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Published May 1, 2000 | public
Journal Article

Long-Range Guanine Oxidation in DNA Restriction Fragments by a Triplex-Directed Naphthalene Diimide Intercalator


Naphthalene diimide (NDI), a powerful oxidant that binds avidly to DNA by intercalation, is seen to damage the 5' guanine of 5'-GG-3' sites by photoactivated charge transport through DNA. When covalently tethered to the center of a triplex-forming oligonucleotide and delivered by triplex formation within a pyrimidine·purine-pyrimidine motif to a specific site on a restriction fragment, NDI can photooxidize guanine over at least 25−38 bp in each direction from the site of binding. Charge migration occurs in both directions from the NDI intercalator and on both DNA strands of the target, but the oxidation is significantly more efficient to the 3' side of the triplex. NDI and octahedral rhodium intercalators, when tethered directly to the 5' terminus of the triplex-forming strand as opposed to the center, generate significant amounts of oxidative damage only in the immediate vicinity of the intercalation site. Given that long-range charge transport depends on DNA stacking, these results suggest that the base stack is distorted at the 5' end of the triplex region in the duplex−triplex junction. Targeting of photooxidative damage by triplex formation extends our previous studies of long-range charge transport to significantly longer DNA sequences through a strategy that does not require covalent attachment of the photooxidant to the DNA being probed. Moreover, triplex targeting of oxidative damage provides for the first time a typical distance distribution for genomic charge transport of ∼200 Å around the oxidant.

Additional Information

© 2000 American Chemical Society. Received February 7, 2000; Revised Manuscript Received March 20, 2000. Publication Date (Web): April 26, 2000. We thank William Greenberg for his helpful suggestions. This work was supported by grants from the NIH (GM53210 to L.W.M. and GM49216 to J.K.B.), as well as funding from the National Foundation for Cancer Research, the Howard Hughes Medical Institute predoctoral fellowship program (M.E.N.), and the Caltech SURF program (K.T.N.).

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October 17, 2023