Entropy loss in long-distance DNA looping

Biophysical Journal

Volumn 85, Issue 1, 2003, Pages 167-173

  Hanke, Andreas ^a,b   Metzler, Ralf ^c,d  

^a UNIVERSITY OF STUTTGART   (Germany)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c NORDITA   (Denmark)

^d MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOPOLYMER; CIRCULAR DNA; DNA;

ARTICLE; CALCULATION; CHEMICAL BOND; DNA DETERMINATION; ENERGY; ENTROPY; MATHEMATICAL ANALYSIS;

EID: 0037974405     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)74463-4     Document Type: Article

References (41)

1. Abramowitz, M., and I. Stegun. 1972. Handbook of Mathematical Functions. Dover, New York.
2. Alberts, B., K. Roberts, D. Bray, J. Lewis, M. Raff, and J. D. Watson. 1994. The molecular biology of the cell. Garland, New York.
3. Amouyal, M., N. Perez, and S. Rolland. 1998. Adjacent cooperation of proteins on DNA are not representative of long-distance interactions. C. R. Acad. Sci. Paris. 321:877-881.
4. Aurell, E., and K. Sneppen. 2002. Epigenetics as a first exit problem. Phys. Rev. Lett. 88:048101.
5. Aurell, E., S. Brown, J. Johanson, and K. Sneppen. 2002. Stability puzzles in phage lambda. Phys. Rev. E. 65:051914.
6. Bell, C. E., and M. Lewis. 2001. Crystal structure of the lambda repressor C-terminal domain octamer. J. Mol. Biol. 314:1127-1136.
7. Bell, C. E., P. Frescura, A. Hochschild, and M. Lewis. 2000. Crystal structure of the lambda repressor C-terminal domain provides a model for cooperative operator binding. Cell. 101:801-811.
8. Blackwood, E. M., and J. T. Kadonaga. 1998. Going the distance: a current view of enhancer action. Science. 281:60-63.
9. Bolsover, S. R., J. S. Hyams, S. Jones, E. A. Shephard, and H. A. White. 2001. From Genes to Cells. Wiley, New York.
10. Breslauer, K. J., R. Frank, H. Blocker, and L. A. Marky. 1986. Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA. 83:3746-3750.
11. Caracciolo, S., M. S. Causo, and A. Pelissetto. 1998. High-precision determination of the critical exponent gamma for self-avoiding walks. Phys. Rev. E. 57:R1215-R1218.
12. Coleman, B. D., D. Swigon, and I. Tobias. 2000. Elastic stability of DNA configurations. II. Supercoiled plasmids with self-contact. Phys. Rev. E. 61:759-770.
13. De Bruin, D., Z. Zaman, R. A. Liberatore, and M. Ptashne. 2001. Telomere looping permits gene activation by a downstream UAS in yeast. Nature. 409:109-113.
14. De Gennes, P.-G. 1979. Scaling concepts in polymer physics. Cornell University Press, Ithaca, New York.
15. Duplantier, B. 1986. Polymer network of fixed topology: renormalization, exact critical exponent gamma in two dimensions, and d = 4-epsilon. Phys. Rev. Lett. 57:941-945.
16. Duplantier, B. 1989. Statistical mechanics of polymer networks of any topology. J. Stat. Phys. 54:581-680.
17. Flory, P. J. 1956. Theory of elastic mechanisms in fibrous proteins. J. Am. Chem. Soc. 78:5222-5235.
18. Griffith, J. D., L. Comeau, S. Rosenfield, R. M. Stansel, A. Bianchi, H. Moss, and T. de Lange. 1999. Mammalian telomeres end in a large duplex loop. Cell. 97:503-514.
19. Guida, R., and J. Zinn-Justin. 1998. Critical exponents of the N-vector model. J. Phys. A. 31:8103-8121.
