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Articles

The nature of the transition mismatches with Watson–Crick architecture: the G*·T or G·T* DNA base mispair or both? A QM/QTAIM perspective for the biological problem

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Pages 925-945 | Received 18 Apr 2014, Accepted 13 May 2014, Published online: 23 Jun 2014

References

  • Arabi, A. A., & Matta, C. F. (2011). Effects of external electric fields on double proton transfer kinetics in the formic acid dimer. Physical Chemistry Chemical Physics, 13, 13738–13748.10.1039/c1cp20175a
  • Atkins, P. W. (1998). Physical chemistry. Oxford: Oxford University Press.
  • Bader, R. F. W. (1990). Atoms in molecules: A quantum theory. Oxford: Oxford University Press.
  • Barone, V., & Cossi, M. (1998). Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. The Journal of Physical Chemistry A, 102, 1995–2001.10.1021/jp9716997
  • Bayley, S. T. (1951). The dielectric properties of various solid crystalline proteins, amino acids and peptides. Transactions of the Faraday Society, 47, 509–517.10.1039/tf9514700509
  • Beard, W. A., & Wilson, S. H. (1998). Structural insights into DNA polymerase β fidelity: Hold tight if you want it right. Chemistry & Biology, 5, R7–R13.10.1016/S1074-5521(98)90081-3
  • Beard, W. A., & Wilson, S. H. (2003). Structural insights into the origins of DNA polymerase fidelity. Structure, 11, 489–496.10.1016/S0969-2126(03)00051-0
  • Bebenek, K., Pedersen, L. C., & Kunkel, T. A. (2011). Replication infidelity via a mismatch with Watson–Crick geometry. Proceedings of the National Academy of Sciences of the United States of America, 108, 1862–1867.10.1073/pnas.1012825108
  • Bondi, A. J. (1964). Van der Waals volumes and radii. The Journal of Physical Chemistry, 68, 441–451.10.1021/j100785a001
  • Boys, S. F., & Bernardi, F. (1970). The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Molecular Physics, 19, 553–566.10.1080/00268977000101561
  • Brovarets’, O. O., & Hovorun, D. M. (2010a). Stability of mutagenic tautomers of uracil and its halogen derivatives: The results of quantum-mechanical investigation. Biopolymers and Cell, 26, 295–298.10.7124/bc
  • Brovarets’, O. O., & Hovorun, D. M. (2010b). How stable are the mutagenic tautomers of DNA bases? Biopolymers and Cell, 26, 72–76.10.7124/bc
  • Brovarets’, O. O., & Hovorun, D. M. (2010c). Molecular mechanisms of transitions induced by cytosine analogue: Comparative quantum-chemical study. Ukrains’kyi Biokhimichnyi Zhurnal, 82, 51–56.
  • Brovarets’, O. O., & Hovorun, D. M. (2010d). Quantum-chemical investigation of tautomerization ways of Watson–Crick DNA base pair guanine-cytosine. Ukrains’kyi Biokhimichnyi Zhurnal, 82, 55–60.
  • Brovarets’, O. O., & Hovorun, D. M. (2010e). Quantum-chemical investigation of the elementary molecular mechanisms of pyrimidine-purine transversions. Ukrains’kyi Biokhimichnyi Zhurnal, 82, 57–67.
