Skip to content
BY-NC-ND 3.0 license Open Access Published by De Gruyter Open Access April 26, 2013

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

Boleslaw Karwowski
From the journal Open Chemistry


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.

[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 Search in Google Scholar

[2] L.C. Panasci, M.A. Alaoui-Jamali, DNA Repair In Cancer Therapy (Humana Press, Totowa, New Jersey, 2004) 10.1007/978-1-59259-735-2Search in Google Scholar

[3] M.S. Cook, M.D. Evans, M. Dizdaroglu, J. Lunec, FASEB J. 17, 1195 (2003) in Google Scholar PubMed

[4] M.K. Eberhardt, Reactive Oxygen Metabolites. Chemistry and Medical Conseqences (Boca Raton, CRC Press, Chicago, 2001) 13 10.1201/9781420041521Search in Google Scholar

[5] A. Sancar, L.A. Lindsey-Boltz, K. Unsal-Kaçmaz, S. Linn, Annual Rev. Biochem. 73, 39, (2004) in Google Scholar PubMed

[6] G.A. Qureshi, S.H. Parvez, Oxidative Stress and Neurodegenerative Disorders (Elsevier, Amsterdam and Oxford, 2007) 89 and 165 Search in Google Scholar

[7] R. Vasita, D.S. Katti, Int. J. Nanomedicine 1, 15 (2006) in Google Scholar PubMed PubMed Central

[8] G.B. Shuster, U. Landman, Top Curr. Chem. 236, 139 (2004) in Google Scholar

[9] J.C. Genereux, J.K. Barton, Chem. Rev. 110, 1642 (2010) in Google Scholar PubMed PubMed Central

[10] Ch. Chatgilialoglu, C. Ferreri, M.A. Trzidis, Chem. Soc. Rev. 40, 1368 (2011) in Google Scholar PubMed

[11] N. Belmadoui, F. Boussicault, M. Guerra, J-L. Ravanat, Ch. Chatgilialoglu, J. Cadet, Org. Biomol. Chem. 8, 3211 (2010) in Google Scholar PubMed

[12] H. Huang, A.K. Basu, M.P. Stone, Chem. Res. Toxicol. 25, 478 (2012) in Google Scholar PubMed PubMed Central

[13] I. Kuraoka, P. Robins, Ch. Masutani, F. Hanaoka, D. Gasparutto, J. Cadet, R.D. Wood, T. Lindahl, JBC 267, 49283 (2001) in Google Scholar PubMed

[14] C. You, X. Dai, B. Yuan, J. Wang, P.J. Brooks, L.J. Niedernhofer, Y. Wang, Nat. Chem. Biol. 8, 817 (2012) in Google Scholar PubMed PubMed Central

[15] I. Kuraoka, Ch. Bender, A. Romieu, J. Cadet, R.W. Wood, T. Lindahl, PNAS 97, 3832 (2000) in Google Scholar PubMed PubMed Central

[16] P. Jaruga, M. Dizdaroglu, DNA Repair 7, 1413 (2008) in Google Scholar PubMed

[17] V.P. Jasti, R.S. Das, B.A. Hilton, S. Weerasooriya, Y. Zou, A.K. Basu, Biochemistry 50, 3862 (2011) in Google Scholar PubMed PubMed Central

[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 in Google Scholar PubMed PubMed Central

[19] A.D. Beck, J. Chem. Phys. 98, 5648 (1993) in Google Scholar

[20] C. Lee, W. Yang, R.G. Parr, Phys. Rev. B 37, 785 (1988) in Google Scholar PubMed

[21] W.J. Hehre, L. Radom, P. Schleyer, R.J.A. Pople, Ab Initio Molecular Orbital Theory (Wiley, New York, 1986) 63–101 Search in Google Scholar

[22] G.A. Petersson, A. Bennett, T.G. Tensfeldt, M.A. Al-Laham, W.A. Shirley, J. Mantzaris, J. Chem. Phys. 89, 2193 (1988) in Google Scholar

[23] G.A. Petersson, M.A. Al-Laham, J. Chem. Phys. 94, 6081 (1991) in Google Scholar

[24] V. Venkatensan, S. Sundararajan, K. Sankaran, K.S. Viswanathan, Spectrochim. Acta. Part A 58, 467 (2002) in Google Scholar

[25] B.T. Karwowski, Comput. Theoret. Chem. 997, 55 (2012) in Google Scholar

[26] Y. Zhao, J. Pu, B.J. Lynch, D.G. Truhlar, PCCP 6, 673 (2004) in Google Scholar

