PL EN


Preferences help
enabled [disable] Abstract
Number of results
Journal
2013 | 11 | 7 | 1079-1090
Article title

The influence of (5′R) and (5′S)-5′,8-cyclo-2′-deoxyadenosine for the electronic properties of nucleosides pairs. The theoretical quantum mechanics studies

Content
Title variants
Languages of publication
EN
Abstracts
EN
Oxidatively generated damage to DNA frequently appears in the human genome as the effect of aerobic metabolism or as the result of exposure to exogenous oxidizing agents such as ionization radiation. In this paper, for the first time, the electronic properties of nucleoside pairs containing 5′,8-cyclo-2′-deoxyadenosine (cdA) in their 5′R and 5′S diastereomeric forms (cdA(R)::T and cdA(S)::T) as the simplest model of ds-DNA have been discussed. The following values of the selected electronic parameters, measured in eV, were found for cdA(R)::T, cdA(S)::T, and dA::T, respectively, adiabatic/vertical electron affinity: 0.39/0.24, 0.35/0.18, 0.33/0.21; and adiabatic/vertical ionization potential: 7.27/7.50, 7.7.25/7.49, 7.03/7.27. Moreover, based on the results of the relaxation energy, the presence of cdA(S)::T should provide the highest barrier for electron transfer in ds-DNA. Analyses of hydrogen bond length deviations reveal that the formation of cationic forms results in higher elongation than that of anionic forms. Moreover, during the electron attachment or detachment for the investigated cdA(R)::T, cdA(S)::T, and dA::T nucleoside pairs, the same scheme of changes in hydrogen bond length was noted. [...]
Publisher
Journal
Year
Volume
11
Issue
7
Pages
1079-1090
Physical description
Dates
published
1 - 7 - 2013
online
26 - 4 - 2013
References
  • [1] J.D. Watson, T.A. Baker, S.P. Bell, A. Gann, M. Levine, R. Losick, Molecular Biology of the Gene, 5th Edition (Benjamin Cummings, Cols Spring Harbor Laboratory Press, San Francisco, 2004) 19 and 181
  • [2] L.C. Panasci, M.A. Alaoui-Jamali, DNA Repair In Cancer Therapy (Humana Press, Totowa, New Jersey, 2004)
  • [3] M.S. Cook, M.D. Evans, M. Dizdaroglu, J. Lunec, FASEB J. 17, 1195 (2003) http://dx.doi.org/10.1096/fj.02-0752rev[Crossref]
  • [4] M.K. Eberhardt, Reactive Oxygen Metabolites. Chemistry and Medical Conseqences (Boca Raton, CRC Press, Chicago, 2001) 13
  • [5] A. Sancar, L.A. Lindsey-Boltz, K. Unsal-Kaçmaz, S. Linn, Annual Rev. Biochem. 73, 39, (2004) http://dx.doi.org/10.1146/annurev.biochem.73.011303.073723[Crossref]
  • [6] G.A. Qureshi, S.H. Parvez, Oxidative Stress and Neurodegenerative Disorders (Elsevier, Amsterdam and Oxford, 2007) 89 and 165
  • [7] R. Vasita, D.S. Katti, Int. J. Nanomedicine 1, 15 (2006) http://dx.doi.org/10.2147/nano.2006.1.1.15[Crossref]
  • [8] G.B. Shuster, U. Landman, Top Curr. Chem. 236, 139 (2004) http://dx.doi.org/10.1007/b94414[Crossref]
  • [9] J.C. Genereux, J.K. Barton, Chem. Rev. 110, 1642 (2010) http://dx.doi.org/10.1021/cr900228f[Crossref]
  • [10] Ch. Chatgilialoglu, C. Ferreri, M.A. Trzidis, Chem. Soc. Rev. 40, 1368 (2011) http://dx.doi.org/10.1039/c0cs00061b[Crossref]
  • [11] N. Belmadoui, F. Boussicault, M. Guerra, J-L. Ravanat, Ch. Chatgilialoglu, J. Cadet, Org. Biomol. Chem. 8, 3211 (2010) http://dx.doi.org/10.1039/c004531d[Crossref]
  • [12] H. Huang, A.K. Basu, M.P. Stone, Chem. Res. Toxicol. 25, 478 (2012) http://dx.doi.org/10.1021/tx2005053[Crossref]
  • [13] I. Kuraoka, P. Robins, Ch. Masutani, F. Hanaoka, D. Gasparutto, J. Cadet, R.D. Wood, T. Lindahl, JBC 267, 49283 (2001) http://dx.doi.org/10.1074/jbc.M107779200[Crossref]
