Determining protein-induced DNA bending in force-extension experiments: Theoretical analysis

Biophysical Journal

Volumn 96, Issue 9, 2009, Pages 3591-3599

  Vologodskii, Alexander ^a  

^a NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CURVED DNA; DNA; DNA BINDING PROTEIN;

ACCURACY; ARTICLE; COMPUTER SIMULATION; DNA CONFORMATION; DNA DETERMINATION; FORCE; MOLECULE; PROTEIN DETERMINATION; THEORETICAL MODEL; ALGORITHM; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; METABOLISM; MONTE CARLO METHOD; THERMODYNAMICS; TIME;

ALGORITHMS; COMPUTER SIMULATION; DNA; DNA-BINDING PROTEINS; MODELS, MOLECULAR; MONTE CARLO METHOD; NUCLEIC ACID CONFORMATION; THERMODYNAMICS; TIME FACTORS;

EID: 67650354846     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.02.022     Document Type: Article

References (44)

1. Swinger, K. K., and P. A. Rice. 2004. IHF and HU: flexible architects of bent DNA. Curr. Opin. Struct. Biol. 14:28-35.
2. Kahn, J. D., and D. M. Crothers. 1993. DNA bending in transcription initiation. Cold Spring Harb. Symp. Quant. Biol. 58:115-122.
3. Becker, N. A., J. D. Kahn, and L. J. Maher, III. 2005. Bacterial repression loops require enhanced DNA flexibility. J. Mol. Biol. 349: 716-730.
4. Vologodskii, A. V., W. Zhang, V. V. Rybenkov, A. A. Podtelezhnikov, D. Subramanian, et al. 2001. Mechanism of topology simplification by type II DNA topoisomerases. Proc. Natl. Acad. Sci. USA. 98:3045-3049.
5. Du, Q., A. Livshits, A. Kwiatek, M. Jayaram, and A. Vologodskii. 2007. Protein-induced local DNA bends regulate global topological complexity of recombination products. J. Mol. Biol. 368:170-182.
6. Horton, N. C., and J. J. Perona. 2000. Crystallographic snapshots along a protein-induced DNA-bending pathway. Proc. Natl. Acad. Sci. USA. 97:5729-5734.
7. Parkhurst, L. J., K. M. Parkhurst, R. Powell, J. Wu, and S. Williams. 2001. Time-resolved fluorescence resonance energy transfer studies of DNA bending in double-stranded oligonucleotides and in DNA-protein complexes. Biopolymers. 61:180-200.
8. Harrington, R. E. 1993. Studies of DNA bending and flexibility using gel electrophoresis. Electrophoresis. 14:732-746.
9. Cherny, D. I., G. Striker, V. Subramaniam, S. D. Jett, E. Palecek, et al. 1999. DNA bending due to specific p53 and p53 core domain-DNA interactions visualized by electron microscopy. J. Mol. Biol. 294:1015-1026.
10. Ten Heggeler-Bordier, B., W. Wahli, M. Adrian, A. Stasiak, and J. Dubochet. 1992. The apical localization of transcibing RNA polymerases on supercoiled DNA prevents their rotation around the template. EMBO J. 11:667-672.
11. Furrer, P., J. Bednar, J. Dubochet, A. Hamiche, and A. Prunell. 1995. DNA at the entry-exit of the nucleosome observed by cryoelectron microscopy. J. Struct. Biol. 114:177-183.
12. Skoko, D., D. Yoo, H. Bai, B. Schnurr, J. Yan, et al. 2006. Mechanism of chromosome compaction and looping by the Escherichia coli nucleoid protein Fis. J. Mol. Biol. 364:777-798.
13. Zhang, H., and J. F. Marko. 2008. Maxwell relations for single-DNA experiments: monitoring protein binding and double-helix torque with force-extension measurements. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 77:031916.
14. Bustamante, C., Z. Bryant, and S. B. Smith. 2003. Ten years of tension: single-molecule DNA mechanics. Nature. 421:423-427.
15. Allemand, J. F., D. Bensimon, and V. Croquette. 2003. Stretching DNA and RNA to probe their interactions with proteins. Curr. Opin. Struct. Biol. 13:266-274.
16. Abbondanzieri, E. A., W. J. Greenleaf, J. W. Shaevitz, R. Landick, and S. M. Block. 2005. Direct observation of base-pair stepping by RNA polymerase. Nature. 438:460-465.
17. Vologodskii, A. 2006. Simulation of equilibrium and dynamic properties of large DNA molecules. In Computational Studies of DNA and RNA. F. Lankas and J. Sponer, editors. Springer, Dordrecht, The Netherlands. 579-604.
