References
- Adhikary A, Khanduri D, Kumar A, Sevilla MD. 2008. Photo-excitation of adenine cation radical [A•+] in the near UV-vis region produces sugar radicals in Adenosine and in its nucleotides. J Phys Chem B 112:15844–15855.
- Adhikary A, Khanduri, D, Sevilla MD. 2009. Direct observation of the protonation state and hole localization site in DNA-oligomers. J Am Chem Soc 131:8614–8619.
- Adhikary A, Kumar A, Becker D, Sevilla MD. 2012. Theory and ESR spectral studies of DNA-radicals. In: Chatgilialoglu C, Struder A, editors. Encyclopedia of radicals in chemistry, biology and materials. Chichester, UK: John Wiley & Sons Ltd. pp 1371–1396.
- Adhikary A, Kumar A, Becker D, Sevilla MD. 2006. The guanine cation radical: Investigation of deprotonation states by ESR and DFT. J Phys Chem B 110:24171–24180.
- Adhikary A, Kumar A, Heizer AN, Palmer BJ, Pottiboyina V, Liang Y, Wnuk SF, Sevilla MD. 2013b. Hydroxyl ion addition to one-electron oxidized thymine: Unimolecular interconversion of C5 to C6 OH-adducts. J Am Chem Soc 135:3121–3135.
- Adhikary A, Kumar A, Munafo SA, Khanduri D, Sevilla MD. 2010. Prototropic equilibria in DNA containing one-electron oxidized GC: Intra-duplex vs. duplex to solvent deprotonation. Phys Chem Chem Phys 12:5353–5368.
- Adhikary A, Kumar A, Palmer BJ, Todd AD, Sevilla MD. 2013a. Formation of S-Cl phosphorothioate adduct radicals in dsDNA-S-oligomers: Hole transfer to guanine vs. disulfide anion radical formation. J Am Chem Soc 135:12827–12838.
- Adhikary A, Malkhasian AYS, Collins S, Koppen J, Becker D, Sevilla MD. 2005. UVA-visible photo-excitation of guanine radical cations produces sugar radicals in DNA and model structures. Nucleic Acids Res 33:5553–5564.
- Becker D, Adhikary A, Sevilla MD. 2007. The role of charge and spin migration in DNA radiation damage. In: Chakraborty T, editor. Charge migration in DNA. Berlin, Heidelberg: Springer-Verlag. pp 139–175.
- Becker D, Adhikary A, Sevilla MD. 2010a. Mechanism of radiation induced DNA damage: Direct effects. In: Rao BSM, Wishart, J, editors. Recent trends in radiation chemistry. Singapore, New Jersey, London: World Scientific Publishing Co. pp 509–542.
- Becker D, Adhikary A, Sevilla MD. 2010b. Physicochemical mechanisms of radiation induced DNA damage. In: Hatano Y, Katsumura Y, Mozumder A, editors. Charged particle and photon interactions with matter – recent advances, applications, and interfaces. Boca Raton, London, New York: CRC Press, Taylor & Francis. pp 503–541.
- Becker D, Bryant-Friedrich A, Trzasko C, Sevilla MD. 2003. Electron spin resonance study of DNA irradiated with an argon-ion beam: Evidence for formation of sugar phosphate backbone radicals. Radiat Res 160:174–185.
- Black P J, Bernhard WA. 2011. EPR detection of an electron scavenging contaminant in irradiated deoxyoligonucleotides: One-electron reduced benzoyl. J Phys Chem B 115:8009–8013.
- Clark SJ, Harrison J, Paul CL, Frommer M. 1994. High sensitivity mapping of methylated cytosines. Nucleic Acids Res 22: 2990–2297.
- Close DM. 2003. Oxidative damage to cytosine: Implication for the study of radiation-induced damage to DNA. J Phys Chem B 107: 864–867.
- Colson A-O, Sevilla MD. 1995. Structure and relative stability of deoxyribose radicals in a model DNA backbone: Ab initio molecular orbital calculations. J Phys Chem 99:3867–3874.
- de La Harpe K, Crespo-Hernández CE, Kohler B. 2009a. The excited- state lifetimes in a G × C DNA duplex are nearly independent of helix conformation and base-pairing motif. ChemPhysChem 10:1421–1425.
- de La Harpe K, Crespo-Hernández CE, Kohler B. 2009b. Deuterium isotope effect on excited-state dynamics in an alternating GC oligonucleotide. J Am Chem Soc 131:17557–17559.
- Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, et al. 2009. Gaussian 09, Gaussian, Inc.: Wallingford, CT.
- Hissung A, von Sonntag C. 1979. The reaction of solvated electrons with cytosine, 5-methyl cytosine and 2′-deoxycytidine in squeous solution. The reaction of the electron adduct intermediates with water, p-nitroacetophenone and oxygen. A pulse spectroscopic and pulse conductometric study. Int J Radiat Biol 35:449–458.