  • Brovarets’, O. O., & Hovorun, D. M. (2011a). Intramolecular tautomerization and the conformational variability of some classical mutagens – cytosine derivatives: Quantum chemical study. Biopolymers and Cell, 27, 221–230.10.7124/bc
  • Brovarets’, O. O., & Hovorun, D. M. (2011b). IR vibrational spectra of H-bonded complexes of adenine, 2-aminopurine and 2-aminopurine+ with cytosine and thymine: Quantum-chemical study. Optics and Spectroscopy, 111, 750–757.10.1134/S0030400X11120058
  • Brovarets’, O. O., & Hovorun, D. M. (2013a). Atomistic understanding of the C·T mismatched DNA base pair tautomerization via the DPT: QM and QTAIM computational approaches. Journal of Computational Chemistry, 34, 2577–2590.10.1002/jcc.v34.30
  • Brovarets’, O. O., & Hovorun, D. M. (2013b). Atomistic nature of the DPT tautomerisation of the biologically important C·C* DNA base mispair containing amino and imino tautomers of cytosine: A QM and QTAIM approach. Physical Chemistry Chemical Physics, 15, 20091–20104.10.1039/c3cp52644e
  • Brovarets’, O. O., & Hovorun, D. M. (2013c). The physicochemical essence of the purine·pyrimidine transition mismatches with Watson–Crick geometry in DNA: A·C* versa A*·C. A QM and QTAIM atomistic understanding. Journal of Biomolecular Structure & Dynamics. doi:10.1080/07391102.2013.852133
  • Brovarets’, O. O., & Hovorun, D. M. (2013d). Prototropic tautomerism and basic molecular principles of hypoxanthine mutagenicity: An exhaustive quantum-chemical analysis. Journal of Biomolecular Structure and Dynamics, 31, 913–936.10.1080/07391102.2012.715041
  • Brovarets’, O. O., & Hovorun, D. M. (2013e). Why the tautomerization of the G·C Watson–Crick base pair via the DPT does not cause point mutations during DNA replication? QM and QTAIM comprehensive analysis. Journal of Biomolecular Structure & Dynamics. doi:10.1080/07391102.2013.822829
  • Brovarets’, O. O., & Hovorun, D. M. (2014a). DPT tautomerisation of the G·Asyn and A*·G*syn DNA mismatches: A QM/QTAIM combined atomistic investigation. Physical Chemistry Chemical Physics, 16, 9074–9085.10.1039/c4cp00488d
  • Brovarets’, O. O., & Hovorun, D. M. (2014b). Can tautomerisation of the A∙T Watson–Crick base pair via double proton transfer provoke point mutations during DNA replication? A comprehensive QM and QTAIM analysis. Journal of Biomolecular Structure & Dynamics, 32, 127–154.
  • Brovarets’, O. O., & Hovorun, D. M. (2014c). How the long G•G* Watson–Crick DNA base mispair comprising keto and enol tautomers of the guanine tautomerises? The results of the QM/QTAIM investigation. Physical Chemistry Chemical Physics. doi:10.1039/C4CP01241 K
  • Brovarets’, O. O., & Hovorun, D. M. (2014d). Does the G•G*syn DNA mismatch containing canonical and rare tautomers of the guanine tautomerise through the DPT? A QM/QTAIM microstructural study. Molecular Physics. doi:10.1080/00268976.2014.927079.
  • Brovarets’, O.O., Kolomiets’, I.M., & Hovorun, D.M. (2012). Elementary molecular mechanisms of the spontaneous point mutations in DNA: A novel quantum-chemical insight into the classical understanding. In T. Tada (Ed.), Quantum chemistry – Molecules for innovations (pp. 59–102). Rijeka: In Tech Open Access.
  • Brovarets’, O. O., Yurenko, Y. P., Dubey, I. Y., & Hovorun, D. M. (2012). Can DNA-binding proteins of replisome tautomerize nucleotide bases? Ab initio model study. Journal of Biomolecular Structure & Dynamics, 29, 1101–1109.