18. Allison, S. A., and J. A. McCammon. 1984. Multistep Brownian dynamics: application to short wormlike chains. Biopolymers. 23:363-375.
19. Allison, S. A. 1986. Brownian dynamics simulation of wormlike chains. Fluorescence depolarization and depolarized light scattering. Macromolecules. 19:118-124.
20. Chirico, G., and J. Langowski. 1992. Calculating hydrodynamic properties of DNA through a second-order Brownian dynamics algorithm. Macromolecules. 25:769-775.
21. 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.
22. Jian, H., A. Vologodskii, and T. Schlick. 1997. Combined wormlike-chain and bead model for dynamic simulations of long linear DNA. J. Comput. Phys. 73:123-132.
23. Huang, J., T. Schlick, and T. Vologodskii. 2001. Dynamics of site juxtaposition in supercoiled DNA. Proc. Natl. Acad. Sci. USA. 98:968-973.
24. Smith, S. B., Y. Cui, and C. Bustamante. 1996. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science. 271:795-799.
25. Frank-Kamenetskii, M. D., A. V. Lukashin, V. V. Anshelevich, and A. V. Vologodskii. 1985. Torsional and bending rigidity of the double helix from data on small DNA rings. J. Biomol. Struct. Dyn. 2:1005-1012.
26. Vologodskii, A. V., and M. D. Frank-Kamenetskii. 1992. Modeling supercoiled DNA. Methods Enzymol. 211:467-480.
27. Vologodskii, A. V. 1994. DNA extension under the action of an external force. Macromolecules. 27:5623-5625.
28. Hagerman, P. J. 1988. Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17:265-286.
29. Stigter, D. 1977. Interactions of highly charged colloidal cylinders with applications to double-stranded DNA. Biopolymers. 16:1435-1448.
30. Rotne, J., and S. Prager. 1969. Variational treatment of hydrodynamic interaction in polymers. J. Chem. Phys. 50:4831-4837.
31. Langowski, J., and U. Giesen. 1989. Configurational and dynamic properties of different length superhelical DNAs measured by dynamic light scattering. Biophys. Chem. 34:9-18.
32. Hammermann, M., C. Stainmaier, H. Merlitz, U. Kapp, W. Waldeck, et al. 1997. Salt effects on the structure and internal dynamics of superhelical DNAs studied by light scattering and Brownian dynamic. Biophys. J. 73:2674-2687.
33. Rybenkov, V. V., A. V. Vologoskii, and N. R. Cozzarelli. 1997. The effect of ionic conditions on the conformations of supercoiled DNA.I. Sedimentation analysis. J. Mol. Biol. 267:299-311.
34. Vologodskii, A. V., and N. R. Cozzarelli. 1995. Modeling of long-range electrostatic interactions in DNA. Biopolymers. 35:289-296.
35. Li, J., P. C. Nelson, and M. D. Betterton. 2006. Entropic elasticity of DNA with a permanent kink. Macromolecules. 39:8816-8821.
36. Wallin, A. E., A. Salmi, and R. Tuma. 2007. Step length measurement-theory and simulation for tethered bead constant-force single molecule assay. Biophys. J. 93:795-805.
37. Vologodskii, A. 2006. Brownian dynamics simulation of knot diffusion along a stretched DNA molecule. Biophys. J. 90:1594-1597.
38. Feller, W. 1968. An Introduction to Probability Theory and Its Applications. John Wiley, New York. 509.
39. Hohng, S., R. Zhou, M. K. Nahas, J. Yu, K. Schulten, et al. 2007. Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the Holliday junction. Science. 318:279-283.
40. Dixit, S., M. Singh-Zocchi, J. Hanne, and G. Zocchi. 2005. Mechanics of binding of a single integration-host-factor protein to DNA. Phys. Rev. Lett. 94:118101.
41. Lia, G., S. Semsey, D. E. Lewis, S. Adhya, D. Bensimon, et al. 2008. The antiparallel loops in gal DNA. Nucleic Acids Res. 36:4204-4210.
42. Strick, T., J. Allemand, V. Croquette, and D. Bensimon. 2000. Twisting and stretching single DNA molecules. Prog. Biophys. Mol. Biol. 74:115-140.
43. Marko, J. F., and E. D. Siggia. 1995. Stretching DNA. Macromolecules. 28:8759-8770.
44. Meiners, J. C., and S. R. Quake. 2000. Femtonewton force spectroscopy of single extended DNA molecules. Phys. Rev. Lett. 84:5014-5017.