Journal
NATURE STRUCTURAL & MOLECULAR BIOLOGY
Volume 11, Issue 12, Pages 1230-1236Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/nsmb864
Keywords
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Funding
- NIGMS NIH HHS [GM56834-09, R01 GM056834] Funding Source: Medline
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Uracil DNA glycosylase (UDG) removes uracil from U.A or U.G base pairs in genomic DNA by extruding the aberrant uracil from the DNA base stack. A question in enzymatic DNA repair is whether UDG and related glycosylases also use an extrahelical recognition mechanism to inspect the integrity of undamaged base pairs. Using NMR imino proton exchange measurements we find that UDG substantially increases the equilibrium constant for opening of T-A base pairs by almost two orders of magnitude relative to free B-DNA. This increase is brought about by enzymatic stabilization of an open state of the base pair without increasing the rate constant for spontaneous base pair opening. These findings indicate a passive search mechanism in which UDG uses the spontaneous opening dynamics of DNA to inspect normal base pairs in a rapid genome-wide search for uracil in DNA.
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