Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA

Proceedings of the National Academy of Sciences of the United States of America

Volumn 100, Issue SUPPL. 2, 2003, Pages 13922-13927

  Hagan, Michael F ^a   Dinner, Aaron R ^b,d   Chandler, David ^b   Chakraborty, Arup K ^a,b,c  

^a University of California   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^d UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BASE PAIRING; BIOSENSOR; CALCULATION; DNA BINDING; DNA CONFORMATION; DNA STRAND BREAKAGE; HYDROGEN BOND; PRIORITY JOURNAL; SAMPLING;

BASE PAIRING; BIOPHYSICS; DNA; HYDROGEN BONDING; KINETICS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; THERMODYNAMICS;

EID: 0344270866     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.2036378100     Document Type: Article

References (34)

1. Demers, L. M., Mirkin, C. A., Mucic, R. C., Reynolds, R. A. I., Letsinger, R. L., Elghanian, R. & Viswanadham, G. (2000) Anal. Chem. 72, 5535-5541.
2. Fritz, J., Baller, M. K., Lang, H. P., Rothuizen, H., Vettiger, P., Meyer, E., Guüntherodt, H., Gerber, C. & Gimzewski, J. K. (2000) Science 288, 316-318.
3. Wu, G., Ji, H., Hansen, K., Thundat, T., Datar, R., Cote, R., Hagan, M. F., Chakraborty, A. K. & Majumdar, A. (2001) Proc. Natl. Acad. Sci. USA 98, 1560-1564.
4. Stimpson, D. I., Hoijer, J. V., Hsieh, W., Jou, C., Gordon, J., Theriault, T., Gamble, R. & Baldeschwieler, J. D. (1994) Proc. Natl. Acad. Sci. USA 92, 6379-6383.
5. Storhoff, J. J., Elghanian, R., Mucic, R. C., Mirkin, C. A. & Letsinger, R. L. (1998) J. Am. Chem. Soc. 120, 1959-1964.
6. Peterlinz, K. A., Georgiadis, R. M., Herne, T. M. & Tarlov, M. J. (1997) J. Am. Chem. Soc. 119, 3401-3402.
7. Wetmur, J. G. (1991) Cril. Rev. Biochem. Mol. Biol. 26, 227-259.
8. Peyrard, M. & Bishop, A. R. (1989) Phys. Rev. Lett. 62, 2755-2758.
9. Zhang, Y., Zheng, W., Liu, J. & Chen, Y. Z. (1997) Phys. Rev. E Slat. Phys. Plasmas Fluids Relat. Interdiscip. Top. 56, 7100-7115.
10. Campa, A. & Giansanti, A. (1999) J. Biol. Phys. 24, 141-155.
11. Drukker, K. & Schatz, G. C. (2000) J. Phys. Chem. B 104, 6108-6111.
12. Jin, R., Wu, G., Li, Z., Mirkin, C. & Schatz, G. C. (2003) J. Am. Chem. Soc. 125, 1643-1654.
13. Norberg, J. & Nilsson, L. (1996) J. Phys. Chem. 100, 2550-2554.
14. Huang, N., Banavali, N. K. & MacKerell, A. D. J. (2003) Proc. Natl. Acad. Sci. USA 100, 68-73.
15. Giudice, E., Varnai, P. & Lavery, R. (2001) Chem. Phys. Chem. 2, 673-677.
16. Giudice, E., Varnai, P. & Lavery, R. (2003) Nucleic Acids Res. 31, 1434-1443.
17. Banavali, N. K. & MacKerrel, A. D. J. (2002) J. Mol. Biol. 319, 141-160.
18. Pohorille, A., Ross, W. S. & Tinoco, I. J. (1990) Int. J. Supercomput. Appl. 4, 81-96.
19. Boczko, E. M. & Brooks, C. L., III (1996) Science 269, 393-396.
20. Dinner, A. R. & Karplus, M. (1999) J. Phys. Chem. B 103, 7976-7994.
21. Bolhuis, P. G. (2003) Proc. Natl. Acad. Sci. USA 100, 12129-12134.
22. Bolhuis, P. G., Chandler, D., Dellago, C. & Geissler, P. L. (2002) Annu. Rev. Phys. Chem. 53, 291-318.
23. Dellago, C., Bolhuis, P. G. & Geissler, P. L. (2001) Adv. Chem. Phys. 123, 1-78.
24. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983) J. Comput. Chem. 4, 187-217.
25. Wetmur, J. G. & Davidson, N. (1968) J. Mol. Biol. 31, 349-370.
26. Bloomfield, V. A., Crothers, D. M. & Tinoco, I. J. (2000) Nucleic Acids: Structures, Properties, and Functions (University Science Books, Sausilito, CA).
27. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H. & Pedersen, L. G. (1995) J. Chem. Phys. 103, 8577-8593.
28. Bolhuis, P. G. (2003) J. Phys. Condens. Matter 15, S113-S120.
29. McCormick, T. (2003) Ph.D. thesis (Univ. of California, Berkeley).
30. Drukker, K., Wu, G. & Schatz, G. C. (2001) J. Chem. Phys. 114, 579-590.
31. Bryngelson, J. D. & Wolynes, P. G. (1987) Proc. Natl. Acad. Sci. USA 84, 7524-7528.
32. Karplus, M. & Shakhnovich, E. (1992) in Protein Folding, ed. Creighton, T. E. (Freeman, New York), pp. 127-193.
33. Dellago, C., Bolhuis, P. G., Csajka, F. S. & Chandler, D. (1998) J. Chem. Phys. 108, 1964-1977.
34. van Erp, T. S., Moroni, D. & Bolhuis, P. G. (2003) J. Chem. Phys. 118, 7762-7774.