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

Journal of Biomolecular Structure and Dynamics

Volumn 33, Issue 5, 2015, Pages 925-945

  Brovarets, Olha O ^a,b   Hovorun, Dmytro M ^a,b  

^a INSTITUTE OF MOLECULAR BIOLOGY AND GENETICS   (Ukraine)

^b TARAS SHEVCHENKO NATIONAL UNIVERSITY OF KYIV   (Ukraine)

Author keywords

B3LYP and MP2; DNA replication; DPT tautomerization; hydrogen bond cooperativity; mutagenic tautomer; QTAIM; spontaneous point mutations; transition mismatches

Indexed keywords

DNA; GUANINE; THYMINE;

ALGORITHM; BASE MISPAIRING; BASE PAIRING; BIOLOGICAL MODEL; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; GENETICS; ISOMERISM; POINT MUTATION; QUANTUM THEORY; THERMODYNAMICS;

ALGORITHMS; BASE PAIR MISMATCH; BASE PAIRING; COMPUTER SIMULATION; DNA; GUANINE; ISOMERISM; MODELS, CHEMICAL; MODELS, GENETIC; POINT MUTATION; QUANTUM THEORY; THERMODYNAMICS; THYMINE;

EID: 84938801340     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2014.924879     Document Type: Article

References (106)

1. 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.
2. Atkins, P. W. (1998). Physical chemistry. Oxford: Oxford University Press.
3. Bader, R. F. W. (1990). Atoms in molecules: A quantum theory. Oxford: Oxford University Press.
4. 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.
5. Bayley, S. T. (1951). The dielectric properties of various solid crystalline proteins, amino acids and peptides. Transactions of the Faraday Society, 47, 509-517.
6. Beard, W. A., & Wilson, S. H. (1998). Structural insights into DNA polymerase â fidelity: Hold tight if you want it right. Chemistry & Biology, 5, R7-R13.
7. Beard, W. A., & Wilson, S. H. (2003). Structural insights into the origins of DNA polymerase fidelity. Structure, 11, 489-496.
8. 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.
9. Bondi, A. J. (1964). Van der Waals volumes and radii. The Journal of Physical Chemistry, 68, 441-451.
10. 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.
11. 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.
12. Brovarets', O. O., & Hovorun, D. M. (2010b). How stable are the mutagenic tautomers of DNA bases? Biopolymers and Cell, 26, 72-76.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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: Quantumchemical study. Optics and Spectroscopy, 111, 750-757.
18. 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.
19. 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.
20. 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
21. 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.
22. 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
23. 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.
24. 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.
25. 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
26. 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.
27. 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.
28. 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.
29. 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
30. 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.
31. 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.
32. 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.
33. 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.
34. 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
35. Brovarets, O. O., Zhurakivsky, R. O., & Hovorun, D. M. (2014b). Does the tautomeric status of the adenine bases change upon the dissociation of the AAsyn Topal Fresco DNA mismatch? A combined QM and QTAIM atomistic insight. Physical Chemistry Chemical Physics, 16, 3715-3725.
36. Brovarets, O. O., Zhurakivsky, R. O., & Hovorun, D. M. (2014c). Structural, energetic and tautomeric properties of the TT./T.T DNA mismatch involving mutagenic tautomer of thymine: A QM and QTAIM insight. Chemical Physics Letters, 592, 247-255.
37. 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
38. 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.
39. 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.
40. 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.
41. 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.
42. Drake, J. W. (1991). Spontaneous mutation. Annual Review of Genetics, 25, 125-146.
43. 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.
44. 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.
45. 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.
46. Frisch, M. J., Head-Gordon, M., & Pople, J. A. (1990). Semidirect algorithms for the MP2 energy and gradient. Chemical Physics Letters, 166, 281-289.
47. 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.
48. 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.
49. 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.
50. Garcia-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.
51. 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.
52. 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.
53. Gutowski, M., Van Lenthe, J. H., Verbeek, J., Van Duijneveldt, F. B., & Chaasinski, G. (1986). The basis set superposition error in correlated electronic structure calculations. Chemical Physics Letters, 124, 370-375.
54. Hariharan, P. C., & Pople, J. A. (1973). The influence of polarization functions on molecular orbital hydrogenation energies. Theoretica Chimica Acta, 28, 213-222.
55. 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.
56. 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.
57. 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.
58. 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.
59. 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. Biochemistry, 44, 4850-4860.
60. Iogansen, A. V. (1999). Direct proportionality of the hydrogen bonding energy and the intensification of the stretching (XH) vibration in infrared spectra. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 55, 1585-1612.
61. Keith, T. A. (2010). AIMAll (Version 10.07.01). Retrieved from aim.tkgristmill.com
62. 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.
63. Kool, E. T. (2002). Active site tightness and substrate fit in DNA replication. Annual Review of Biochemistry, 71, 191-219.
64. Kornberg, A., & Baker, T. A. (1992). DNA Replication. New York, NY: W. H. Freeman.
65. 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.
66. 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.
67. 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.
68. 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.
69. 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.
70. Löwdin, P.-O. (1963). Proton tunneling in DNA and its biological implications. Reviews of Modern Physics, 35, 724-732.
71. 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.
72. 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.
73. 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.
74. 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.
75. 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.
76. 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.
77. 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.
78. 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.
79. 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.
80. 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.
81. Palafox, M. A. (2000). Scaling factors for the prediction of vibrational spectra. I. Benzene molecule. International Journal of Quantum Chemistry, 77, 661-684.
82. 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.
83. 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.
84. 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.
85. Parr, R. G., & Yang, W. (1989). Density-functional theory of atoms and molecules. Oxford: Oxford University Press.
86. 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.
87. Peng, C., & Schlegel, H. B. (1993). Combining synchronous transit and quasi-Newton methods to find transition states. Israel Journal of Chemistry, 33, 449-454.
88. 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.
89. 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.
90. Politzer, P., Murray, J. S., & Jaque, P. (2013). Perspectives on the reaction force constant. Journal of Molecular Modeling, 19, 4111-4118.
91. Poltev, V. I., & Bruskov, V. I. (1977). Molecular mechanisms of spontaneous transversions and transitions. Molecular Biology (Molekuliarnaia biologiia), 11, 661-670.
92. 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.
93. 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.
94. Rogozin, I. B., & Pavlov, Y. I. (2003). Theoretical analysis of mutation hotspots and their DNA sequence context specificity. Mutation Research, 544, 65-85.
95. Saenger, W. (1984). Principles of nucleic acid structure. New York, NY: Springer.
96. 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.
97. 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.
98. 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.
99. 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.
100. 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.
101. Topal, M. D., & Fresco, J. R. (1976). Complementary base pairing and the origin of substitution mutations. Nature, 263, 285-289.
102. Von Borstel, R. C. (1994). Origins of spontaneous base substitutions. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 307, 131-140.
103. 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.
104. Watson, J. D., & Crick, F. H. C. (1953). Genetical implications of the structure of deoxyribonucleic acid. Nature, 171, 964-967.
105. 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.
106. 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.