Modelling DNA loops using continuum and statistical mechanics

Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences

Volumn 362, Issue 1820, 2004, Pages 1355-1371

  Balaeff, A ^a,c   Koudella, C R ^b,d   Mahadevan, L ^b,d   Schulten, K ^a  

^a University of Illinois at Urbana Champaign   (United States)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c IBM T J WATSON RESEARCH CENTER   (United States)

^d HARVARD UNIVERSITY   (United States)

Author keywords

Brownian dynamics; Catabolite gene activator protein (CAP); DNA loops; Elastic rod model; Lac repressor; Loop formation kinetics

Indexed keywords

EID: 3042632970     PISSN: 1364503X     EISSN: None     Source Type: Journal    
DOI: 10.1098/rsta.2004.1384     Document Type: Article

References (40)

1. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K. & Walter, P. 2002 Molecular biology of the cell, 4th edn. Garland Science.
2. Bader, G. & Ascher, U. 1987 A new basis implementation for a mixed order boundary value ODE solver. SIAM J. Sci. Statist. Comput. 8, 483.
3. Balaeff, A., Mahadevan, L. & Schulten, K. 1999 Elastic rod model of a DNA loop in the lac operon. Phys. Rev. Lett. 83, 1900.
4. Balaeff, A., Mahadevan, L. & Schulten, K. 2003 Modeling DNA loops using the theory of elasticity. E-print archive arXiv.org, pub. no. 0301006. (Available at http://arxiv.org/abs/physics/0301006.)
5. Balaeff, A., Mahadevan, L. & Schulten, K. 2004 Structural basis for cooperative DNA binding by CAP and lac repressor. Structure 12, 123-132.
6. Busby, S. & Ebright, R. 1999 Transcription activation by catabolite activator protein (CAP). J. Mol. Biol. 293, 199.
7. Coleman, B. D., Tobias, I. & Swigon, D. 1995 Theory of the influence of end conditions on self-contact in DNA loops. J. Chem. Phys. 103, 9101.
8. Cox, R. G. 1970 The motion of long slender bodies in a viscous fluid. Part 1. General theory. J. Fluid Mech. 44, 791.
9. Cox, R. G. 1971 The motion of long slender bodies in a viscous fluid. Part 2. Shear flow. J. Fluid Mech. 45, 625.
10. Dua, A. & Cherayil, B. J. 2002 The dynamics of chain closure in semiflexible polymers. J. Chem. Phys. 116, 399.
11. Edelman, L. M., Cheong, R. & Kahn, J. D. 2003 Fluorescence resonance energy transfer over ≈130 basepairs in hyperstable lac repressor-DNA loops. Biophys. J. 84, 1131.
12. Finzi, L. & Gelles, J. F. 1995 Measurement of lactose represser-mediated loop formation and breakdown in sinngle DNA molecules. Science 267, 378.
13. Hinch, E. J. 1994 Brownian motion with stiff bonds and rigid contraints. J. Fluid Mech. 271, 219.
14. Hudson, J. M. & Fried, M. G. 1990 Co-operative interactions between the catabolite gene activator protein and the lac repressor at the lactose promoter. J. Mol. Biol. 214, 381.
15. Kirchhoff, G. R. 1883 Vorlesungen über mathematische Physik, Mechanik, Vorlesung 28, Dritte Auflage. Leipzig: B. G. Teubner.
16. Klenin, K., Merlitz, H. & Langowski, J. 1998 A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes. Biophys. J. 74, 780.
17. Lewis, M., Chang, G., Horton, N. C., Kercher, M. A., Pace, H. C., Schumacher, M. A., Brennan, A. G. & Lu, P. 1996 Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science 271, 1247.
18. Lia, G., Bensimon, D., Croquette, V., Allemand, J.-F., Dunlap, D., Lewis, D. E. A., Adhya, S. & Finzi, L. 2003 Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping. Proc. Natl. Acad. Sci. USA 100, 11 373.
19. Love, A. E. H. 1927 A treatise on the mathematical theory of elasticity. Dover.
20. Madras, N. & Sokal, A. D. 1988 The pivot algorithm: a highly efficient Monte Carlo algorithm for the self-avoiding random walk. J. Stat. Phys. 50, 109.
21. Mahadevan, L. & Keller, J. B. 1996 Coiling of flexible ropes. Proc. R. Soc. Lond. A 452, 1679.
22. Manning, R. S., Maddocks, J. H. & Kahn, J. D. 1996 A continuum rod model of sequence-dependent DNA structure. J. Chem. Phys. 105, 5626.
23. Matthews, K. 1992 DNA looping. Microbiol. Mol. Biol. Rev. 56, 123.
24. Merlitz, H., Rippe, K., Klenin, K. V. & Langowski, J. 1998 Looping dynamics of linear DNA molecules and the effect of DNA curvature: a study by Brownian dynamics simulation. Biophys. J. 74, 773.
25. Oehler, S., Eismann, E. R., Krämer, H. & Müller-Hill, B. 1990 The three operators of the lac operon cooperate in repression. EMBO J. 9, 973.
26. Olson, W. K. 1996 Simulating DNA at low resolution. Curr. Opin. Struct. Biol. 6, 242.
27. Olson, W. K. & Zhurkin, V. B. 2000 Modeling DNA deformations. Curr. Opin. Struct. Biol. 10, 286.
28. Olson, W. K. (and 14 others) 2001 A standard reference frame for the description of nucleic acid base-pair geometry. J. Mol. Biol. 313, 229.
29. Olson, W. K., Marky, N. L., Jernigan, R. L. & Zhurkin, V. B. 1993 Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. J. Mol. Biol. 232, 530.
30. Öttinger, H. C. 1996 Stochastic processes in polymeric fluids. Springer.
31. Parkinson, G., Wilson, C., Gunasekera, A., Ebright, Y. W., Ebright, R. E. & Herman, H. M. 1996 Structure of the CAP-DNA complex at 2.5 A resolution: a complete picture of the protein-DNA interface. J. Mol. Biol. 260, 395.
32. Pastor. R. W., Zwanzig, R. & Szabo, A. 1996 Diffusion limited first contact of the ends of a polymer: comparison of theory with simulation. J. Chem. Phys. 105, 3878.
33. Perros, M., Steitz, T. A., Fried, M. G. & Hudson, J. M. 1996 DNA looping and lac repressor-lac CAP interaction. Science 274, 1929.
34. Ptashne, M. 1992 A genetic switch, 2nd edn. Blackwell Science.
35. Schleif, R. 1992 DNA looping. A. Rev. Biochem. 61, 199.
36. Schlick, T. 1995 Modeling superhelical DNA: recent analytical and dynamic approaches. Curr. Opin. Struct. Biol. 5, 245.
37. Strick, T. R., Allemand, J.-F., Bensimon, D. & Croquette, V. 2000 Stress-induced structural transitions in DNA and proteins. A. Rev. Biophys. Biomol. Struct. 29, 523.
38. Tsodikov, O. V., Saecker, R. M., Melcher, S. E., Levandoski, M. M., Frank, D. E., Capp, M. W. & Record Jr, M. T. 1999 Wrapping of flanking non-operator DNA in lac represser-operator complexes: implications for DNA looping. J. Mol. Biol. 294, 639.
39. Villa, E., Balaeff, A., Mahadevan, L. & Schulten, K. 2004 Multi-scale method for simulating protein-DNA complexes. Multiscale Model. Simul. (In the press.)
40. Westcott, T. P., Tobias, I. & Olson, W. K. 1997 Modeling self-contact forces in the elastic theory of DNA supercoiling. J. Chem. Phys. 107, 3967.