Journal of Chemical Physics
Feedback | Help | Exit
The Journal of Chemical Physics
Search:
   
 
 
 
Previous Article
Isolating excitonic Raman coherence in semiconductors using two-dimensional correlation spectroscopy
We present the experimental and simulation results of two-dimensional optical coherent correlation spectroscopy signals along the phase-matching direction kI=−k1+k2+k3 projected on the two-dimen...
Next Article
Analytical and numerical studies of sequence dependence of passage times for translocation of heterobiopolymers through nanopores
We consider chaperone-assisted translocation of biopolymers with two distinct monomers or bases A and B, with the size of the chaperones being , where is a monomer's size. The probability that A and ...

Charge-transport-mediated recruitment of DNA repair enzymes

J. Chem. Phys. 129, 235101 (2008); doi:10.1063/1.3026735

Published 15 December 2008

You are not logged in to this journal. Log in

Pak-Wing Fok,1,2 Chin-Lin Guo,3 and Tom Chou2,4
1Applied and Computational Mathematics, California Institute of Technology, Pasadena, California 91125, USA
2Department of Biomathematics, UCLA, Los Angeles, California 90095-1766, USA
3Applied Physics and Bioengineering, California Institute of Technology, Pasadena, California 91125, USA
4Department of Mathematics, UCLA, Los Angeles, California 90095-1766, USA
Damaged or mismatched bases in DNA can be repaired by base excision repair enzymes (BER) that replace the defective base. Although the detailed molecular structures of many BER enzymes are known, how they colocalize to lesions remains unclear. One hypothesis involves charge transport (CT) along DNA [Yavin et al., Proc. Natl. Acad. Sci. U.S.A. 102, 3546 (2005)]. In this CT mechanism, electrons are released by recently adsorbed BER enzymes and travel along the DNA. The electrons can scatter (by heterogeneities along the DNA) back to the enzyme, destabilizing and knocking it off the DNA, or they can be absorbed by nearby lesions and guanine radicals. We develop a stochastic model to describe the electron dynamics and compute probabilities of electron capture by guanine radicals and repair enzymes. We also calculate first passage times of electron return and ensemble average these results over guanine radical distributions. Our statistical results provide the rules that enable us to perform implicit-electron Monte Carlo simulations of repair enzyme binding and redistribution near lesions. When lesions are electron absorbing, we show that the CT mechanism suppresses wasteful buildup of enzymes along intact portions of the DNA, maximizing enzyme concentration near lesions. ©2008 American Institute of Physics
History: Received 15 July 2008; accepted 24 October 2008; published 15 December 2008
Permalink: http://link.aip.org/link/?JCPSA6/129/235101/1
BUY THIS ARTICLE   (US$24)
Download HTML Download Sectioned HTML Download PDF (347 kB) View Cart

KEYWORDS and PACS

Keywords
PACS

RELATED DATABASES


To view database links for this article,
you need to log in.
To view database links for this article,
you need to log in.

PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
Publisher:
AIP is a member of CrossRef AIP