  • [14] C. You, X. Dai, B. Yuan, J. Wang, P.J. Brooks, L.J. Niedernhofer, Y. Wang, Nat. Chem. Biol. 8, 817 (2012) http://dx.doi.org/10.1038/nchembio.1046[Crossref]
  • [15] I. Kuraoka, Ch. Bender, A. Romieu, J. Cadet, R.W. Wood, T. Lindahl, PNAS 97, 3832 (2000) http://dx.doi.org/10.1073/pnas.070471597[Crossref]
  • [16] P. Jaruga, M. Dizdaroglu, DNA Repair 7, 1413 (2008) http://dx.doi.org/10.1016/j.dnarep.2008.06.005[Crossref]
  • [17] V.P. Jasti, R.S. Das, B.A. Hilton, S. Weerasooriya, Y. Zou, A.K. Basu, Biochemistry 50, 3862 (2011) http://dx.doi.org/10.1021/bi2004944[Crossref]
  • [18] D. Bhattacharyya, S. Ramachandran, S. Sharma, W. Pathmasiri, C.L. King, I. Baskerville-Abraham, G. Boysen, J.A. Swenberg, S.L. Campbell, N.V. Dokholyan, S.G. Chaney, PLoS ONE 6(8), e23582 (2011) doi:10.1371/journal.pone.0023582 http://dx.doi.org/10.1371/journal.pone.0023582[Crossref]
  • [19] A.D. Beck, J. Chem. Phys. 98, 5648 (1993) http://dx.doi.org/10.1063/1.464913[Crossref]
  • [20] C. Lee, W. Yang, R.G. Parr, Phys. Rev. B 37, 785 (1988) http://dx.doi.org/10.1103/PhysRevB.37.785[Crossref]
  • [21] W.J. Hehre, L. Radom, P. Schleyer, R.J.A. Pople, Ab Initio Molecular Orbital Theory (Wiley, New York, 1986) 63–101
  • [22] G.A. Petersson, A. Bennett, T.G. Tensfeldt, M.A. Al-Laham, W.A. Shirley, J. Mantzaris, J. Chem. Phys. 89, 2193 (1988) http://dx.doi.org/10.1063/1.455064[Crossref]
  • [23] G.A. Petersson, M.A. Al-Laham, J. Chem. Phys. 94, 6081 (1991) http://dx.doi.org/10.1063/1.460447[Crossref]
  • [24] V. Venkatensan, S. Sundararajan, K. Sankaran, K.S. Viswanathan, Spectrochim. Acta. Part A 58, 467 (2002) http://dx.doi.org/10.1016/S1386-1425(01)00555-8[Crossref]
  • [25] B.T. Karwowski, Comput. Theoret. Chem. 997, 55 (2012) http://dx.doi.org/10.1016/j.comptc.2012.07.036[Crossref]
  • [26] Y. Zhao, J. Pu, B.J. Lynch, D.G. Truhlar, PCCP 6, 673 (2004) http://dx.doi.org/10.1039/b316260e[Crossref]
  • [27] Y. Zhao, D.G. Truhlar, J. Phys. Chem. A. 109, 5656 (2005) http://dx.doi.org/10.1021/jp050536c[Crossref]
  • [28] A. Dkhissi, R. Blossey, Chem. Phys. Lett. 439, 35 (2007) http://dx.doi.org/10.1016/j.cplett.2007.03.065[Crossref]
  • [29] J.C. Rienstra-Kiracofe, G.S. Tschumper, H.F. Schaefer III, S. Nandi, B. Ellison, Chem. Rev. 102, 231 (2002) http://dx.doi.org/10.1021/cr990044u[Crossref]
  • [30] Ch-G. Zhan, J.A. Nichols, D.A. Dixon, J. Phys. Chem. A 107, 4184 (2003) http://dx.doi.org/10.1021/jp0225774[Crossref]
  • [31] M. Spotheim-Maurizot, M. Mostafavi, T. Duoki, J. Belloni, Radiation Chemistry from Basics to Applications in Material and Life Sciences (EDP Scievces, Cedex A, France, 2008) 191–201
  • [32] M.D. Sevilla, D. Becker, M. Yan, S.R. Summerfield, J. Phys. Chem. 95, 3409 (1991) http://dx.doi.org/10.1021/j100161a080[Crossref]
  • [33] J.B. Foresman, A. Frisch, Exploring Chemistry with Electronic Structure Method 2nd edition (Gaussian, Inc., Pittsburgh, PA, 1996) 141–160
  • [34] M.J. Frisch, J.G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, J.A. Montgomery, T. Vreven, Jr., K.N. Kudin, J.C. Burant, J.M. Millam, S.S Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G.A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J.E. Knox, H.P. Hratchian, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, P.Y. Ayala, K. Morokuma, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich, A.D. Daniels, M.C. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Clifford, J. Cioslowski, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, C. Gonzalez, and J.A. Pople, Gaussian 03 Revision D.01 (Gaussian, Inc., Wallingford CT, 2004)
