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Long-distance radical cation reactions in DNA three-way junctions: inter-arm interaction and migration through the junction.

ABSTRACT: DNA three-way junctions (TWJ) are branched molecules having three 'arms'. We studied long-distance radical cation migration in these assemblies by incorporating anthraquinone (AQ) groups linked by a covalent tether to one strand of one arm of the TWJ. Excitation of the AQ at 350 nm results in one-electron oxidation of the DNA, which generates a base radical cation. This leads to relatively inefficient (compared with duplex DNA) strand cleavage at guanines following piperidine treatment of the irradiated samples. When the AQ is linked to the 5'-terminus of arm III by a flexible tether, gel electrophoretic analysis shows that strand cleavage occurs at the guanines in all three arms. We also investigated a TWJ in which the anthraquinone is specifically intercalated in arm III. In this case, a different pattern of strand cleavage is detected. We conclude that there are at least two mechanisms for long-distance radical cation migration in TWJs: (i) by inefficient charge hopping through the junction; (ii) by a through-space, cross-arm interaction when the AQ is on a flexible tether.

SUBMITTER: Santhosh U

PROVIDER: S-EPMC206456 | biostudies-literature | 2003 Oct

REPOSITORIES: biostudies-literature

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Long-distance radical cation reactions in DNA three-way junctions: inter-arm interaction and migration through the junction.

Santhosh U U Schuster Gary B GB

Nucleic acids research 20031001 19

DNA three-way junctions (TWJ) are branched molecules having three 'arms'. We studied long-distance radical cation migration in these assemblies by incorporating anthraquinone (AQ) groups linked by a covalent tether to one strand of one arm of the TWJ. Excitation of the AQ at 350 nm results in one-electron oxidation of the DNA, which generates a base radical cation. This leads to relatively inefficient (compared with duplex DNA) strand cleavage at guanines following piperidine treatment of the ir ...[more]

PMID: 14500833

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Project description:To directly compare the reactivity of positively charged carbon-centered aromatic σ-radicals toward methanol in solution and in the gas phase, the 2-, 3-, and 4-dehydropyridinium cations (distonic isomers of the pyridine radical cation) were generated by ultraviolet photolysis of the corresponding iodo precursors in a mixture of water and methanol at varying pH. The reaction mixtures were analyzed by using liquid chromatography/mass spectrometry. Hydrogen atom abstraction was the only reaction observed for the 3- and 4-dehydropyridinium cations (and pyridines) in solution. This also was the major reaction observed earlier in the gas phase. Depending on the pH, the hydrogen atom can be abstracted from different molecules (i.e., methanol or water) and from different sites (in methanol) by the 3- and 4-dehydropyridinium cations/pyridines in solution. In the pH range 1-4, the methyl group of methanol is the main hydrogen atom donor site for both 3- and 4-dehydropyridinium cations (just like in the gas phase). At higher pH, the hydroxyl groups of water and methanol also act as hydrogen atom donors. This finding is rationalized by a greater abundance of the unprotonated radicals that preferentially abstract hydrogen atoms from the polar hydroxyl groups. The percentage yield of hydrogen atom abstraction by these radicals was found to increase with lowering the pH in the pH range 1.0-3.2. This pH effect is rationalized by polar effects: the lower the pH, the greater the fraction of protonated (more polar) radicals in the solution. This finding is consistent with previous results obtained in the gas phase and suggests that gas-phase studies can be used to predict solution reactivity, but only as long as the same reactive species is studied in both experiments. This was found not to be the case for the 2-iodopyridinium cation. Photolysis of this precursor in solution resulted in the formation of two major addition products, 2-hydroxy- and 2-methoxypyridinium cations, in addition to the hydrogen atom abstraction product. These addition products were not observed in the earlier gas-phase studies on 2-dehydropyridinium cation. Their observation in solution is explained by the formation of another reactive intermediate, the 2-pyridylcation, upon photolysis of 2-iodopyridinium cation (and 2-iodopyridine). The same intermediate was observed in the gas phase but it was removed before examining the reactions of the desired radical, 2-dehydropyridinium cation (which cannot be done in solution).

Dataset Information

Long-distance radical cation reactions in DNA three-way junctions: inter-arm interaction and migration through the junction.

Publications

Long-distance radical cation reactions in DNA three-way junctions: inter-arm interaction and migration through the junction.

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