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Nontarget DNA binding shapes the dynamic landscape for enzymatic recognition of DNA damage.

ABSTRACT: The DNA repair enzyme human uracil DNA glycosylase (UNG) scans short stretches of genomic DNA and captures rare uracil bases as they transiently emerge from the DNA duplex via spontaneous base pair breathing motions. The process of DNA scanning requires that the enzyme transiently loosen its grip on DNA to allow stochastic movement along the DNA contour, while engaging extrahelical bases requires motions on a more rapid timescale. Here, we use NMR dynamic measurements to show that free UNG has no intrinsic dynamic properties in the millisecond to microsecond and subnanosecond time regimes, and that the act of binding to nontarget DNA reshapes the dynamic landscape to allow productive millisecond motions for scanning and damage recognition. These results suggest that DNA structure and the spontaneous dynamics of base pairs may drive the evolution of a protein sequence that is tuned to respond to this dynamic regime.

SUBMITTER: Friedman JI

PROVIDER: S-EPMC2699497 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature

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Nontarget DNA binding shapes the dynamic landscape for enzymatic recognition of DNA damage.

Friedman Joshua I JI Majumdar Ananya A Stivers James T JT

Nucleic acids research 20090401 11

The DNA repair enzyme human uracil DNA glycosylase (UNG) scans short stretches of genomic DNA and captures rare uracil bases as they transiently emerge from the DNA duplex via spontaneous base pair breathing motions. The process of DNA scanning requires that the enzyme transiently loosen its grip on DNA to allow stochastic movement along the DNA contour, while engaging extrahelical bases requires motions on a more rapid timescale. Here, we use NMR dynamic measurements to show that free UNG has n ...[more]

PMID: 19339520

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