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A. J Mol Graph Model 2006, 25, 247-260.
27. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Andres, J. L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98, Revision A. 6 Gaussian, Inc.: Pittsburgh, PA, 1998.
28. Bessler, B. H.; Merz, K. M., Jr.; Kollman, P. A. J Comp Chem 1990, 11, 431-439.
29. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J Chem Phys 1983, 79, 926-935.
30. Darden, T.; Perera, L.; Li, P.; Penderson, L. Structure 1999, 7,R55-R60.
31. Darden, T.; York, D.; Penderson, L. J Chem Phys 1993, 98, 10089-10092.
32. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J Comp Phys 1977, 23, 327-341.
33. Pastor, R. W.; Brooks, B. R.; Szabo, A. Mol Phys 1988, 65, 1409-1419.
34. Auffinger, P.; Westhof, E. J Mol Biol 2000, 300, 1113-1131.
35. Humphrey, W.; Dalke, A.; Schulten, K. J Mol Graph 1996, 14, 33-38.
36. Feig, M.; Karanicolas, J.; Brooks, C. L., III. J Mol Graph Model 2004, 22, 377-395.
37. Lu, X.-J.; Olsen, W. K. Nucleic Acids Res 2003, 31, 5108-5121.
38. Xiong, Y.; Sundaralingam, M. Structure 1998, 6, 1493-1501.
39. Lavery, R.; Zakrzeweska, K. In Base and Base Pair Morphologies, Helical Parameters, and Definitions. Oxford Handbook of Nucleic Acid structure; Neidle, S., Ed.; Oxford University Press, New York, 2003.
40. Sudarsanakumar, C.; Xiong, Y.; Sundaralingam, M. J Mol Biol 2000, 299, 103-112.
41. Dickerson, A. E. Methods Enzymol 1992, 211, 67-111.
42. Reichert, J.; Jabs, A.; Slickers, P.; Suhnel, J. Nucleic Acids Res 2000, 28, 246-249.
43. Olson, W. K. Nucleic Acids Res 1982, 10, 777-787.
44. Lu, X.-J.; Shakked, Z.; Olson, W. K. J Mol Biol 2000, 300, 819-840.
45. Suzuki, M.; Yagi, N. J Mol Biol 1996, 255, 677-687.
46. Vargason, J. M.; Henderson, K.; Ho, P. S. PNAS 2001, 98, 7265-7270.
47. Berger, I.; Tereshko, V.; Ikeda, H.; Marquez, V. E.; Egli, M. Nucleic Acids Res 1998, 26, 2473-2480.
48. Gao, H. L. J.; Kool, E. T. J Org Chem 2005, 70, 639-647.