Damage site location by uracil DNA glycosylase involves short‐range sliding and efficient DNA hopping

The astonishingly efficient location and excision of damaged DNA bases by DNA repair glycosylases is an especially intriguing mechanistic problem. The problem is exemplified by the paradigm enzyme uracil DNA glycosylase (UNG) that excises rare uracil bases from genomic DNA. Here we explore the efficiency and mechanism by which UNG executes intramolecular transfer and excision of two uracil sites embedded at increasing distances from each other in duplex DNA. At low salt concentrations, the efficiency of intramolecular site excision ( f intra ) decreased from 61 to zero percent as the base pair spacing between uracil sites increased from 20 to 800 bp. The mechanism of transfer is dominated by one‐dimensional sliding for spacings less than about 56 bps with an estimated diffusion constant of 7 × 10 5 bp 2 /s, with predominantly three‐dimensional hopping for spacings greater than about 200 bps. At intermediate spacings, both sliding and hopping pathways are operative. Physiological salt concentration decreased f intra by 76 % at a site spacing of 56 bp, with only 1 in 10 UNG molecules cleaving the second site in an intramolecular transfer event. We develop a generally useful kinetic model for interpreting ensemble site transfer data that provides the fractional contribution of sliding and hopping pathways as a function of site spacing. Our analysis indicates that intramolecular hopping and 3D diffusion through bulk solution are the principal pathways for efficient patrolling of long genomic DNA sequences for damage. Thus, short‐range sliding events only function to allow redundant inspection of very local DNA sequences. This work was supported by NIH grant GM56834‐10 awarded to J.T.S.