How different DNA-binding proteins affect long-range oxidative damage to DNA

Here the effect on DNA-mediated charge transport of binding by a variety of proteins is examined. DNA assemblies were constructed that contain a tethe red rhodium intercalator, as photooxidant, as well as two 5 ' -GG-3 ' sites flanking the DNA-binding site for the different proteins. By monitoring th e ratio of oxidative damage promoted at the guanine doublet situated distal to the protein-binding site versus that at the proximal site as a function of protein binding, the effects of binding the proteins on DNA-mediated ch arge transport were determined. Proteins examined included both the wild-ty pe and mutant methyltransferase, M.HhaI, which are base-flipping enzymes, t he restriction endonuclease R.PvuII, a TATA-binding protein, which kinks th e DNA, and the transcription factor Antennapedia homeodomain protein, which binds DNA through a helix-turn-helix motif. In general, it was observed th at yields of long-range oxidative damage correlate with protein-dependent a lterations in DNA base stacking. Interactions that disturb the DNA pi -stac k inhibit DNA charge transport. Alternatively, interactions that promote no helix distortion but, as a result of tight packing, may rigidify the pi -s tack, serve instead to enhance the ability of the DNA base pairs to serve a s a conduit for charge transport. Thus, protein binding to DNA modulates lo ng-range charge transport both negatively and positively, depending upon th e specific protein/DNA interactions in play. Long-range DNA charge transpor t and this modulation by protein binding may be important to consider physi ologically.