Geometry of mediating protein affects the probability of loop formation in DNA

Biophysical Journal

Volumn 94, Issue 8, 2008, Pages 3150-3158

  Agrawal, Neeraj J ^a   Radhakrishnan, Ravi ^a   Purohit, Prashant K ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BINDING PROTEIN;

ARTICLE; BINDING SITE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; PROTEIN BINDING; STATISTICAL MODEL; ULTRASTRUCTURE;

BINDING SITES; COMPUTER SIMULATION; DNA; DNA-BINDING PROTEINS; MODELS, CHEMICAL; MODELS, MOLECULAR; MODELS, STATISTICAL; NUCLEIC ACID CONFORMATION; PROTEIN BINDING;

EID: 43149113705     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.122986     Document Type: Article

References (40)

1. Schleif, R. 1992. DNA looping. Annu. Rev. Biochem. 61:199-223.
2. Halford, S. E., A. J. Welsh, and M. D. Szczelkun. 2004. Enzyme-mediated DNA looping. Annu. Rev. Biophys. Biomol. Struct. 33:1-24.
3. Garcia, H. G., P. Grayson, L. Han, M. Inamdar, J. Kondev, P. C. Nelson, R. Phillips, J. Widom, and P. A. Wiggins. 2007. Biological consequences of tightly bent DNA: the other life of a macromolecular celebrity. Biopolymers. 85:115-130.
4. Shimada, J., and H. Yamakawa. 1984. Ring-closure probabilities for twisted wormlike chains - application to DNA. Macromolecules. 17:689-698.
5. Cloutier, T. E., and J. Widom. 2004. Spontaneous sharp bending of double-stranded DNA. Mol. Cell. 14:355-362.
6. Du, Q., C. Smith, N. Shiffeldrim, M. Vologodskaia, and A. Vologodskii. 2005. Cyclization of short DNA fragments and bending fluctuations of the double helix. Proc. Natl. Acad. Sci. USA. 102:5397-5402.
7. Wiggins, P. A., R. Phillips, and P. C. Nelson. 2005. Exact theory of kinkable elastic polymers. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 71:021909.
8. Lankas, F., R. Lavery, and J. H. Maddocks. 2006. Kinking occurs during molecular dynamics simulations of small DNA minicircles. Structure. 14:1527-1534.
9. Finzi, L., and J. Gelles. 1995. Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules. Science. 267:378-380.
10. Lia, G., D. Bensimon, V. Croquette, J.-F. Allemand, D. Dunlap, D. E. A. Lewis, S. Adhya, and L. Finzi. 2003. Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping. Proc. Natl. Acad. Sci. USA. 100:11373-11377.
11. Zurla, C., A. Franzini, G. Galli, D. D. Dunlap, D. E. A. Lewis, S. Adhya, and L. Finzi. 2006. Novel tethered particle motion analysis of CI protein-mediated DNA looping in the regulation of bacteriophage-λ. J. Phys. Condens. Matter. 18:S225-S234.
12. van den Broek, B., F. Vanzi, D. Normanno, F. S. Pavone, and G. J. L. Wuite. 2006. Real-time observation of DNA looping dynamics of type IIE restriction enzymes NaeI and NarI. Nucleic Acids Res. 34:167-174.
13. Gemmen, G. J., R. Millin, and D. E. Smith. 2006. DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force. Nucleic Acids Res. 34:2864-2877.
14. Purohit, P. K., and P. C. Nelson. 2006. Effect of supercoiling on formation of protein-mediated DNA loops. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 74:061906.
15. Czapla, L., D. Swigon, and W. K. Olson. 2006. Sequence-dependent effects in the cyclization of short DNA. J. Chem. Theory Comput. 2:685-695.
16. 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.
17. Jacobson, H., and W. H. Stockmayer. 1950. Intramolecular reaction in polycondensations. 1. The theory of linear systems. J. Chem. Phys. 18:1600-1606.
18. Kindt, J. T. 2002. Pivot-coupled grand canonical Monte Carlo method for ring simulations. J. Chem. Phys. 116:6817-6825.
19. Kulic, I. M., H. Mohrbach, V. Lobaskin, R. Thaokar, and H. Schiessel. 2005. Apparent persistence length renormalization of bent DNA. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 72:041905.
20. Frederick, K. K., M. S. Marlow, K. G. Valentine, and A. J. Wand. 2007. Conformational entropy in molecular recognition by proteins. Nature. 448:325-330.
21. Marko, J. F., and E. D. Siggia. 1995. Stretching DNA. Macromolecules. 28:8759-8770.
22. Friedman, A. M., T. O. Fischmann, and T. A. Steitz. 1995. Crystal-structure of Lac repressor core tetramer and its implications for DNA looping. Science. 268:1721-1727.
23. Mehta, R. A., and J. D. Kahn. 1999. Designed hyperstable Lac repressor center dot DNA loop topologies suggest alternative loop geometries. J. Mol. Biol. 294:67-77.
24. Harmer, T., M. Wu, and R. Schleif. 2001. The role of rigidity in DNA looping-unlooping by AraC. Proc. Natl. Acad. Sci. USA. 98:427-431.
25. Klenin, K., H. Merlitz, and J. Langowski. 1998. A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes. Biophys. J. 74:780-788.
26. Vologodskii, A. V., S. D. Levene, K. V. Klenin, M. Frank-Kamenetskii, and N. R. Cozzarelli. 1992. Conformational and thermodynamic properties of supercoiled DNA. J. Mol. Biol. 227:1224-1243.
27. Allen, M. P., and D. J. Tildesley. 1987. Computer Simulation of Liquids. Oxford Science, Oxford.
28. Hoffman, J. D. 1992. Numerical Methods for Engineers and Scientists. McGraw-Hill, New York.
29. Andricioaei, I., and M. Karplus. 2001. On the calculation of entropy from covariance matrices of the atomic fluctuations. J. Chem. Phys. 115:6289-6292.
30. Wang, F. G., and D. P. Landau. 2001. Efficient, multiple-range random walk algorithm to calculate the density of states. Phys. Rev. Lett. 86:2050-2053.
31. Reif, F. 1965. Fundamentals of Statistical and Thermal Physics, Ch. 2. McGraw-Hill, Singapore.
32. Pathria, R. K. 1996. Statistical Mechanics. Butterworth Heinemann, Oxford.
33. Yamakawa, H. 1971. Modern Theory of Polymer Solutions. Harper and Row, New York.
34. Douarche, N., and S. Cocco. 2005. Protein-mediated DNA loops: effects of protein bridge size and kinks. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 72:061902.
35. Sankararaman, S., and J. F. Marko. 2005. Formation of loops in DNA under tension. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 71:021911.
36. Rippe, K. 2001. Making contacts on a nucleic acid polymer. Trends Biochem. Sci. 26:733-740.
37. Reuter, M., D. Kupper, A. Meisel, C. Schroeder, and D. H. Kruger. 1998. Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites. J. Biol. Chem. 273:8294-8300.
38. Fain, B., J. Rudnick, and S. Ostlund. 1997. Conformations of linear DNA. Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics. 55:7364-7368.
39. Perkins, T. T., S. R. Quake, D. E. Smith, and S. Chu. 1994. Relaxation of a single DNA molecule observed by optical microscopy. Science. 264:822-826.
40. Sutherland, B. 1973. Some exact results for one-dimensional models of solids. Phys. Rev. A. 8:2514-2516.