TY - JOUR
T1 - Timing facilitated site transfer of an enzyme on DNA
AU - Schonhoft, Joseph D.
AU - Stivers, James T.
N1 - Funding Information:
We thank J. Parker (Harvard Medical School) for purified hUNG used in this study. This work was supported by US National Institutes of Health grant GM056834.
PY - 2012/2
Y1 - 2012/2
N2 - Many enzymes that react with specific sites in DNA have the property of facilitated diffusion, in which the DNA chain is used as a conduit to accelerate site location. Despite the importance of such mechanisms in gene regulation and DNA repair, there have been few viable approaches to elucidate the microscopic process of facilitated diffusion. Here we describe a new method in which a small-molecule trap (uracil) is used to clock a DNA repair enzyme as it hops and slides between damaged sites in DNA. The 'molecular clock' provides unprecedented information: the mean length for DNA sliding, the one-dimensional diffusion constant, the maximum hopping radius and the time frame for DNA hopping events. In addition, the data establish that the DNA phosphate backbone is a sufficient requirement for DNA sliding.
AB - Many enzymes that react with specific sites in DNA have the property of facilitated diffusion, in which the DNA chain is used as a conduit to accelerate site location. Despite the importance of such mechanisms in gene regulation and DNA repair, there have been few viable approaches to elucidate the microscopic process of facilitated diffusion. Here we describe a new method in which a small-molecule trap (uracil) is used to clock a DNA repair enzyme as it hops and slides between damaged sites in DNA. The 'molecular clock' provides unprecedented information: the mean length for DNA sliding, the one-dimensional diffusion constant, the maximum hopping radius and the time frame for DNA hopping events. In addition, the data establish that the DNA phosphate backbone is a sufficient requirement for DNA sliding.
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U2 - 10.1038/nchembio.764
DO - 10.1038/nchembio.764
M3 - Article
C2 - 22231272
AN - SCOPUS:84856117713
SN - 1552-4450
VL - 8
SP - 205
EP - 210
JO - Nature chemical biology
JF - Nature chemical biology
IS - 2
ER -