  • Brovarets’, O. O., Yurenko, Y. P., & Hovorun, D. M. (2013a). Intermolecular CH···O/N H-bonds in the biologically important pairs of natural nucleobases: A thorough quantum-chemical study. Journal of Biomolecular Structure & Dynamics. doi:10.1080/07391102.2013.799439
  • Brovarets’, O. O., Zhurakivsky, R. O., & Hovorun, D. M. (2010). Is there adequate ionization mechanism of the spontaneous transitions? Quantum-chemical investigation. Biopolymers and Cell, 26, 398–405.10.7124/bc
  • Brovarets’, O. O., Zhurakivsky, R. O., & Hovorun, D. M. (2013b). The physico-chemical “anatomy” of the tautomerization through the DPT of the biologically important pairs of hypoxanthine with DNA bases: QM and QTAIM perspectives. Journal of Molecular Modeling, 19, 4119–4137.10.1007/s00894-012-1720-9
  • Brovarets’, O. O., Zhurakivsky, R. O., & Hovorun, D. M. (2013c). DPT tautomerization of the long A∙A* Watson–Crick base pair formed by the amino and imino tautomers of adenine: Combined QM and QTAIM investigation. Journal of Molecular Modeling, 19, 4223–4237.10.1007/s00894-013-1880-2
  • Brovarets’, O. O., Zhurakivsky, R. O., & Hovorun, D. M. (2013d). The physico-chemical mechanism of the tautomerisation via the DPT of the long Hyp∗·Hyp Watson–Crick base pair containing rare tautomer: A QM and QTAIM detailed look. Chemical Physics Letters, 578, 126–132.10.1016/j.cplett.2013.05.067
  • Brovarets’, O. O., Zhurakivsky, R. O., & Hovorun, D. M. (2014a). DPT tautomerisation of the wobble guanine•thymine DNA base mispair is not mutagenic: QM and QTAIM arguments. Journal of Biomolecular Structure and Dynamics. doi:10.1080/07391102.2014.897259
  • Brovarets’, O. O., Zhurakivsky, R. O., & Hovorun, D. M. (2014b). Does the tautomeric status of the adenine bases change upon the dissociation of the A*·Asyn Topal–Fresco DNA mismatch? A combined QM and QTAIM atomistic insight. Physical Chemistry Chemical Physics, 16, 3715–3725.10.1039/c3cp54708f
  • Brovarets’, O. O., Zhurakivsky, R. O., & Hovorun, D. M. (2014c). Structural, energetic and tautomeric properties of the T·T∗/T∗·T DNA mismatch involving mutagenic tautomer of thymine: A QM and QTAIM insight. Chemical Physics Letters, 592, 247–255.10.1016/j.cplett.2013.12.034
  • Brovarets’, O. O., Zhurakivsky, R. O., & Hovorun, D. M. (2014d). A QM/QTAIM microstructural analysis of the tautomerisation via the DPT of the hypoxanthine·adenine nucleobase pair. Molecular Physics. doi:10.1080/00268976.2013.877170
  • Cossi, M., Rega, N., Scalmani, G., & Barone, V. (2003). Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model. Journal of Computational Chemistry, 24, 669–681.10.1002/jcc.10189
  • Danilov, V. I., Anisimov, V. M., Kurita, N., & Hovorun, D. (2005). MP2 and DFT studies of the DNA rare base pairs: The molecular mechanism of the spontaneous substitution mutations conditioned by tautomerism of bases. Chemical Physics Letters, 412, 285–293.10.1016/j.cplett.2005.06.123
  • Danilov, V. I., Van Mourik, T., Kurita, N., Wakabayashi, H., Tsukamoto, T., & Hovorun, D. M. (2009). On the mechanism of the mutagenic action of 5-bromouracil: A DFT study of uracil and 5-bromouracil in a water cluster. The Journal of Physical Chemistry A, 113, 2233–2235.10.1021/jp811007j
  • Dewar, M. J. S., & Storch, D. M. (1985). Alternative view of enzyme reactions. Proceedings of the National Academy of Sciences of the United States of America, 82, 2225–2229.10.1073/pnas.82.8.2225
  • Drake, J. W. (1991). Spontaneous mutation. Annual Review of Genetics, 25, 125–146.10.1146/annurev.ge.25.120191.001013
  • Dunning, T. H., Jr. (1989). Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. The Journal of Chemical Physics, 90, 1007–1023.10.1063/1.456153
  • Espinosa, E., Molins, E., & Lecomte, C. (1998). Hydrogen bond strengths revealed by topological analyses of experimentally observed electron densities. Chemical Physics Letters, 285, 170–173.10.1016/S0009-2614(98)00036-0
  • Friedberg, E. C., Walker, G. C., Siede, W., Wood, R. D., Schultz, R. A., & Ellenberger, T. (2006). DNA repair and mutagenesis. Washington, DC: ASM Press.
