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BIOLOGICAL SCIENCES / BIOPHYSICS
A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA
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Departments of *Chemistry and Chemical Biology and Molecular and Cellular Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
Edited by Peter H. von Hippel, University of Oregon, Eugene, OR, and approved February 14, 2006 (received for review November 8, 2005)
A central mystery in the function of site-specific DNA-binding proteins is the detailed mechanism for rapid location and binding of target sites in DNA. Human oxoguanine DNA glycosylase 1 (hOgg1), for example, must search out rare 8-oxoguanine lesions to prevent transversion mutations arising from oxidative stress. Here we report high-speed imaging of single hOgg1 enzyme molecules diffusing along DNA stretched by shear flow. Salt-concentration-dependent measurements reveal that such diffusion occurs as hOgg1 slides in persistent contact with DNA. At near-physiologic pH and salt concentration, hOgg1 has a subsecond DNA-binding time and slides with a diffusion constant as high as 5 x 106 bp2/s. Such a value approaches the theoretical upper limit for one-dimensional diffusion and indicates an activation barrier for sliding of only 0.5 kcal/mol (1 kcal = 4.2 kJ). This nearly barrierless Brownian sliding indicates that DNA glycosylases locate lesion bases by a massively redundant search in which the enzyme selectively binds 8-oxoguanine under kinetic control.
nonspecific binding | shear flow stretching | single-molecule imaging | DNA glycosylase mechanism | hopping
Present address: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115. Author contributions: G.L.V., X.S.X., and P.C.B. designed research; P.C.B. performed research; P.C.B. and A.B. contributed new reagents/analytic tools; P.C.B. analyzed data; and P.C.B., G.L.V., X.S.X., and A.M.v.O. wrote the paper.
Conflict of interest statement: No conflicts declared.
This paper was submitted directly (Track II) to the PNAS office.
¶To whom correspondence may be addressed. E-mail: verdine{at}chemistry.harvard.edu or xie{at}chemistry.harvard.edu
© 2006 by The National Academy of Sciences of the USA
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