REFERENCES (40)
View in Separate Window/Tab
For access to fully linked references, you need to log in. For access to fully linked references, you need to Log in.
  1. S. D. Bruner, P. G. Norman, and G. L. Verdine, Nature (London) 403, 859 (2000).
  2. H. M. Nash, S. D. Bruner, O. D. Schärer, T. Kawate, T. A. Addona, E. Spooner, W. S. Lane, and G. L. Verdine, Curr. Biol. 6, 968 (1996).
  3. S. S. Parikh, C. D. Mol, and J. A. Tainer, Structure 5, 1543 (1997).
  4. E. Yavin, A. K. Boal, E. D. A. Stemp, E. M. Boon, A. L. Livingston, V. L. O'Shea, S. S. David, and J. K. Barton, Proc. Natl. Acad. Sci. U.S.A. 102, 3546 (2005).
  5. E. M. Boon, A. L. Livingston, M. H. Chmiel, S. S. David, and J. K. Barton, Proc. Natl. Acad. Sci. U.S.A. 100, 12543 (2003).
  6. P. C. Blainey, A. M. van Oijen, A. Banerjee, G. L. Verdine, and X. S. Xie, Proc. Natl. Acad. Sci. U.S.A. 103, 5752 (2006).
  7. A. D. Riggs, S. Bourgeois, and M. Cohn, J. Mol. Biol. 53, 401 (1970).
  8. A. D. Riggs, H. Suzuki, and S. Bourgeois, J. Mol. Biol. 53, 401 (1970).
  9. O. G. Berg, R. B. Winter, and P. H. von Hippel, Biochemistry 20, 6929 (1981).
  10. R. B. Winter, O. G. Berg, and P. H. von Hippel, Biochemistry 20, 6961 (1981).
  11. P. H. von Hippel and O. G. Berg, J. Biol. Chem. 264, 675 (1989).
  12. O. G. Berg and P. H. von Hippel, J. Mol. Biol. 193, 723 (1987).
  13. L. A. Mirny, Nat. Phys. 4, 93 (2008).
  14. Z. Wunderlich and L. A. Mirny, Nucleic Acids Res. 36, 3570 (2008).
  15. K. Klenin, H. Merlitz, J. Longowski, and C. -X. Wu, Phys. Rev. Lett. 96, 018104 (2006).
  16. M. Slutsky and L. A. Mirny, Biophys. J. 87, 4021 (2004).
  17. T. Hu, A. Y. Grosberg, and B. I. Shklovskii, Biophys. J. 90, 2731 (2006).
  18. A. G. Cherstvy, A. B. Kolomeisky, and A. A. Kornyshev, J. Phys. Chem. 112, 4741 (2008).
  19. S. E. Halford and J. F. Marko, Nucleic Acids Res. 32, 3040 (2004).
  20. Y. M. Wang, R. H. Austin, and E. C. Cox, Phys. Rev. Lett. 97, 048302 (2006).
  21. C. Loverdo, O. Bénichou, M. Moreau, and R. Voituriez, Nat. Phys. 4, 134 (2008).
  22. A. K. Boal, E. Yavin, O. A. Lukianova, V. L. O'Shea, S. S. David, and J. K. Barton, Biochemistry 44, 8397 (2005).
  23. B. Giese, Annu. Rev. Biochem. 71, 51 (2002).
  24. G. B. Schuster, Acc. Chem. Res. 33, 253 (2000).
  25. N. J. Turro and J. K. Barton, J. Biol. Inorg. Chem. 3, 201 (1998).
  26. C. J. Murphy, M. R. Arkin, Y. Jenkins, N. D. Ghatlia, S. H. Bossman, N. J. Turro, and J. K. Barton, Science 262, 1025 (1993).
  27. K. A. Eriksen, Theor. Biol. Med. Model. 2, 15 (2005).
  28. S. Redner, A Guide to First-Passage Processes (Cambridge University Press, Cambridge, 2001).
  29. D. J. Bicout, Phys. Rev. E 56, 6656 (1997).
  30. J. E. Broadwell, Phys. Fluids 7, 1243 (1964.
  31. J. E. Broadwell, J. Fluid Mech. 19, 401 (1964).
  32. A. J. Christlieb, J. A. Rossmanith, and P. Smereka, Commun. Math. Sci. 2, 443 (2004).
  33. M. R. D'Orsogna and J. Rudnick, Phys. Rev. E 66, 041804 (2002).
  34. R. Bruinsma, G. Gruner, M. R. D'Orsogna, and J. Rudnick, Phys. Rev. Lett. 85, 4393 (2000).
  35. H. J. Helbock, K. B. Beckman, M. K. Shigenaga, P. B. Walter, A. A. Woodall, H. C. Yeo, and B. N. Ames, Proc. Natl. Acad. Sci. U.S.A. 95, 288 (1998).
  36. H. Bai and A. -L. Lu, J. Bacteriol. 189, 902 (2006).
  37. M. R. D'Orsogna and T. Chou, J. Phys. A 38, 531 (2005).
  38. G. -W. Li, O. G. Berg, and J. Elf, e-print arXiv:0809.1063.
  39. For E. Coli, the maximum deposition rate can be obtained by assuming a nucleoid radius of approximately b[approximate]0.3  µm. Upon assuming a MutY diffusivity of D~3×10−7  cm2/s, the Debye–Smoluchowski estimate is kon~4piDb[approximate]6×1010  M−1 s−1. For MutY concentration of C[approximate]20  enzymes/femtoliter, the average time between depositions is (kC)−1[approximate]0.0005  s.
  40. While passive enzymes converge more quickly to enzymes when measured in terms of the deposition number n, CT repair enzymes converge more quickly when measured in terms of the number of adsorptions m=O(n1/3). In fact, the enzyme-lesion distance for repair enzymes scales as O(n−2/3)=O(m−2) compared to O(m−1) for passive enzymes with m=n (every deposition results in an adsorption).

CITING ARTICLES
For access to citing articles, you need to log in.
For access to citing articles, you need to Log in.


Copyright © American Institute of Physics