Orientation of DNA on a Surface from Simulation

Biopolymers

Volumn 73, Issue 5, 2004, Pages 570-578

  Wong, Ka Yiu ^a   Pettitt, B Montgomery ^a  

^a University of Houston   (United States)

Author keywords

DNA chip; DNA orientation; Hybridization; Molecular dynamics

Indexed keywords

COATING TECHNIQUES; MOLECULAR DYNAMICS; SILANES;

HELICAL PARAMETERS; HYBRIDIZATIONS;

DNA;

ARTICLE; CALCULATION; DNA CONFORMATION; DNA MICROARRAY; HYBRIDIZATION; MOLECULAR DYNAMICS; SURFACE PROPERTY;

COMPUTER SIMULATION; DNA; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SURFACE PROPERTIES;

EID: 1842632558     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/bip.20004     Document Type: Article

References (36)

1. Heller, M. J. Annu Rev Biomed Eng 2002, 4, 129-153.
2. Rampal, J. B., Ed. Methods in Molecular Biology. Vol. 170: DNA Arrays: Methods and Protocols; Humana: Totowa, NJ, 2001.
3. Duggan, D. J.; Bittner, M.; Chen, Y.; Meltzer, P.; Trent, J. M. Nature Genet 1999, 21, 10-14.
4. Debouck, C.; Goodfellow, P. N. Nature Genet 1999, 21, 48-50.
5. Rusling, J. F., Ed. Biomolecular Films: Design, Function, and Applications: Marcel Dekker, New York, 2003.
6. Kelley, S. O.; Barton, J. K.; Jackson, N. M.; McPherson, L. D.; Potter, A. B.; Spain, E. M.; Allen, M. J.; Hill, M. G. Langmuir 1998, 24, 6781-6784.
7. Vainrub, A.; Pettitt, B. M. Phys Rev E 2002, 66, 041905.
8. Vainrub, A.; Pettitt, B. M. Biopolymers 2003, 68, 265-270.
9. Vainrub, A.; Pettitt, B. M. Chem Phys Lett 2000, 323, 160-166.
10. Zhang, Z.-L.; Pang, D.-W.; Zhang, R.-Y. Bioconj Chem 2002, 13, 104-109.
11. Dong, L. Q.; Zhou, J. Z.; Wu, L. L.; Dong, P.; Lin, Z. H. Chem Phys Lett 2002, 354, 458-465.
12. Sam, M.; Boon, E. M.; Barton, J. K.; Hill, M. G.; Spain, E. M. Langmuir 2001, 17, 5727-5730.
13. Patole, S. N.; Pike, A. R.; Connolly, B. A.; Horrocks, B. R.; Houlton, A. Langmuir 2003, 19, 5457-5463.
14. Vainrub, A.; Pettitt, B. M. J Am Chem Soc 2003, 125, 7798-7799.
15. Charles, P. T.; Vora, G. J.; Andreadis, J. D.; Fortney, A. J.; Meador, C. E.; Dulcey, C. S.; Stenger, D. A. Langmuir 2003, 19, 1586-1591.
16. Erts, D.; Polyakov, B.; Olin, H.; Tuite, E. J Phys Chem B 2003, 107, 3591-3597.
17. Wong, K.-Y.; Pettitt, B. M. Theor Chem Acc 2001, 106, 233-235.
18. Lamture, J. B.; Beattie, K. L.; Burke, B. E.; Eggers, M. D.; Ehrlich, D. J.; Fowler, R.; Hollis, M. A.; Kosicki, B. B.; Reich, R. K.; Smith, S. R.; Varma, R. S.; Hogan, M. E. Nucleic Acids Res 1994, 22, 2121-2125.
19. Saenger, W. Principles of Nucleic Acid Structure; Springer Verlag: New York, 1984.
20. Wong, K.-Y.; Pettitt, B. M. Chem Phys Lett 2000, 326, 193-198.
21. Chuang, I.-S.; Maciel, G. E. J Phys Chem B 1997, 101, 3052-3064.
22. Discover 2.9.8/96.0, Molecular Simulations, San Diego, CA, May 1996.
23. Rovere, M.; Ricci, M. A.; Vellati, D.; Bruni, F. J Chem Phys 1998, 108, 9859-9867.
24. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B. ; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J Phys Chem B 1998, 102, 3586-3616.
25. Foloppe, N.; MacKerell, A. D., Jr. J Comput Chem 2000, 21, 86-104.
26. Macke, T. J.; Case, D. A. In Molecular Modeling of Nucleic Acids; Leontis, N. B.; SantaLucia, J., Jr., Eds.; American Chemical Society: Washington, DC, 1998; pp 379-393.
27. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J Chem Phys 1983, 79, 926-935.
28. Beglov, D.; Roux, B. J Chem Phys 1994, 100, 9050-9063.
29. Smith, P. E.; Holder, M. E.; Dang, L. X.; Feig, M.; Pettitt, B. M. ESP, University of Houston, 1996.
30. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University: New York, 1987.
31. de Leeuw, S. W.; Perram, J. W.; Smith, E. R. Proc Roy Soc Lond 1980, A373, 27-56.
32. Andersen, H. C. J Comput Phys 1983, 52, 24-34.
33. Swope, W. C.; Andersen, H. C.; Berens, P. H.; Wilson, K. R. J Chem Phys 1982, 76, 637-649.
34. MacKerell, A. D., Jr.; Banavali, N. K. J Comput Chem 2000, 21, 105-120.
35. Lu, X.-J.; Olson, W. K. Nucleic Acids Res 2003, 31, 5108-5121.
36. Humphrey, W.; Dalke, A.; Schulten, K. J Mol Graphics 1996, 14, 33-38.