A kinetic Trapping Method for Evaluating One and Three Dimensional Target Site Location Mechanisms of Human Uracil DNA Glycosylase (UNG)

Abstract

Maintaining the integrity of the encoded information within the human genome is a significant challenge for DNA repair systems. One such system is uracil base excision repair (BER) which begins by the action of Uracil DNA Glycosylase (UNG) that functions to remove incorporated uracils within the genome. While the enzymatic mechanisms and structures of BER glycosylase enzymes including UNG have been extensively studied, the diffusional mechanism by which these enzymes locate their target lesions efficiently among the high background of normal DNA is not well understood. A strategy that has been proposed is the use of facilitated transfer of the enzyme along DNA by non-specific DNA-protein interactions, which serves to increase the speed of target site location by reducing the search dimensionality from three to one dimension. While UNG and other glycosylases are considered to employ this strategy, the exact details are largely unknown. Here we describe a novel approach to unravel the short range DNA transfer mechanism of UNG using small molecule inhibitors that kinetically trap transient dissociated intermediates along the transfer pathway. We find that there is a very high probability that an UNG molecule will dissociate from DNA in the process of transferring between two uracil sites separated by only 20 bp along DNA. We use this kinetic trapping approach to estimate the net rate of intermolecular transfer between uracil sites as a function of site spacing, providing the first quantitative ensemble measurements of site transfer rates of a DNA repair enzyme.