  • Frisch, M. J., Head-Gordon, M., & Pople, J. A. (1990). Semi-direct algorithms for the MP2 energy and gradient. Chemical Physics Letters, 166, 281–289.10.1016/0009-2614(90)80030-H
  • Frisch, M. J., Pople, J. A., & Binkley, J. S. (1984). Self-consistent molecular orbital methods 25. Supplementary functions for Gaussian basis sets. The Journal of Chemical Physics, 80, 3265–3269.10.1063/1.447079
  • Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., & Cheeseman, J. R., … Pople, J. A. (2010). GAUSSIAN 09 (Revision B.01). Wallingford, CT: Gaussian.
  • Furmanchuk, A., Isayev, O., Gorb, L., Shishkin, O. V., Hovorun, D. M., & Leszczynski, J. (2011). Novel view on the mechanism of water-assisted proton transfer in the DNA bases: Bulk water hydration. Physical Chemistry Chemical Physics, 13, 4311–4317.10.1039/c0cp02177f
  • García-Moreno, B. E., Dwyer, J. J., Gittis, A. G., Lattman, E. E., Spencer, D. S., & Stites, W. E. (1997). Experimental measurement of the effective dielectric in the hydrophobic core of a protein. Biophysical Chemistry, 64, 211–224.10.1016/S0301-4622(96)02238-7
  • Goodman, M. F. (1997). Hydrogen bonding revisited: Geometric selection as a principal determinant of DNA replication fidelity. Proceedings of the National Academy of Sciences of the United States of America, 94, 10493–10495.10.1073/pnas.94.20.10493
  • Govorun, D. N., Danchuk, V. D., & Mishchuk, Y. R. (1992). AM1 calculation of the nucleic acid bases structure and vibrational spectra. Journal of Molecular Structure, 267, 99–103.10.1016/0022-2860(92)87016-O
  • Gutowski, M., Van Lenthe, J. H., Verbeek, J., Van Duijneveldt, F. B., & Chałasinski, G. (1986). The basis set superposition error in correlated electronic structure calculations. Chemical Physics Letters, 124, 370–375.10.1016/0009-2614(86)85036-9
  • Hariharan, P. C., & Pople, J. A. (1973). The influence of polarization functions on molecular orbital hydrogenation energies. Theoretica Chimica Acta, 28, 213–222.10.1007/BF00533485
  • Hovorun, D. M., Gorb, L., & Leszczynski, J. (1999). From the nonplanarity of the amino group to the structural nonrigidity of the molecule: A post-Hartree-Fock ab initio study of 2-aminoimidazole. International Journal of Quantum Chemistry, 75, 245–253.10.1002/(ISSN)1097-461X
  • Hratchian, H. P., & Schlegel, H. B. (2004). Accurate reaction paths using a Hessian based predictor–corrector integrator. The Journal of Chemical Physics, 120, 9918–9924.10.1063/1.1724823
  • Hratchian, H. P., & Schlegel, H. B. (2005a). Finding minima, transition states, and following reaction pathways on ab initio potential energy surfaces. In C. E. Dykstra, G. Frenking, K. S. Kim, & G. Scuseria (Eds.), Theory and applications of computational chemistry (pp. 195–249). Amsterdam: Elsevier.10.1016/B978-044451719-7/50053-6
  • Hratchian, H. P., & Schlegel, H. B. (2005b). Using Hessian updating to increase the efficiency of a Hessian based predictor-corrector reaction path following method. Journal of Chemical Theory and Computation, 1, 61–69.10.1021/ct0499783
  • Hwang, H., & Taylor, J.-S. (2005). Evidence for Watson−Crick and not Hoogsteen or wobble base pairing in the selection of nucleotides for insertion opposite pyrimidines and a thymine dimer by yeast DNA Pol η. Biochemistry, 44, 4850–4860.10.1021/bi048244+
  • Iogansen, A. V. (1999). Direct proportionality of the hydrogen bonding energy and the intensification of the stretching ν(XH) vibration in infrared spectra. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 55, 1585–1612.10.1016/S1386-1425(98)00348-5
  • Keith, T. A. (2010). AIMAll (Version 10.07.01). Retrieved from aim.tkgristmill.com
  • Kendall, R. A., Dunning, T. H., Jr, & Harrison, R. J. (1992). Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions. The Journal of Chemical Physics, 96, 6796–6806.10.1063/1.462569
  • Kool, E. T. (2002). Active site tightness and substrate fit in DNA replication. Annual Review of Biochemistry, 71, 191–219.10.1146/annurev.biochem.71.110601.135453
  • Kornberg, A., & Baker, T. A. (1992). DNA Replication. New York, NY: W. H. Freeman.
