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      Electron attachment-induced DNA single-strand breaks at the pyrimidine sites

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      1 , 2 , * , 2 , 2 , *
      Nucleic Acids Research
      Oxford University Press

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          Abstract

          To elucidate the contribution of pyrimidine in DNA strand breaks caused by low-energy electrons (LEEs), theoretical investigations of the LEE attachment-induced C 3′–O 3′, and C 5′–O 5′ σ bond as well as N-glycosidic bond breaking of 2′-deoxycytidine-3′,5′-diphosphate and 2′-deoxythymidine-3′,5′-diphosphate were performed using the B3LYP/DZP++ approach. The base-centered radical anions are electronically stable enough to assure that either the C–O or glycosidic bond breaking processes might compete with the electron detachment and yield corresponding radical fragments and anions. In the gas phase, the computed glycosidic bond breaking activation energy (24.1 kcal/mol) excludes the base release pathway. The low-energy barrier for the C 3′–O 3′ σ bond cleavage process (∼6.0 kcal/mol for both cytidine and thymidine) suggests that this reaction pathway is the most favorable one as compared to other possible pathways. On the other hand, the relatively low activation energy barrier (∼14 kcal/mol) for the C 5′–O 5′ σ bond cleavage process indicates that this bond breaking pathway could be possible, especially when the incident electrons have relatively high energy (a few electronvolts). The presence of the polarizable medium greatly increases the activation energies of either C–O σ bond cleavage processes or the N-glycosidic bond breaking process. The only possible pathway that dominates the LEE-induced DNA single strands in the presence of the polarizable surroundings (such as in an aqueous solution) is the C 3′–O 3′ σ bond cleavage (the relatively low activation energy barrier, ∼13.4 kcal/mol, has been predicted through a polarizable continuum model investigation). The qualitative agreement between the ratio for the bond breaks of C 5′–O 5′, C 3′–O 3′ and N-glycosidic bonds observed in the experiment of oligonucleotide tetramer CGAT and the theoretical sequence of the bond breaking reaction pathways have been found. This consistency between the theoretical predictions and the experimental observations provides strong supportive evidences for the base-centered radical anion mechanism of the LEE-induced single-strand bond breaking around the pyrimidine sites of the DNA single strands.

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          Most cited references53

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          Resonant formation of DNA strand breaks by low-energy (3 to 20 eV) electrons.

          Most of the energy deposited in cells by ionizing radiation is channeled into the production of abundant free secondary electrons with ballistic energies between 1 and 20 electron volts. Here it is shown that reactions of such electrons, even at energies well below ionization thresholds, induce substantial yields of single- and double-strand breaks in DNA, which are caused by rapid decays of transient molecular resonances localized on the DNA's basic components. This finding presents a fundamental challenge to the traditional notion that genotoxic damage by secondary electrons can only occur at energies above the onset of ionization, or upon solvation when they become a slowly reacting chemical species.
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            DNA strand breaks induced by 0-4 eV electrons: the role of shape resonances.

            Collisions of 0-4 eV electrons with thin DNA films are shown to produce single strand breaks. The yield is sharply structured as a function of electron energy and indicates the involvement of pi* shape resonances in the bond breaking process. The cross sections are comparable in magnitude to those observed in other compounds in the gas phase in which pi* electrons are transferred through the molecule to break a remote bond. The results therefore support aspects of a theoretical study by Barrios et al. [J. Phys. B 106, 7991 (2002)]] indicating that such a mechanism could produce strand breaks in DNA.
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              Single, double, and multiple double strand breaks induced in DNA by 3-100 eV electrons.

              Nonthermal secondary electrons with initial kinetic energies below 100 eV are an abundant transient species created in irradiated cells and thermalize within picoseconds through successive multiple energy loss events. Here we show that below 15 eV such low-energy electrons induce single (SSB) and double (DSB) strand breaks in plasmid DNA exclusively via formation and decay of molecular resonances involving DNA components (base, sugar, hydration water, etc.). Furthermore, the strand break quantum yields (per incident electron) due to resonances occur with intensities similar to those that appear between 25 and 100 eV electron energy, where nonresonant mechanisms related to excitation/ionizations/dissociations are shown to dominate the yields, although with some contribution from multiple scattering electron energy loss events. We also present the first measurements of the electron energy dependence of multiple double strand breaks (MDSB) induced in DNA by electrons with energies below 100 eV. Unlike the SSB and DSB yields, which remain relatively constant above 25 eV, the MDSB yields show a strong monotonic increase above 30 eV, however with intensities at least 1 order of magnitude smaller than the combined SSB and DSB yields. The observation of MDSB above 30 eV is attributed to strand break clusters (nano-tracks) involving multiple successive interactions of one single electron at sites that are distant in primary sequence along the DNA double strand, but are in close contact; such regions exist in supercoiled DNA (as well as cellular DNA) where the double helix crosses itself or is in close proximity to another part of the same DNA molecule.
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                Author and article information

                Journal
                Nucleic Acids Res
                nar
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                September 2010
                September 2010
                29 April 2010
                29 April 2010
                : 38
                : 16
                : 5280-5290
                Affiliations
                1Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, CAS, Shanghai 201203 P. R. China and 2Interdisciplinary Nanotoxicity Center, Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA
                Author notes
                *To whom correspondence should be addressed. Jiande Gu. Tel: +86 21 5080 6720; Fax: +86 21 5080 7088; Email: jiandegush@ 123456go.com
                Correspondence may also be addressed to Jerzy Leszczynski. Tel: +1 601 979 3482; Fax: +1 601 979 7823; Email: jerzy@ 123456icnanotox.org
                Article
                gkq304
                10.1093/nar/gkq304
                2938206
                20430827
                1cafc405-142d-4a9e-87e7-fb9b80db321b
                © The Author(s) 2010. Published by Oxford University Press.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 2 March 2010
                : 7 April 2010
                : 12 April 2010
                Categories
                Computational Biology

                Genetics
                Genetics

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