Timing facilitated site transfer of an enzyme on DNA.
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.
Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
Joseph D
JD
Schonhoft
James T
JT
Stivers
D001665:Binding Sites; D004247:DNA / Q000378:metabolism*; D004260:DNA Repair; D045643:DNA Repair Enzymes / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004058:Diffusion; D007700:Kinetics; D008722:Methods; D009068:Movement; D010710:Phosphates / Q000378:metabolism; D014498:Uracil
D004268:DNA-Binding Proteins; D010710:Phosphates; D014498:Uracil; D004247:DNA; D045643:DNA Repair Enzymes