High-Performance Computing Infrastructure for South East Europe's Research Communities pp 109-115 | Cite as
Solvatochromic Effect for the Denaturation and Mutation Processes in DNA: Computational Study
Chapter
Abstract
The influence of the environment on the proton transfer between nucleotide bases has crucial importance for denaturation and mutation processes in DNA. For quantitative description of these processes, activation (ΔE#) and reaction (ΔE) energies of the proton transfer as well as lactam-lactim (KT LL) and amino-imino (KT AI) tautomeric equilibrium constants by the quantum-chemical DFT method are calculated. It is shown that decrease in the environment polarity (Er) due to mixing of ethanol with water (solvatochromic effect) leads to a decrease in the activation energy of the proton transfer and to an increase of the mutation frequency (vm), and at the same time to the tendency of DNA to denaturation. Hence, energy and kinetic characteristics of the proton transfer may be used for quantitative estimation of a solvatochromic effect in DNA. The validity of the solvatochromic effect is confirmed by the bathochromic shift of the DNA absorption band in the UV spectrum.
Keywords
solvatochromic effect DNA denaturation mutation DFT calculationsPreview
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References
- 1.Gorb, L., Podolyan, Y., Dziekonski, P., Sokolski, W., Leszczynski, J.: Double Proton Transfer in AT and GC Base Pairs. J. Am. Chem. Soc. 126, 10119–10129 (2004), doi:10.1021/ja049155nCrossRefGoogle Scholar
- 2.Fogarasi, G.: Water-mediated tautomerization of Cytosine to the rare imino form. Chem., Phys. 349, 204–209 (2008), doi:Doi.org/101016/j.chemphys.2008.02.016Google Scholar
- 3.Ceron Carrasco, J.P., Requena, A., Michaux, C., Perpete, E.A., Jacquemin, D.: Effects of Hydration of the Proton Transfer Mechanism in the Adenine-Thymine Base Pair. J. Phys. Chem. A 113, 7892–7898 (2009), doi:10.1021/jp900782h)CrossRefGoogle Scholar
- 4.Ceron Carrasco, J.P., Requena, A.J., Zuniga, J., Michaux, C., Perpete, E.A., Jacquemin, D.: Intermolecular Proton Transfer in Microhydrated GC Base Pairs: A New Mechanism for Spontaneous Mutation in DNA. J. Phys. Chem. A 113, 10549–10556 (2009), doi:10.1021/jp906551fCrossRefGoogle Scholar
- 5.Cui, S., Yu, J., Kuhner, F., Schulten, K., Gaub, H.F.: Double Stranded DNA Dissociates into Sigle Strands When Dragged into a Poor Solvent. J. Am. Chem. Soc. 129, 14710–14716 (2007), doi:10.1021/ja74776cCrossRefGoogle Scholar
- 6.Geidushek, E.P., Herskovits, T.: Nonaqueous Solvents of DNA. Reversible and irreversible denaturation in methanol. Arch. Biochem. Biophys. 95, 114–129 (1961), doi:org/10.1016/0003-9861(61) 90116-3Google Scholar
- 7.Sinanogly, O., Abdulnur, S.: Hydrophobing stacking of bases and the solvent denaturation of DNA. Photochem. and Photobiol. 3, 333–342 (1964), doi:10.1111/j.1751-1097.1964.tb08156.x)CrossRefGoogle Scholar
- 8.Bonner, G., Klibanov, A.M.: Structural Stability of DNA in nonaqueous solvents. Biotech. Bioeng. 68, 339–344 (2000), doi:(10.1002/CSICI) 1097-0290(20000505)68Google Scholar
- 9.Arscott, P.G., Ma, C., Wennar, G.R., Bloomfield, V.A.: DNA condensation by cobalt hexamine in alcohol-water mixtures: Dielectric constant and other solvent effects. Biopolymers 36, 345–364 (1995), doi:10.1002/bip.360360309CrossRefGoogle Scholar
- 10.Feig, M., Pettitt, B.M.: A molecular simulation picture of DNA hydration around A-and B- DNA. Biopolymers 48, 199–209 (1998), doi:10.1002/(SICI)1097-0282(1998)48CrossRefGoogle Scholar
- 11.Chalikyan, T.V., Sarvazyan, A.P., Plum, G.E., Breshauer, K.J.: Influence of Base composition, base sequence. and duplex structure on DNA hydration. Biochemistry 33, 2394–2401 (1994), doi:10.1021/bi00175a007CrossRefGoogle Scholar
- 12.Kohn, W., Becke, A.D., Parr, R.G.: Density Functional Theory of Electronic Structure. J. Phys. Chem. 100, 12974–12980 (1996), doi:10.1021/jp960669lCrossRefGoogle Scholar
- 13.Laikov, D.N., Ustynyuk, Y.A.: Priroda_04: a quantum-chemical program suite. New possibilities in the study of molecular systems with the application of parallal computing. Russ. Chem. Bull., Int. Edn. 54, 820–826 (2005)CrossRefGoogle Scholar
- 14.Perdew, J.P., Burke, K., Ernzerhof, M.: Generalized Gradient Approximation Made Simple. Phys. Rev. Lett. 77, 3865–3868 (1996), doi:10.1103/PhysRev.lett.77.3865CrossRefGoogle Scholar
- 15.Adamo, C., Barone, V.J.: Physically motified density functional with improved performances: The modified Perdew-Burke-Ernzerhof model. J. Chem. Phys. 116, 5933–5941 (2002), doi.org./101063/1.1458927Google Scholar
- 16.Becke, A.D.: Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A38, 3098–3100 (1988), doi:10.1103/PhysRevA38.3098Google Scholar
- 17.Reichardt, C.: Solvatochromic dyes as solvent polarity indicators. Chem. Rev. 94, 2319–2358 (1994), doi:10.1021/cr00032a006CrossRefGoogle Scholar
- 18.Lowdin, P.: Some Aspects on the Biological Problems of heredity, Mutations, Agingand Tumors in View of the quantum theory of the DNA molecule. Advances in Quantum Chemistry 2, 213–360 (1966), doi:org/10.1016/S0065-3276(08)60069-6Google Scholar
- 19.Kereselidze, J.A., Zarqua, T., S. Kikalishvili, T.J., Churgulia, E.J.M.C., Makaridze, M.C.: Somenew views on the tautomerisation mechanism. Russ. Chem. Rev. 71, 993–1003 (2002)CrossRefGoogle Scholar
- 20.Rogers, M.T., Burdett, J.T.: Keto-enoltautomerism in β-dicarbonyls studied by nuclear magnetic resonance spectroscopy. J. Am. Chem. Soc. 86, 2105–2109 (1964), doi:10.1021/ja01065a003CrossRefGoogle Scholar
- 21.Prezhdo, V.V., Khimenko, N.L., Surov, Y.N.: Influence of the solvent on tautomeric transformation of acetoacetic ester. Ukr. Khim. Zh. 52, 57–63 (1986)Google Scholar
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