  • Kosenkov, D., Kholod, Y., Gorb, L., Shishkin, O., Hovorun, D. M., Mons, M., & Leszczynski, J. (2009). Ab initio kinetic simulation of gas-phase experiments: Tautomerization of cytosine and guanine. The Journal of Physical Chemistry B, 113, 6140–6150.10.1021/jp810570w
  • Krishnan, R., Binkley, J. S., Seeger, R., & Pople, J. A. (1980). Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions. The Journal of Chemical Physics, 72, 650–654.10.1063/1.438955
  • Lee, C., Yang, W., & Parr, R. G. (1988). Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Physical Review B, 37, 785–789.10.1103/PhysRevB.37.785
  • Lee, H., Popodi, E., Tang, H., & Foster, P. L. (2012). Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. Proceedings of the National Academy of Sciences of the United States of America, 109, E2774–E2783.10.1073/pnas.1210309109
  • Li, Y., & Waksman, G. (2001). Crystal structures of a ddATP-, ddTTP-, ddCTP, and ddGTP- trapped ternary complex of Klentaq1: Insights into nucleotide incorporation and selectivity. Protein Science, 10, 1225–1233.10.1110/(ISSN)1469-896X
  • Löwdin, P.-O. (1963). Proton tunneling in DNA and its biological implications. Reviews of Modern Physics, 35, 724–732.10.1103/RevModPhys.35.724
  • Löwdin, P.-O. (1966). Quantum genetics and the aperiodic solid: Some aspects on the biological problems of heredity, mutations, aging, and tumors in view of the quantum theory of the DNA molecule. In P.-O. Löwdin (Ed.), Advances in quantum chemistry, (Vol. 2, pp. 213–360). New York, NY: Academic Press.
  • Lozynski, M., Rusinska-Roszak, D., & Mack, H.-G. (1998). Hydrogen bonding and density functional calculations: The B3LYP approach as the shortest way to MP2 results. The Journal of Physical Chemistry A, 102, 2899–2903.10.1021/jp973142x
  • Mata, I., Alkorta, I., Espinosa, E., & Molins, E. (2011). Relationships between interaction energy, intermolecular distance and electron density properties in hydrogen bonded complexes under external electric fields. Chemical Physics Letters, 507, 185–189.10.1016/j.cplett.2011.03.055
  • Matta, C. F. (2010). How dependent are molecular and atomic properties on the electronic structure method? Comparison of Hartree-Fock, DFT, and MP2 on a biologically relevant set of molecules. Journal of Computational Chemistry, 31, 1297–1311.