20. Hanke, A., and R. Metzler. 2002. Towards the molecular workshop: entropy-driven designer molecules, entropy activation, and nanomechanical devices. Chem. Phys. Lett. 359:22-26.
21. Lee, C. S., R. E. Pyeritz, and C. A. Thomas, Jr. 1976. Kinetic studies on cyclization of T7 and T1 DNAs. Biopolymers. 15:671-686.
22. Marko, J. F., and E. D. Siggia. 1996. Stretching DNA. Macromolecules. 28:8759-8770.
23. Merlitz, H., K. Rippe, K. V. Klenin, and J. Langowski. 1998. Looping dynamics of linear DNA molecules and the effect of DNA curvature: a study by Brownian dynamics simulation. Biophys. J. 74:773-779.
24. Metzler, R. 2001. The future is noisy: on the role of spatial fluctuations and the merits of cooperativity in genetic switching. Phys. Rev. Lett. 87:068103.
25. Metzler, R., A. Hanke, P. G. Dommersnes, Y. Kantor, and M. Kardar. 2002a. Equilibrium shapes of flat knots. Phys. Rev. Lett. 88:188101.
26. Metzler, R., A. Hanke, P. G. Dommersnes, Y. Kantor, and M. Kardar. 2002b. Tightness of slip-linked polymer chains. Phys. Rev. E. 65:061103.
27. Montigny, W. J., C. R. Houchens, S. Illenye, J. Gilbert, E. Coonrod, Y.-C. Chang, and N. H. Heintz. 2001. Condensation by DNA looping facilitates transfer of large DNA molecules into mammalian cells. Nucleic Acids Res. 29:1982-1988.
28. Ohno, K., and K. Binder. 1988. Scaling theory of star polymers and general polymer networks in bulk and semi-infinite good solvents. J. Phys. (Paris). 49:1329-1351.
29. Poland, D. C., and H. A. Scheraga. 1965. Statistical mechanics of non-covalent bonds in polyamino acids. VIII. Covalent loops in protein. Biopolymers. 3:379-399.
30. Ptashne, M., and A. Gunn. 2002. Genes and signals. Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
31. Ptashne, M. 1992. A Genetic Switch. Cell Press and Blackwell Science, Cambridge, Massachusetts.
32. Révet, B., B. van Wilcken-Bergmann, H. Bessert, A. Barker, and B. Müller-Hill. 1999. Four dimers of lambda repressor bound to two suitably spaced pairs of lambda operators form octamers and DNA loops over large distances. Curr. Biol. 9:151-154.
33. Schäfer, L., C. van Ferber, U. Lehr, and B. Duplantier. 1992. Renormalization of polymer networks and stars. Nucl. Phys. B. 374:473-495.
34. Schellmann, J. A. editor. 1955. The stability of hydrogen-bonded peptide structures in aqueous solution. C. R. Trav. Lab. Carlsberg Ser. Chim. 29:230-259.
35. Semlyen, J. A. 1997. Large Ring Molecules. John Wiley and Sons, Chichester, West Sussex, England.
36. Semsey, S., M. Geanacopoulos, D. E. A. Lewis, and S. Adhya. 2002. Operator-bound GalR dimers close DNA loops by direct interaction: tetramerization and inducer binding. EMBO J. 21:4349-4356.
37. Snustad, D. P., and M. J. Simmons. 2003. Principles of Genetics. John Wiley and Sons, New York.
38. Tobias, I., D. Swigon, and B. D. Coleman. 2000. Elastic stability of DNA configurations. I. General theory. Phys. Rev. E. 61:747-758.
39. Wang, M. C., and G. E. Uhlenbeck. 1955. On the theory of the Brownian motion II. Rev. Mod. Phys. 17:323-342.
40. Xu, H., and T. R. Hoover. 2001. Transcriptional regulation at a distance in bacteria. Curr. Op. Microbiol. 4:138-144.
41. Zaman, Z., C. Heid, and M. Ptashne. 2002. Telomere looping permits repression 'at a distance' in yeast. Curr. Biol. 12:930-933.