Our laboratory continues the development of a comprehensive model of DNA radiation induced to damage, one that describes physicochemical events from the initial track structure and DNA ion-radical-excited state formation through hole and electron transfer, to chemical events involving free radical processes that lead to secondary radicals and, finally, to combination and redox processes that result in DNA damage such as base and sugar damage, strand scission and associated base release. The spatial distribution of the damage sites is a critical portion of our model as it determines the biological effectivenes of the radiation damage. The overall goal of the current proposed effort is to test several aspects this overall model, to modify it as appropriate and thereby elucidate fundamental mechanisms of radiation damage to DNA by radiations of varying linear energy transfer (LET). These studies will be performed under conditions that emphasize the direct effect of radiation, and will employ magnetic resonance spectroscopies (ESR), product analyses, gamma and cyclotron heavy ion-beam irradiation, as well as theoretical modeling including time dependent density functional theory (TD- DFT).
The first aim will test the hypotheses that the mechanism of hole transfer process from the sugar- phosphate backbone to the DNA bases is base sequence and temperature dependent. Oligomer sequences chosen for study will provide the sequence dependence and temperature dependence of the mechanism of long range hole transfer from the DNA backbone through A runs to a remote G in DNA.
The second aim will test the hypothesis that the yields of two strand break radicals, at C5'and C3'sites in the DNA sugar phosphate backbone are LET dependent and are produced by specific oxidative and reductive mechanisms, respectively. We will test the hypothesis that, as LET increases, spatial clustering of these radicals increases to form multiple proximate strand breaks (multiple damage sites);however, the highest yields of sugar radicals do not occur precisely at the Bragg peak of the ion beam path. This would suggest that ion and radical recombinations inhibits cluster formation at the track ends.
The third aim will employ theoretical calculations to further test and confirm molecular mechanisms proposed in each of the aims. Especially significant will be the use of DFT theory to accurately predict core-excited states and test the hypotheses that one low energy electron can induce a double strand break and further that double oxidation of sugar sites leads to strand breaks without radical involvement. We believe these efforts will allow us to establish new insights into fundamental radiation processes important for biomedical research.
The goal of this research is to develop a comprehensive model of radiation damage to DNA by elucidating fundamental mechanisms of formation of damage sites in DNA using radiations of varying linear energy transfer (LET). Our model for DNA radiation damage that describes events from the initial formation of DNA ion-radicals and excited states, to hole and electron transfer, to sugar radical formation and finally to molecular products will be tested at several critical steps to illuminate the fundamental processes resulting in the formation of stable DNA damage products. These studies, which are performed under conditions that emphasize the direct-type effects of radiation, will employ gamma and cyclotron heavy ion-beam irradiations, magnetic resonance spectroscopes, density functional theory and product analysis techniques and will address major unanswered questions in DNA radiation damage that are important and pertinent to biomedical research.
|Adhikary, Amitava; Kumar, Anil; Rayala, Ramanjaneyulu et al. (2014) One-electron oxidation of gemcitabine and analogs: mechanism of formation of C3' and C2' sugar radicals. J Am Chem Soc 136:15646-53|
|Adhikary, Amitava; Kumar, Anil; Palmer, Brian J et al. (2014) Reactions of 5-methylcytosine cation radicals in DNA and model systems: thermal deprotonation from the 5-methyl group vs. excited state deprotonation from sugar. Int J Radiat Biol 90:433-45|
|Chomicz, Lidia; Petrovici, Alex; Archbold, Ian et al. (2014) An ESR and DFT study of hydration of the 2'-deoxyuridine-5-yl radical: a possible hydroxyl radical intermediate. Chem Commun (Camb) 50:14605-8|
|Petrovici, Alex; Adhikary, Amitava; Kumar, Anil et al. (2014) Presolvated electron reactions with methyl acetoacetate: electron localization, proton-deuteron exchange, and H-atom abstraction. Molecules 19:13486-97|
|Kumar, Anil; Sevilla, Michael D (2014) Proton transfer induced SOMO-to-HOMO level switching in one-electron oxidized A-T and G-C base pairs: a density functional theory study. J Phys Chem B 118:5453-8|
|Adhikary, Amitava; Kumar, Anil; Palmer, Brian J et al. (2013) Formation of S-Cl phosphorothioate adduct radicals in dsDNA S-oligomers: hole transfer to guanine vs disulfide anion radical formation. J Am Chem Soc 135:12827-38|
|Kheir, Jeanette; Chomicz, Lidia; Engle, Alyson et al. (2013) Presolvated low energy electron attachment to peptide methyl esters in aqueous solution: C-O bond cleavage at 77 K. J Phys Chem B 117:2872-7|
|Kumar, Anil; Sevilla, Michael D (2013) ýý- vs ýý-radical states of one-electron-oxidized DNA/RNA bases: a density functional theory study. J Phys Chem B 117:11623-32|
|Adhikary, Amitava; Kumar, Anil; Heizer, Alicia N et al. (2013) Hydroxyl ion addition to one-electron oxidized thymine: unimolecular interconversion of C5 to C6 OH-adducts. J Am Chem Soc 135:3121-35|
|Kumar, Anil; Sevilla, Michael D (2013) Excited state proton-coupled electron transfer in 8-oxoG-C and 8-oxoG-A base pairs: a time dependent density functional theory (TD-DFT) study. Photochem Photobiol Sci 12:1328-40|
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