[27] Y. Zhao, D.G. Truhlar, J. Phys. Chem. A. 109, 5656 (2005) in Google Scholar PubMed

[28] A. Dkhissi, R. Blossey, Chem. Phys. Lett. 439, 35 (2007) in Google Scholar

[29] J.C. Rienstra-Kiracofe, G.S. Tschumper, H.F. Schaefer III, S. Nandi, B. Ellison, Chem. Rev. 102, 231 (2002) in Google Scholar PubMed

[30] Ch-G. Zhan, J.A. Nichols, D.A. Dixon, J. Phys. Chem. A 107, 4184 (2003) in Google Scholar

[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 Search in Google Scholar

[32] M.D. Sevilla, D. Becker, M. Yan, S.R. Summerfield, J. Phys. Chem. 95, 3409 (1991) in Google Scholar

[33] J.B. Foresman, A. Frisch, Exploring Chemistry with Electronic Structure Method 2nd edition (Gaussian, Inc., Pittsburgh, PA, 1996) 141–160 Search in Google Scholar

[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) Search in Google Scholar

[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 Search in Google Scholar

[36] P.T. Henderson, D. Jones, G. Hampikian, Y. Kan, G.B. Shuster, Proc. Natl. Acad. Sci.USA 96, 8353 (1999) in Google Scholar PubMed PubMed Central

[37] J. Jotmer, M. Bixon, A. Langenbacher, M.E. Michel-Beyerle, Proc. Natl. Acad. Sci.USA 95, 12759 (1998) in Google Scholar PubMed PubMed Central

[38] G.B. Schuster, U. Landman, Top Curr. Chem. 236, 139 (2004) in Google Scholar

[39] B. Giese, J. Amaudurut, A-K. Kohler, M. Sporman, S. Wessely, Nature 412, 318 (2001) in Google Scholar

[40] B. Giese, Acc. Chem. Res. 33, 631 (2000) in Google Scholar

[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 10.1007/978-1-4020-8184-2_1Search in Google Scholar

[42] J. Sponer, J. Leszczynski, P. Hobza, Biopolymers (Nucleic Acid Sciences) 61, 3 (2002)<3::AID-BIP10048>3.0.CO;2-410.1002/1097-0282(2001)61:1<3::AID-BIP10048>3.0.CO;2-4Search in Google Scholar

[43] L. Rao, H. Ke, G. Fu, X. Xu, Y. Yan, J. Chem. Theory Comput. 5, 86 (2009) in Google Scholar

[44] Y. Zhao, D.G. Truhlar, J. Phys. Chem. A 109, 5656 (2005) in Google Scholar

[45] Y. Zhao, D.G. Truhlar, J. Phys. Chem. A 108, 6908 (2004) in Google Scholar

[46] A. Dkhissi, R. Blossey, Chem. Phys. Lett. 439, 35 (2007) in Google Scholar

[47] E.K. Riley, M. Pitonak, P. Jurecka, P. Hobza, Chem. Rev. 110, 5023 (2010) in Google Scholar

[48] J. Gu, Y. Xie, H.F. Schaefer III, J. Phys. Chem. B 109, 13067 (2005) in Google Scholar PubMed

[49] B.T. Karwowski, Cent. Eur. J. Chem. 8, 70 (2010) in Google Scholar

[50] C. Altona, M. Sundaralingam, J. Am. Chem. Soc. 94, 8205 (1972) in Google Scholar PubMed

[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 Search in Google Scholar

[52] X. Li, Z. Cai, M.D. Sevilla, J. Phys. Chem. A. 106, 9345 (2002) in Google Scholar

[53] H. Sugiyama, I. Saito, J. Am. Chem. Soc. 118, 7063 (1996) in Google Scholar

[54] C. Dherin, D. Gasparutto, T.R. O’Connor, J. Cadet, S. Bpitex, Int. J. Radiat. Biol. 80, 21 (2004) in Google Scholar PubMed

[55] N.A. Richardson, J. Gu, S. Wang, Y. Xie, H.F. Schaefer III., J. Am. Chem. Soc. 126, 4404 (2004) in Google Scholar PubMed

[56] K. Miaskiewicz, J.H. Miller, F. Fuciarelli, Nucl. Acids Res. 23, 515 (1995) in Google Scholar PubMed PubMed Central

[57] J. Cadet, T. Douki, D. Gasparutto, J-L. Ravanat, Mutation Res. 5315 (2003) Search in Google Scholar

Published Online: 2013-4-26
Published in Print: 2013-7-1

© 2013 Versita Warsaw

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Scroll Up Arrow