Apparent directional scanning for DNA repair

Biophysical Journal

Volumn 94, Issue 1, 2008, Pages 47-52

  Zhao, Tong ^a   Dinner, Aaron R ^a,b  

^a UNIVERSITY OF CHICAGO   (United States)

^b Gordon Center for Integrative Science   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTIN; STREPTAVIDIN;

ARTICLE; BINDING KINETICS; DIFFUSION; DNA DETERMINATION; DNA REPAIR; DNA SEQUENCE; PROTEIN BINDING;

EID: 37749042380     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.107.110619     Document Type: Article

References (20)

1. Riggs, A. D., S. Bourgeois, and M. Cohn. 1970. The lac repressor-operator interaction. III. Kinetic studies. J. Mol. Biol. 53:401-417.
2. von Hippel, P. H., and O. G. Berg. 1989. Facilitated target location in biological systems. J. Biol. Chem. 264:675-678.
3. Adam, G., and M. Delbruck. 1968. Reduction in dimensionality in biological diffusion processes. In Structural Chemistry and Molecular Biology. W. H. Freeman and Co., New York. 198-215.
4. Berg, O. G., R. B. Winter, and P. H. von Hippel. 1981. Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry. 20:6929-6948.
5. Shimamoto, N. 1999. One-dimensional diffusion of proteins along DNA. J. Biol. Chem. 274:15293-15296.
6. Slutsky, M., and L. A. Mirny. 2004. Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. Biophys. J. 87:4021-4035.
7. Halford, S. E., and J. F. Marko. 2004. How do site-specific DNA-binding proteins find their target? Nucleic Acids Res. 32:3040-3052.
8. Sokolov, I. M., R. Metzler, K. Pant, and M. C. Williams. 2005. Target search of N sliding proteins on a DNA. Biophys. J. 89:895-902.
9. Alberts, B., A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter. 2002. Molecular Biology of the Cell, 4th Ed. Garland Science, New York.
10. Howard, J. 2001. Mechanics of Motor Proteins and the Cytoskeleton. Sinauer Associates, New York.
11. Daniels, D. S., T. T. Woo, K. X. Luu, D. M. Noll, N. D. Clarke, A. E. Pegg, and J. A. Tainer. 2004. DNA binding and nucleotide flipping by the human DNA repair protein AGT. Nat. Struct. Mol. Biol. 11:714-720.
12. Begley, T. J., and L. D. Samson. 2004. Reversing DNA damage with a directional bias. Nat. Struct. Mol. Biol. 11:688-690.
13. 6-alkylguanine-DNA alkyltransferase. J. Biol. Chem. 278:7973-7980.
14. 6-alkylguanine-DNA alkyltransferase (AGT) with short single-stranded DNAs. J. Biol. Chem. 282:3357-3366.
15. Bortz, A. B., M. H. Kalos, and J. L. Lebowitz. 1975. A new algorithm for Monte Carlo simulation of Ising spin systems. J. Comput. Phys. 17:10-18.
16. Gillespie, D. T. 1977. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81:2340-2361.
17. Newman, M. E. J., and G. T. Barkema. 1999. Monte Carlo Methods in Statisical Physics. Clarendon Press, Oxford, UK.
18. Blainey, P. C., A. M. van Oijen, A. Banerjee, G. L. Verdine, and X. S. Xie. 2006. A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proc. Natl. Acad. Sci. USA. 103:5752-5757.
19. Schurr, J. M. 1979. The one-dimensional diffusion coefficient of proteins absorbed on DNA. Hydrodynamic considerations. Biophys. Chem. 9:413-414.
20. 6-alkylguanine-DNA alkyltransferase. J. Biol. Chem. 280:30873-30881.