Ab initio molecular orbital calculations on DNA base pair radical ions: effect of base pairing on proton-transfer energies, electron affinities, and ionization potentials

Colson, Anny‐Odile; Besler, Brent; Sevilla, Michael D.

doi:10.1021/j100203a039

Cited by 157 publications

(176 citation statements)

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“…Based on the gas-phase IEs, G is the easiest to oxidize, however, the positive charge does not necessarily remain on G and can migrate along the DNA strand as far as 200Å [1][2][3] to the other low IE sites (i.e., extended G runs). Charge migration is coupled with ionization-induced proton transfer [4][5][6][7][8][9][10], which separates the hole and the radical center. These processes ultimately lead to the formation of oxo-guanine (8-oxo-7,8-dihydroguanine) and fused thymine dimers [11].…”

Section: Introductionmentioning

confidence: 99%

Electronic Structure and Spectroscopy of Nucleic Acid Bases: Ionization Energies, Ionization-Induced Structural Changes, and Photoelectron Spectra

et al. 2010

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We report high-level ab initio calculations and single-photon ionization mass spectrometry study of ionization of adenine (A), thymine (T), cytosine (C) and guanine (G). For thymine and adenine, only the lowest-energy tautomers were considered, whereas for cytosine and guanine we characterized five lowest-energy tautomeric forms. The first adiabatic and several vertical ionization energies were computed us-

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Section: Introductionmentioning

confidence: 99%

Electronic Structure and Spectroscopy of Nucleic Acid Bases: Ionization Energies, Ionization-Induced Structural Changes, and Photoelectron Spectra

et al. 2010

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“…Theoretical studies of electron attachment to DNA subunits were pioneered by Colson, Belson, and Sevilla approximately 25 years ago using the Hartree-Fock (HF) approximation [119]. Subsequently, EA values were refined using post-HF methods that introduce electron correlation at different levels, including second order Møller-Plesset perturbation theory -MP2 -, coupled-clusters including perturbative triple excitations -CCSD(T) -, and multiconfigurational perturbation theory -CASPT2.…”

Section: Electron Affinitiesmentioning

confidence: 99%

Interactions between low energy electrons and DNA: a perspective from first-principles simulations

Kohanoff¹,

McAllister²,

Tribello³

et al. 2017

J. Phys.: Condens. Matter

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Abstract. DNA damage caused by irradiation has been studied for many decades. Such studies allow us to better assess the dangers posed by radiation, and to increase the efficiency of the radiotherapies that are used to combat cancer. A full description of the irradiation process involves multiple size and time scales. It starts from the interaction of radiation -either photons or swift ions -with the biological medium. Such interactions cause electronic excitation and ionisation. The two main products of ionising radiation are thus electrons and radicals. Both of these species can cause damage to biological molecules, in particular DNA. In the long run, this molecular level damage can prevent cells from replicating and can hence lead to cell death. For a long time it was assumed that the main actors in the damage process were the radicals. However, experiments in a seminal paper by the group of Leon Sanche in 2000 showed that low-energy electrons (LEE), such as those generated when ionising biological targets, can also cause bond breaks in biomolecules, in particular strand breaks in plasmid DNA [1]. These results prompted a significant amount of experimental and theoretical work aimed at elucidating the role played by LEE in DNA damage.In this Topical Review we provide a general overview of the problem. We discuss experimental findings and theoretical results hand in hand with the aim of describing the physics and chemistry that occurs during the process of radiation damage, from the initial stages of electronic excitation, through the inelastic propagation of electrons in the medium, the interaction of electrons with DNA, and the chemical end-point effects on DNA. A very important aspect of this discussion is the consideration of a realistic, physiological environment. The role played by the aqueous solution and the amino acids from the histones in chromatin must be considered. Moreover, thermal fluctuations must be incorporated when studying these phenomena. Hence, a special place in this Topical Review is occupied by our recent first-principles molecular dynamics simulations that address the issue of how the environment favours or prevents LEEs from causing damage to DNA. We finish by summarising the conclusions achieved so far, and by suggesting a number of possible directions for further study.

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“…The ionization potentials of DNA bases in GC and AT hydrogen-bonded base pairs were calculated by Colson et al 47 using HF/3-21G and HF/6-31þG(d)//HF/3-21G methods in Koopmans' approximations which were further refined by Li et al 48,49 using the B3LYP method and the 6-31þG(d) basis set (Hutter and Clark 50 and Bertran et al 51 ). The calculated IP vert for GC and AT base pairs, by Li et al 48,49 , were found to be 7.23 and 7.80 eV; however, the zero-point energy (ZPE)-corrected adiabatic IP of GC and ATwere found to be 6.90 and 7.68 eV, respectively.…”

Section: Ionization Potential Of Dna Bases and Base Pairsmentioning

confidence: 99%

Theoretical Modeling of Radiation‐Induced DNA Damage

Kumar

Sevilla

2009

Radical and Radical Ion Reactivity in Nucleic Acid Chemistry

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Ab initio molecular orbital calculations on DNA base pair radical ions: effect of base pairing on proton-transfer energies, electron affinities, and ionization potentials

Cited by 157 publications

References 6 publications

Electronic Structure and Spectroscopy of Nucleic Acid Bases: Ionization Energies, Ionization-Induced Structural Changes, and Photoelectron Spectra

Electronic Structure and Spectroscopy of Nucleic Acid Bases: Ionization Energies, Ionization-Induced Structural Changes, and Photoelectron Spectra

Interactions between low energy electrons and DNA: a perspective from first-principles simulations

Theoretical Modeling of Radiation‐Induced DNA Damage

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