Hostname: page-component-586b7cd67f-2brh9 Total loading time: 0 Render date: 2024-11-25T17:59:01.175Z Has data issue: false hasContentIssue false
  • English
  • Français

Dynamics of DNA conformations and DNA-protein interactions

Published online by Cambridge University Press:  26 February 2011

Ralf Metzler ,
Tobias Ambjörnsson ,
Michael A. Lomholt  and
Oleg Krichevsky
Ralf Metzler
Affiliation:
metz@nordita.dk, NORDITA, Blegdamsvej 17, Copenhagen OE, N/A, 2100, Denmark, +45 353 25507
Tobias Ambjörnsson
Affiliation:
ambjorn@nordita.dk, NORDITA, Denmark
Michael A. Lomholt
Affiliation:
mlomholt@nordita.dk, NORDITA, Denmark
Oleg Krichevsky
Affiliation:
okrichev@bgumail.bgu.ac.il, Ben Gurion University, Israel
Get access

Abstract

Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA denaturation (bubble breathing), deriving its dynamic response to external physical parameters and the DNA sequence in terms of the bubble relaxation time spectrum and the autocorrelation function of bubble breathing. The interaction with binding proteins that selectively bind to the DNA single strand exposed in a denaturation bubble are shown to involve an interesting competition of time scales, varying between kinetic blocking of protein binding up to full binding protein-induced denaturation of the DNA. We will also address the potential to use DNA physics for the design of nanosensors. Finally, we report recent findings on the search process of proteins for a specific target on the DNA.

Keywords

diffusionpolymerbiological
Type
Research Article
Information
MRS Online Proceedings Library (OPL) , Volume 899: Symposium N – Dynamics in Small Confining Systems VIII , 2005 , 0899-N03-06
Copyright
Copyright © Materials Research Society 2006

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

REFERENCES

1. Crick, F., Nature 227, 561 (1970).Google Scholar
2. Alberts, B., Roberts, K., Bray, D., Lewis, J., Raff, M. and Watson, J. D., The molecular biology of the cell (Garland, New York, 1994).Google Scholar
3. Kornberg, A., DNA Synthesis, (Freeman, W. H., San Francisco, CA 1974).Google Scholar
4. Delcourt, S. G. and Blake, R. D., J. Biol. Chem. 266, 15160 (1991).Google Scholar
5. Blake, R. D., Bizzaro, J. W., Blake, J. D., Day, G. R., Delcourt, S. G., Knowles, J., Marx, K. A., and SantaLucia, J. Jr., Bioinformatics 15, 370 (1999).Google Scholar
6. Blossey, R. and Carlon, E., Phys. Rev. E 68, 061911 (2003).Google Scholar
7. Ambjörnsson, T. and Metzler, R., in preparation.Google Scholar
8. SantaLucia, J. Jr., Proc. Natl. Acad. Sci. USA 95, 1460 (1998).Google Scholar
9. Gu’eron, M., Kochoyan, M., and Leroy, J.-L., Nature 328, 89 (1987).Google Scholar
10. Altan-Bonnet, G., Libchaber, A., and Krichevsky, O., Phys. Rev. Lett. 90, 138101 (2003).Google Scholar
11. Ambjörnsson, T. and Metzler, R., J. Phys. Cond. Mat., at press. Google Scholar
12. Poland, D. and Scheraga, H. A., Theory of Helix-Coil Transitions in Biopolymers (Academic, New York, 1970).Google Scholar
13. Ambjörnsson, T., Krichevsky, O., and Metzler, R., in preparation.Google Scholar
14. Jensen, D. E. and von Hippel, P. H., J. Biol. Chem. 251, 7198 (1976).Google Scholar
15. Pant, K., Karpel, R. L., and Williams, M. C., J. Mol. Biol. 327, 571 (2003).Google Scholar
16. Karpel, R. L., IUBMB Life 53, 161 (2002).Google Scholar
17. Ambjörnsson, T. and Metzler, R., Phys. Rev. E 72, 030901(R) (2005).Google Scholar
18. Ambjörnsson, T., Lomholt, M., and Metzler, R., J. Phys. Cond. Mat. 17, S3945 (2005); Ambjörnsson, T. and Metzler, R., Phys. Biol. 1, 77 (2004).Google Scholar
19. Bakk, A. and Metzler, R., FEBS Lett. 563, 66 (2004); J. Theor. Biol. 231, 525 (2004), and Refs. therein. Google Scholar
20. Slutsky, M. and Mirny, L. A., Biophys. J. 87, 4021 (2004).Google Scholar
21. Sokolov, I. M., Metzler, R., Pirant, K., and Williams, M. C., Biophys. J. 89, 895 (2005); Phys. Rev. E 72, at press.Google Scholar
22. Metzler, R. and Klafter, J., Phys. Rep. 339, 1 (2000).Google Scholar
23. Sokolov, I. M., Mai, J. and Blumen, A., Phys. Rev. Lett. 79, 857 (1997); D.Brockmann and T. Geisel, Phys. Rev. Lett. 91, 048303; A. Hanke and R. Metzler, Biophys. J. 85, 167 (2003).Google Scholar
24. Berg, O. G., Winter, R. B., and von Hippel, P. H., Biochem. 20, 6961 (1981).Google Scholar
25. Lomholt, M. A., Ambjörnsson, T., and Metzler, R., Phys. Rev. Lett., accepted.Google Scholar
26. Chechkin, A. V., Metzler, R., Klafter, J., Gonchar, V. Y., and Tanatarov, L. V., J. Phys. A36, L537 (2003).Google Scholar
27. Coppey, M., B’enichou, O., Voituriez, R., and Moreau, M., Biophys. J. 87, 1640 (2004).Google Scholar