  • [35] D. Khanduri, A. Adhikary, M.D. Sevilla, In: M.M. Greenberg (Ed.), Radical and Radical Ion Reactivity in Nucleic Acid Chemistry (John Wiley Sons, Inc., New Jersey, 2009) 1
  • [36] P.T. Henderson, D. Jones, G. Hampikian, Y. Kan, G.B. Shuster, Proc. Natl. Acad. Sci.USA 96, 8353 (1999) http://dx.doi.org/10.1073/pnas.96.15.8353[Crossref]
  • [37] J. Jotmer, M. Bixon, A. Langenbacher, M.E. Michel-Beyerle, Proc. Natl. Acad. Sci.USA 95, 12759 (1998) http://dx.doi.org/10.1073/pnas.95.22.12759[Crossref]
  • [38] G.B. Schuster, U. Landman, Top Curr. Chem. 236, 139 (2004) http://dx.doi.org/10.1007/b94414[Crossref]
  • [39] B. Giese, J. Amaudurut, A-K. Kohler, M. Sporman, S. Wessely, Nature 412, 318 (2001) http://dx.doi.org/10.1038/35085542[Crossref]
  • [40] B. Giese, Acc. Chem. Res. 33, 631 (2000) http://dx.doi.org/10.1021/ar990040b[Crossref]
  • [41] M.K. Shukla, J. Leszczynski, In: M.K. Shukla, J. Leszczynski (Eds.), Radiation Induced Molecular Phenomena in Nucleic Acid (Springer Science+Business Media B.V., Netherlands, 2008) 1
  • [42] J. Sponer, J. Leszczynski, P. Hobza, Biopolymers (Nucleic Acid Sciences) 61, 3 (2002) http://dx.doi.org/10.1002/1097-0282(2001)61:1<3::AID-BIP10048>3.0.CO;2-4[Crossref]
  • [43] L. Rao, H. Ke, G. Fu, X. Xu, Y. Yan, J. Chem. Theory Comput. 5, 86 (2009) http://dx.doi.org/10.1021/ct800237n[Crossref]
  • [44] Y. Zhao, D.G. Truhlar, J. Phys. Chem. A 109, 5656 (2005) http://dx.doi.org/10.1021/jp050536c[Crossref]
  • [45] Y. Zhao, D.G. Truhlar, J. Phys. Chem. A 108, 6908 (2004) http://dx.doi.org/10.1021/jp048147q[Crossref]
  • [46] A. Dkhissi, R. Blossey, Chem. Phys. Lett. 439, 35 (2007) http://dx.doi.org/10.1016/j.cplett.2007.03.065[Crossref]
  • [47] E.K. Riley, M. Pitonak, P. Jurecka, P. Hobza, Chem. Rev. 110, 5023 (2010) http://dx.doi.org/10.1021/cr1000173[Crossref]
  • [48] J. Gu, Y. Xie, H.F. Schaefer III, J. Phys. Chem. B 109, 13067 (2005) http://dx.doi.org/10.1021/jp0515535[Crossref]
  • [49] B.T. Karwowski, Cent. Eur. J. Chem. 8, 70 (2010) http://dx.doi.org/10.2478/s11532-009-0105-0[Crossref]
  • [50] C. Altona, M. Sundaralingam, J. Am. Chem. Soc. 94, 8205 (1972) http://dx.doi.org/10.1021/ja00778a043[Crossref]
  • [51] Ch. Thibaudeau, P. Acharya, J. Chattopadhyaya, Stereoelectronic Effects in Nucleosides and Nucleotides and their Structural Implications, 2nd edition (Upsala University Press, Sweden, 2005) 22
  • [52] X. Li, Z. Cai, M.D. Sevilla, J. Phys. Chem. A. 106, 9345 (2002) http://dx.doi.org/10.1021/jp021322n[Crossref]
  • [53] H. Sugiyama, I. Saito, J. Am. Chem. Soc. 118, 7063 (1996) http://dx.doi.org/10.1021/ja9609821[Crossref]
  • [54] C. Dherin, D. Gasparutto, T.R. O’Connor, J. Cadet, S. Bpitex, Int. J. Radiat. Biol. 80, 21 (2004) http://dx.doi.org/10.1080/09553000310001632976[Crossref]
  • [55] N.A. Richardson, J. Gu, S. Wang, Y. Xie, H.F. Schaefer III., J. Am. Chem. Soc. 126, 4404 (2004) http://dx.doi.org/10.1021/ja030487m[Crossref]
  • [56] K. Miaskiewicz, J.H. Miller, F. Fuciarelli, Nucl. Acids Res. 23, 515 (1995) http://dx.doi.org/10.1093/nar/23.3.515[Crossref]
  • [57] J. Cadet, T. Douki, D. Gasparutto, J-L. Ravanat, Mutation Res. 5315 (2003)
Document Type
Publication order reference
YADDA identifier
bwmeta1.element.-psjd-doi-10_2478_s11532-013-0242-3
Identifiers
JavaScript is turned off in your web browser. Turn it on to take full advantage of this site, then refresh the page.