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A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA

Journal Article


Abstract


  • 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 × 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. © 2006 by The National Academy of Sciences of the USA.

Publication Date


  • 2006

Citation


  • Blainey, P. C., Van Oijen, A. M., Banerjee, A., Verdine, G. L., & Xie, X. S. (2006). A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proceedings of the National Academy of Sciences of the United States of America, 103(15), 5752-5757. doi:10.1073/pnas.0509723103

Scopus Eid


  • 2-s2.0-33645807371

Start Page


  • 5752

End Page


  • 5757

Volume


  • 103

Issue


  • 15

Abstract


  • 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 × 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. © 2006 by The National Academy of Sciences of the USA.

Publication Date


  • 2006

Citation


  • Blainey, P. C., Van Oijen, A. M., Banerjee, A., Verdine, G. L., & Xie, X. S. (2006). A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proceedings of the National Academy of Sciences of the United States of America, 103(15), 5752-5757. doi:10.1073/pnas.0509723103

Scopus Eid


  • 2-s2.0-33645807371

Start Page


  • 5752

End Page


  • 5757

Volume


  • 103

Issue


  • 15