DNA charge transport as a first step in coordinating the detection of lesions by repair proteins
Damaged bases in DNA are known to lead to errors in replication and transcription, compromising the integrity of the genome. We have proposed a model where repair proteins containing redox-active [4Fe-4S] clusters utilize DNA charge transport (CT) as a first step in finding lesions. In this model, the population of sites to search is reduced by a localization of protein in the vicinity of lesions. Here, we examine this model using single-molecule atomic force microscopy (AFM). XPD, a 5′-3′ helicase involved in nucleotide excision repair, contains a [4Fe-4S] cluster and exhibits a DNA-bound redox potential that is physiologically relevant. In AFM studies, we observe the redistribution of XPD onto kilobase DNA strands containing a single base mismatch, which is not a specific substrate for XPD but, like a lesion, inhibits CT. We further provide evidence for DNA-mediated signaling between XPD and Endonuclease III (EndoIII), a base excision repair glycosylase that also contains a [4Fe-4S] cluster. When XPD and EndoIII are mixed together, they coordinate in relocalizing onto the mismatched strand. However, when a CT-deficient mutant of either repair protein is combined with the CT-proficient repair partner, no relocalization occurs. These data not only indicate a general link between the ability of a repair protein to carry out DNA CT and its ability to redistribute onto DNA strands near lesions but also provide evidence for coordinated DNA CT between different repair proteins in their search for damage in the genome.
© 2012 by the National Academy of Sciences. Contributed by Jacqueline K. Barton, December 13, 2011 (sent for review November 1, 2011). Published online before print January 23, 2012. We thank Alison Parisian for technical assistance and Eric Olmon for preparation and purification of WT and Y82A EndoIII protein. We are also grateful to the Beckman Institute MMRC for AFM instrumentation. We also thank the National Institutes of Health (NIH) (GM49216 to J.K.B.; CA112093 to J.A.T.), and the Department of Energy (DOE) (ENIGMA program under Contract No. DE-AC02-05CH11231 to J.A.T.) for funding. We also thank the National Science Foundation (NSF) for a graduate fellowship to T.P.M. Author contributions: P.A.S., T.P.M., and J.K.B. designed research; P.A.S. and T.P.M. performed research; J.O.F. and J.A.T. contributed new reagents/analytic tools; P.A.S., T.P.M., J.O.F., J.A.T., and J.K.B. analyzed data; and P.A.S., T.P.M., J.O.F., J.A.T., and J.K.B. wrote the paper. The authors declare no conflict of interest. This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1120063109/-/DCSupplemental.
Published - Sontz2012p17255P_Natl_Acad_Sci_Usa.pdf
Supplemental Material - pnas.1120063109_SI.pdf