  • Matta, C. F., Castillo, N., & Boyd, R. J. (2006). Extended weak bonding interactions in DNA: π-Stacking (base–base), base−backbone, and backbone−backbone interactions. The Journal of Physical Chemistry B, 110, 563–578.10.1021/jp054986g
  • Mertz, E. L., & Krishtalik, L. I. (2000). Low dielectric response in enzyme active site. Proceedings of the National Academy of Sciences of the United States of America, 97, 2081–2086.10.1073/pnas.050316997
  • Minnick, D. T., Liu, L., Grindley, N. D., Kunkel, T. A., & Joyce, C. M. (2002). Discrimination against purine–pyrimidine mispairs in the polymerase active site of DNA polymerase I: A structural explanation. Proceedings of the National Academy of Sciences of the United States of America, 99, 1194–1199.10.1073/pnas.032457899
  • Mishchuk, Y. R., Potyagaylo, A. L., Hovorun, D. M. (2000). Structure and dynamics of 6-azacytidine by MNDO/H quantum-chemical method. Journal of Molecular Structure, 552, 283–289.10.1016/S0022-2860(00)00492-0
  • Nikolaienko, T. Y., Bulavin, L. A., & Hovorun, D. M. (2011). How flexible are DNA constituents? The quantum-mechanical study Journal of Biomolecular Structure and Dynamics, 29, 563–575.10.1080/07391102.2011.10507406
  • Nikolaienko, T. Y., Bulavin, L. A., & Hovorun, D. M. (2012). Bridging QTAIM with vibrational spectroscopy: The energy of intramolecular hydrogen bonds in DNA-related biomolecules. Physical Chemistry Chemical Physics, 14, 7441–7447.10.1039/c2cp40176b
  • Palafox, M. A. (2000). Scaling factors for the prediction of vibrational spectra. I. Benzene molecule. International Journal of Quantum Chemistry, 77, 661–684.10.1002/(ISSN)1097-461X
  • Palafox, M. A. (2014). Molecular structure differences between the antiviral nucleoside analogue 5-iodo-2′-deoxyuridine and the natural nucleoside 2′-deoxythymidine using MP2 and DFT methods: Conformational analysis, crystal simulations, DNA pairs and possible behaviour. Journal of Biomolecular Structure and Dynamics, 32, 831–851.10.1080/07391102.2013.789402
  • Palafox, M. A., Iza, N., & Gil, M. (2002). The hydration effect on the uracil frequencies: An experimental and quantum chemical study. Journal of Molecular Structure: THEOCHEM, 585, 69–92.10.1016/S0166-1280(02)00033-7
  • Palafox, M. A., & Rastogi, V. K. (2002). Quantum chemical predictions of the vibrational spectra of polyatomic molecules: The uracil molecule and two derivatives. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 58, 411–440.10.1016/S1386-1425(01)00509-1
  • Parr, R. G., & Yang, W. (1989). Density-functional theory of atoms and molecules. Oxford: Oxford University Press.
  • Peng, C., Ayala, P. Y., Schlegel, H. B., & Frisch, M. J. (1996). Using redundant internal coordinates to optimize equilibrium geometries and transition states. Journal of Computational Chemistry, 17, 49–56.10.1002/(ISSN)1096-987X
  • Peng, C., & Schlegel, H. B. (1993). Combining synchronous transit and quasi-Newton methods to find transition states. Israel Journal of Chemistry, 33, 449–454.10.1002/ijch.v33.4
  • Petruska, J., Sowers, L. C., & Goodman, M. (1986). Comparison of nucleotide interactions in water, proteins, and vacuum: Model for DNA polymerase fidelity. Proceedings of the National Academy of Sciences of the United States of America, 83, 1559–1562.10.1073/pnas.83.6.1559
  • Platonov, M. O., Samijlenko, S. P., Sudakov, O. O., Kondratyuk, I. V., & Hovorun, D. M. (2005). To what extent can methyl derivatives be regarded as stabilized tautomers of xanthine? Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 62, 112–114.10.1016/j.saa.2004.12.012
  • Politzer, P., Murray, J. S., & Jaque, P. (2013). Perspectives on the reaction force constant. Journal of Molecular Modeling, 19, 4111–4118.10.1007/s00894-012-1713-8
  • Poltev, V. I., & Bruskov, V. I. (1977). Molecular mechanisms of spontaneous transversions and transitions. Molecular Biology (Molekuliarnaia biologiia), 11, 661–670.
