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Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)

Search of Damaged Bases by DNA Repair Enzymes: Random Walks in One and Three Dimensions

Many DNA-dependent proteins, such as restriction endonucleases, transcription factors, or DNA repair enzymes face the challenge of finding rare specific sequences or structural elements of DNA in a vast excess of competing non-specific DNA (1, 2). Proteins may locate targets in DNA using either diffusion in three dimensions of movement along the DNA contour. The proteins that move along DNA use two fundamentally different movement mechanisms: directed movement coupled with ATP hydrolysis and random one-dimensional diffusion driven by Brownian fluctuations. We have developed a new approach to quantitatively analyze the latter mechanism (3) and used it to study the process of lesion search by several DNA repair enzymes: Escherichia coli and human uracil DNA glycosylases, 8-oxoguanine-DNA glycosylases, and AP endonucleases. All these enzymes were able to move along DNA by one-dimensional diffusion over distances up to 80 base pairs, with the probability of passage decreasing with the increasing travel distance. The average travel distance was significantly influenced by ionic strength, Mg2+ ions, and competing non-specific DNA-binding molecules but was barely affected by crowding agents. Nicks and short gaps in DNA, as well as specifically bound small ligands, were efficiently overpassed, and DNA strands could be switched during the search, indicating that the enzymes are able to use hopping, a mode of movement involving dissociation of the protein–DNA complex and immediate reassociation of the protein with DNA in the close vicinity of its previous position. Differences in the behavior of uracil-DNA glycosylase on blunt and hairpin DNA ends was observed, suggesting that the ends serve neither as points of irreversible loss nor total reflection of the moving protein. An analytical model has been developed that describes the one-dimensional random walk of proteins along DNA in terms of probabilities of the enzyme to move or dissociate at each step.

This research has been supported by RFBR (11-04-00807-а) and Presidium of RAS “Molecular and Cell Biology” program (6.14).

References
  1. O. G. Berg, R. B. Winter, P. H. von Hippel, Biochemistry 27, 6929-6948 (1981).
  2. D. O. Zharkov, A. P. Grollman, Mutat. Res. 577, 24-54 (2005).
  3. V. S. Sidorenko, G. V. Mechetin, G. A. Nevinsky, D. O. Zharkov, FEBS Lett. 582, 410-414 (2008).

Dmitry O. Zharkov1
Grigory V. Mechetin1
and Boris A. Veytsman2

1SB RAS Institute of Chemical Biology and Fundamental Medicine Novosibirsk, Russia, 630090
2Computational Materials Science Center George Mason University Fairfax, VA 22030, USA

Ph: +7 (383) 363-5128
Fx: +7 (383) 363-5150

dzharkov@niboch.nsc.ru