DNA charge transport as a first step in coordinating the detection of lesions by repair proteins

Abstract

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 redoxactive [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 DNAbound 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.DNA electron transfer | iron-sulfur clusters | oxidative damage

Active transcriptomic and proteomic reprogramming in theC. elegansnucleotide excision repair mutant xpa-1

“…DNA charge transport has been suggested to activate MAPK signaling. 56,57 MAPK activation was also suggested from transcriptome analysis of another NER mutant, ercc-1 39 , where we found a strong correlation between genes regulated by the PMK-1 p38 MAPK and the ercc-1 data set. Together, these results suggest that NER function is not lifespan-limiting in C. elegans partially due to an adaptive transcriptome reprogramming involving activation of p38 MAPK stress-response signaling.…”

Solution, surface, and single molecule platforms for the study of DNA-mediated charge transport

“…Remarkably, when its localization near DNA damage is studied by AFM, XPD is found to cooperate with EndoIII to promote redistribution around mismatches, despite the fact that these proteins are derived from entirely different organisms. 136 This result highlights the universal nature of DNA CT as a mechanism for long-distance biological signaling and coordination of protein activities even, between proteins of diverse structure and function.…”

Unified model for conductance through DNA with the Landauer-Büttiker formalism

“…[4][5][6] Many efforts [7][8][9][10][11][12][13][14][15][16] have been devoted to understanding the mechanism of charge transfer and transport in DNA. From an electrical device perspective, double barrier resonant tunneling structures, 17 spin specific electron conductor, 18,19 field effect transistor, 20 trinary logic, 21 optomechanical molecular motor, 22 negative differential resistance, 23 detection of lesions by repair proteins 24 and doping 25 are in principle possible with DNA. Furthermore, recent work has also shown that it is possible to detect diseases by measuring the electrical conductivity of DNA.…”