  • Poltev, V. I., Shulyupina, N. V., & Bruskov, V. I. (1998). Fidelity of nucleic acid biosynthesis. Comparison of computer modeling results with experimental data. Molecular Biology (Molekuliarnaia biologiia), 32, 233–240.
  • Ponomareva, A. G., Yurenko, Y. P., Zhurakivsky, R. O., van Mourik, T., & Hovorun, D. M. (2012). Complete conformational space of the potential HIV-1 reverse transcriptase inhibitors d4U and d4C. A quantum chemical study. Physical Chemistry Chemical Physics, 14, 6787–6795.10.1039/c2cp40290d
  • Rogozin, I. B., & Pavlov, Y. I. (2003). Theoretical analysis of mutation hotspots and their DNA sequence context specificity. Mutation Research, 544, 65–85.10.1016/S1383-5742(03)00032-2
  • Saenger, W. (1984). Principles of nucleic acid structure. New York, NY: Springer.10.1007/978-1-4612-5190-3
  • Samijlenko, S. P., Yurenko, Y. P., Stepanyugin, A. V., & Hovorun, D. M. (2012). Tautomeric equilibrium of uracil and thymine in model protein–nucleic acid contacts. Spectroscopic and quantum chemical approach. The Journal of Physical Chemistry B, 114, 1454–1461.
  • Shishkin, O. V., Pelmenschikov, A., Hovorun, D. M., & Leszczynski, J. (2000). Theoretical analysis of low-lying vibrational modes of free canonical 2΄-deoxyribonucleosides. Chemical Physics, 260, 317–325.10.1016/S0301-0104(00)00251-2
  • Sordo, J. A. (2001). On the use of the Boys–Bernardi function counterpoise procedure to correct barrier heights for basis set superposition error. Journal of Molecular Structure: THEOCHEM, 537, 245–251.10.1016/S0166-1280(00)00681-3
  • Sordo, J. A., Chin, S., & Sordo, T.L. (1988). On the counterpoise correction for the basis set superposition error in large systems. Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), 74, 104–110.
  • Tirado-Rives, J., & Jorgensen, W. L. (2008). Performance of B3LYP density functional methods for a large set of organic molecules. Journal of Chemical Theory and Computation, 4, 297–306.10.1021/ct700248 k
  • Topal, M. D., & Fresco, J. R. (1976). Complementary base pairing and the origin of substitution mutations. Nature, 263, 285–289.10.1038/263285a0
  • Von Borstel, R. C. (1994). Origins of spontaneous base substitutions. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 307, 131–140.10.1016/0027-5107(94)90285-2
  • Wang, W., Hellinga, H. W., & Beese, L. S. (2011). Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. Proceedings of the National Academy of Sciences of the United States of America, 108, 17644–17648.10.1073/pnas.1114496108
  • Watson, J. D., & Crick, F. H. C. (1953). Genetical implications of the structure of deoxyribonucleic acid. Nature, 171, 964–967.10.1038/171964b0
  • Wigner, E. (1932). Über das Überschreiten von Potentialschwellen bei chemischen Reaktionen [Crossing of potential thresholds in chemical reactions]. Zeitschrift für Physikalische Chemie, B19, 203–216.
  • Yurenko, Y. P., Zhurakivsky, R. O., Samijlenko, S. P., & Hovorun, D. M. (2011). Intramolecular CH···O hydrogen bonds in the AI and BI DNA-like conformers of canonical nucleosides and their Watson–Crick pairs. Quantum chemical and AIM analysis. Journal of Biomolecular Structure and Dynamics, 29, 51–65.10.1080/07391102.2011.10507374

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