- IQmol.. Free open-source molecular editor and visualization package; available at http://www.iqmol.org.
- Joseph J, Schuster GB. 2012. Oxidatively generated damage to DNA at 5-methylcytosine mispairs. Photochem Photobiolog Sci 11: 998–1003.
- Kanvah S, Schuster GB. 2004. One-electron oxidation of DNA: The effect of replacement of cytosine with 5-methylcytosine on long-distance radical cation transport and reaction. J Am Chem Soc 126:7341–7344.
- Kawai K, Osakada Y, Majima T. 2009. Importance of protonation state of guanine radical cation during hole transfer in DNA. Chemphyschem 10:1766–1769.
- Kawai K, Wata Y, Hara M, Tojo S, Majima T. 2002. Regulation of one-electron oxidation rate of guanine by base pairing with cytosine derivatives. J Am Chem Soc 124:3586–3590.
- Khanduri D, Adhikary A, Sevilla MD. 2011. Highly Oxidizing excited states of one-electron oxidized guanine in DNA: Wavelength and pH dependence. J Am Chem Soc 133:4527–4537.
- Krivokapić A, Øhman KT, Munthe M, Nelson WH, Hole EO, Sagstuen E. 2010. Radicals in 5-methylcytosine induced by ionizing radiation. Electron magnetic resonance for structural and mechanistic analyses. Radiat Res 173:689–702.
- Krivokapić A, Øhman KT, Nelson WH, Hole EO, Sagstuen E. 2009. Primary oxidation products of 5-methylcytosine: Methyl dynamics and environmental influences. J Phys Chem A 113:9633–9640.
- Kumar A, Sevilla MD. 2006. Photoexcitation of dinucleoside radical cations: A time-dependent density functional study. J Phys Chem B 110:24181–24188.
- Kumar A, Sevilla MD. 2008a. Radiation effects on DNA: Theoretical investigations of electron, hole and excitation pathways to DNA damage. In: Shukla MK, Leszczynski J, editors. Radiation induced molecular phenomena in nucleic acid: A comprehensive theoretical and experimental analysis. Berlin, Heidelberg: Springer-Verlag. pp 577–617.
- Kumar A, Sevilla MD. 2008b. The role of πσ* excited states in electron-induced DNA strand break formation: A time-dependent density functional theory study. J Am Chem Soc 130:2130–2131.
- Kumar A, Sevilla MD. 2009. Theoretical modeling of radiation-induced DNA damage. In: Greenberg MM, editor . Radical and radical ion activity in nucleic acid chemistry. New Jersey: John Wiley & Sons, Inc. pp 1–40.
- Li M-J, Liu L, Wei K, Yao F, Guo Q-X. 2006. Significant effects of phosphorylation on relative stabilities of DNA and RNA sugar radicals: Remarkably high susceptibility of H-2′ abstraction in RNA. J Phys Chem B 110:13582–13589.
- Li Z, Zheng Y, Cloutier P, Sanche L, Wagner JR. 2008. Low energy electron induced DNA damage: Effects of terminal phosphate and base moieties on the distribution of damage. J Am Chem Soc 130:5612–5613.
- Malone ME, Cullis PM, Symons MCR, Parker AW. 1995. Biphotonic photoionization of cytosine and its derivatives with UV radiation at 248 nm: An EPR study in low-temperature perchlorate glasses. J Phys Chem 99:9299–9308.
- Ohlmann J, Hüttermann J. 1993. Reactions of water radiolysis intermediates with pyrimidine and purine bases in aqueous BeF2 glasses: an EPR study. Int J Radiat Biol 63:427–436.
- Raiti MJ, Sevilla MD. 1999. Density functional theory investigation of the electronic structure and spin density distribution in peroxyl radicals. J Phys Chem A 103:1619–1626.
- Sevilla MD, Van Paemel C, Nichols C. 1972. An electron spin resonance study of several DNA base cation radicals produced by photoionization. J Phys Chem 76:3571–3577.
- Shkrob IA, Marin TW, Adhikary A, Sevilla MD. 2011. Photooxidation of nucleic acids on metal oxides: Physico-chemical and astrobiological perspectives. J Phys Chem C 115:3393–3403.
- Wang W, Razskazovskii Y, Sevilla MD. 1997. Secondary radical attack on DNA nucleotides: Reaction by addition to DNA bases and abstraction from sugars. Int J Radiat Biol 71:387–399.
- Zhang Q, Wang Y. 2003. Independent generation of 5- (2′-deoxycytidinyl)methyl radical and the formation of a novel cross-link lesion between 5-methylcytosine and guanine. J Am Chem Soc 125:12795–12802.
- Zuo S, Boorstein RJ, Teebor GW. 1995. Oxidative damage to 5-methylcytosine in DNA. Nucleic Acids Res 23:3239–3243.