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Topology matters: Some aspects of DNA physics

Published online by Cambridge University Press:  01 February 2011

Ralf Metzler
Ralf Metzler*
Affiliation:
NORDITA, Blegdamsvej 17, 2100 København Ø, Denmark
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Abstract

Biological cells, in some sense, are all about topology: Biomembranes separating different volumes from one another, ions or even macromolecules having to cross these membranes in controlled fashion through membrane pores; or certain proteins moving along the DNA to find their target sequence instead of searching for this site in the full 3-dimensional cell volume. Even on the single biopolymer level, topology is an essential ingredient: Intriguingly, in bacteria DNA occurs knotted, i.e., in a state topologically different from a simply connected ring. It is a key question to understand the statistical behaviour of such knotted DNA to understand a number of physiological processes having to overcome this knottedness, or to quantify results from DNA separation techniques such as electrophoresis, in which the knottedness influences the mobility. At the same time, double-stranded DNA continuously opens up floppy single-stranded bubbles, which fluctuate in size, exposing the single Watson-Crick bases to binding proteins. Again, statistical mechanical tools can be employed to examine the bubble dynamics. Here, we introduce some recent results on DNA knots and bubble fluctuations.

Type
Research Article
Information
MRS Online Proceedings Library (OPL) , Volume 790: Symposium P – Dynamics in Small Confining Systems–2003 , 2003 , P4.2
Copyright
Copyright © Materials Research Society 2004

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References

REFERENCES

1. Rybenkov, V.V., Ullsperger, C., Vologodskii, A.V., and Cozzarelli, N.R., Science 277, 690 (1997).Google Scholar
2. Miller, K.G., Liu, L.F., and Englund, P.T., J. Biol. Chem. 256, 9334 (1981).Google Scholar
3. Wassermann, S.A., Dungan, J.M., and Cozzarelli, N.R., Science 229, 171 (1985).Google Scholar
4. Yan, J., Magnasco, M.O. and Marko, J.F., Nature 401, 932 (1999).Google Scholar
5. Metzler, R., Hanke, A., Dommersnes, P. G., Kantor, Y., and Kardar, M., Phys. Rev. Lett. 88, 188101 (2002).Google Scholar
6. Marko, J.F. and Siggia, E.D., Macromol. 28, 8759 (1996).Google Scholar
7. Deutsch, J.M., Phys. Rev. E 59, R2539 (1999).Google Scholar
8. Duplantier, B., J. Stat. Phys. 54, 581 (1989).Google Scholar
9. Metzler, R., Hanke, A., Dommersnes, P. G., Kantor, Y., and Kardar, M., Phys. Rev. E 65, 061103 (2002).Google Scholar
10. Hanke, A. and Metzler, R., Chem. Phys. Lett. 359, 22 (2002).Google Scholar
11. Maier, B. and Räadler, J.O., Phys. Rev. Lett. 82, 1911 (1999).Google Scholar
12. Valle, F. and Dietler, G., personal communication.Google Scholar
13. Hastings, M.B., Daya, Z.A., Ben-Naim, E., and Ecke, R.E., Phys. Rev. E 66, 025102 (2002).Google Scholar
14. Janse van Rensburg, E. J. and Whittington, S. G., J. Phys. A 24, 3935 (1991).Google Scholar
15. Quake, S. R., Phys. Rev. Lett. 73, 3317 (1994).Google Scholar
16. Grosberg, A. Yu., Feigel, A., and Rabin, Y., Phys. Rev. E 54, 6618 (1996).Google Scholar
17. Grosberg, A. Yu., Phys. Rev. Lett. 85, 3858 (2000).Google Scholar
18. Metzler, R., New J. Phys. 4, 91.1 (2002).Google Scholar
19. Farago, O., Kantor, Y., and Kardar, M., Europhys. Lett. 60, 53 (2002).Google Scholar
20. Hanke, A., Metzler, R., Dommersnes, P. G., Kantor, Y., and Kardar, M., Euro. Phys. J., at press.Google Scholar
21. Orlandini, E., Stella, A. L., and Vanderzande, C., Phys. Rev. E 68, 031804 (2003).Google Scholar
22. Metzler, R., Kantor, Y., and Kardar, M., Phys. Rev. E 66, 022102 (2002).Google Scholar
23. Hanke, A. and Metzler, R., Biophys. J. 85, 167 (2003).Google Scholar
24. Karpel, R. L., IUBMB Life 53, 161 (2002).Google Scholar
25. Pant, K., Karpel, R. L., and Williams, M. C., J. Mol. Biol. 327, 571 (2003).Google Scholar
26. Altan-Bonnet, G., Libchaber, A., and Krichevsky, O., Phys. Rev. Lett. 90, 138101 (2003).Google Scholar
27. Poland, D. and Scheraga, H. A., Theory of Helix-Coil Transitions in Biopolymers (Academic, New York, 1970).Google Scholar
28. Fisher, M. E., J. Chem. Phys. 45, 1469 (1966).Google Scholar
29. Kafri, Y., Mukamel, D. and Peliti, L., Phys. Rev. Lett. 85, 4988 (2000).Google Scholar
30. Hanke, A. and Metzler, R., Phys. Rev. Lett. 90, 159801 (2003).Google Scholar
31. Blossey, R. and Carlon, E., Phys. Rev. E, at press.Google Scholar
32. 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
33. Hanke, A. and Metzler, R., J. Phys. A 36, L473 (2003).Google Scholar
34. Hwa, T., Marinari, E., Sneppen, K., and Tang, L.-H., P. Natl. Acad. Sci. (USA) 100, 4411 (2003).Google Scholar
35. Metzler, R. and Klafter, J., Phys. Rep. 339, 1 (2000).Google Scholar
36. Metzler, R. and Klafter, J., Biophys. J. 85, 2776 (2003).Google Scholar