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Nucleic Acids Research, 2001, Vol. 29, No. 10 2026-2033
© 2001 Oxford University Press

Charge transport through DNA four-way junctions

Duncan T. Odom, Erik A. Dill and Jacqueline K. Barton*

Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA

Long range oxidative damage as a result of charge transport is shown to occur through single crossover junctions assembled from four semi-complementary strands of DNA. When a rhodium complex is tethered to one of the arms of the four-way junction assembly, thereby restricting its intercalation into the {pi}-stack, photo-induced oxidative damage occurs to varying degrees at all guanine doublets in the assembly, though direct strand scission only occurs at the predicted site of intercalation. In studies where the Mg2+ concentration was varied, so as to perturb base stacking at the junction, charge transport was found to be enhanced but not to be strongly localized to the arms that preferentially stack on each other. These data suggest that the conformations of four-way junctions can be relatively mobile. Certainly, in four-way junctions charge transport is less discriminate than in the more rigidly stacked DNA double crossover assemblies.

* To whom correspondence should be addressed. Tel: +1 626 395 6075; Fax: +1 626 577 4976; Email: jkbarton{at}caltech.edu


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