The effects of tautomerization and protonation on the adenine–cytosine mismatches: a density functional theory study

References

• Aihara, J. (2002). Nucleus-independent chemical shifts and local aromaticities in large polycyclic aromatic hydrocarbons. Chemical Physics Letters, 365, 34–39.10.1016/S0009-2614(02)01415-X
   Web of Science ®Google Scholar
• Bader, R. F. W. (1990). Atoms in molecules: A quantum theory. Oxford: Oxford University Press.
   Google Scholar
• Barone, V., & Cossi, M. (1998). Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. Journal of Physical Chemistry A, 102, 1995–2001.10.1021/jp9716997
   Web of Science ®Google Scholar
• Biegler König, F., & Schönbohm, J. (2002). Update of the AIM2000-program for atoms in molecules. Journal of Computational Chemistry, 23, 1489–1494.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2009). Physicochemical mechanism of the wobble DNA base pairs Gua·Thy and Ade·Cyt transition into the mismatched base pairs Gua*·Thy and Ade·Cyt* formed by the mutagenic tautomers. Ukrainica Bioorganica Acta., 2, 12–18.
   Google Scholar
• Brovarets’, O. O., & Hovorun D. M. (2010). 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
   Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2013a). 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
   PubMed Web of Science ®Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2013b). 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
   PubMed Web of Science ®Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2014). 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, 32, 1474–1499.
   PubMed Web of Science ®Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2015a). Tautomeric transition between wobble A·C DNA base mispair and Watson–Crick-like A·C* mismatch: Microstructural mechanism and biological significance. Physical Chemistry Chemical Physics, 17, 15103–15110.10.1039/C5CP01568E
   PubMed Web of Science ®Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2015b). 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 & Dynamics, 33, 925–945.
   PubMed Web of Science ®Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2015c). 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, 33, 28–55.
   PubMed Web of Science ®Google Scholar
• Brovarets’, O. O., Yurenko, Y. P., & Hovorun, D. M. (2014). Intermolecular CH···O/N H-bonds in the biologically important pairs of natural nucleobases: A thorough quantum-chemical study. Journal of Biomolecular Structure & Dynamics, 32, 993–1022.
   PubMed Web of Science ®Google Scholar
• Brovarets’, O. O., Yurenko, Y. P., & Hovorun, D. M. (2015). The significant role of the intermolecular CH⋯O/N hydrogen bonds in governing the biologically important pairs of the DNA and RNA modified bases: A comprehensive theoretical investigation. Journal of Biomolecular Structure & Dynamics, 33, 1624–1652.
   PubMed Web of Science ®Google Scholar
• 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
   Google Scholar
• Brovarets’, O. O., Zhurakivsky, R. O., & Hovorun, D. M. (2013a). 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
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Brovarets’, O. O., Zhurakivsky, R. O., & Hovorun, D. M. (2013c). 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
   Web of Science ®Google Scholar
• Brovarets’, O. O., Zhurakivsky, R. O., & Hovorun, D. M. (2014). 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
   PubMed Web of Science ®Google Scholar
• Brovarets’, O. O., Zhurakivsky, R. O., & Hovorun, D. M. (2015). DPT tautomerisation of the wobble guanine·thymine DNA base mispair is not mutagenic: QM and QTAIM arguments. Journal of Biomolecular Structure & Dynamics, 33, 674–689.
   PubMed Web of Science ®Google Scholar
• Chęcińska, L., & Grabowski, S. J. (2006). F–H⋯F–C hydrogen bonds – The influence of hybridization of carbon atom connected with F-acceptor on their properties. Chemical Physics, 327, 202–208.10.1016/j.chemphys.2006.04.011
   Web of Science ®Google Scholar
• Cheong, N. R., Nam, S. H., Park, H. S., Ryu, S., Song, J. K., Park, S. M., ... Jouvet, C. (2011). Photofragmentation in selected tautomers of protonated adenine. Physical Chemistry Chemical Physics, 13, 291–295.10.1039/C000961J
   PubMed Web of Science ®Google Scholar
• Colominas, C., Luque, F. J., & Orozco, M. (1996). Tautomerism and protonation of guanine and cytosine. implications in the formation of hydrogen-bonded complexes. Journal of the American Chemical Society, 118, 6811–6821.10.1021/ja954293l
   Web of Science ®Google Scholar
• Corminboeuf, C., Heine, T., Seifert, G., Schleyer, P. V. R., & Weber, J. (2004). Induced magnetic fields in aromatic [n]-annulenes – Interpretation of NICS tensor components. Physical Chemistry Chemical Physics, 6, 273–276.10.1039/b313383b
   Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• 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
   Web of Science ®Google Scholar
• Das, G., & Lyngdoh, R. H. D. (2014). Configuration of wobble base pairs having pyrimidines as anticodon wobble bases: Significance for codon degeneracy. Journal of Biomolecular Structure & Dynamics, 32, 1500–1520.
   PubMed Web of Science ®Google Scholar
• Dolney, D. M., Hawkins, G. D., Winget, P., Liotard, D. A., Cramer, C. J., & Truhlar, D. G. (2000). Universal solvation model based on conductor-like screening model. Journal of Computational Chemistry, 21, 340–366.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Domagała, M., & Grabowski, S. J. (2005). CH···N and CH···S hydrogen bonds-influence of hybridization on their strength. The Journal of Physical Chemistry A, 109, 5683–5688.10.1021/jp0511496
   PubMed Web of Science ®Google Scholar
• Ebrahimi, A., Habibi, M., Masoodi, H. R., & Gholipour, A. R. (2009). Relationship between calculated NMR data and intermolecular hydrogen bond properties in X-pyridine⋯HF. Chemical Physics, 355, 67–72.10.1016/j.chemphys.2008.11.004
   Web of Science ®Google Scholar
• Erikson, L. A. (Ed.). (2001). Theoretical biochemistry: Processes and properties of biological systems. Amsterdam: Elsevier Science.
   Google Scholar
• 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
   Web of Science ®Google Scholar
• Fonseca Guerra, C., Bickelhaupt, F. M., Saha, S., & Wang, F. (2006). Adenine tautomers: Relative stabilities, ionization energies, and mismatch with cytosine. The Journal of Physical Chemistry A, 110, 4012–4020.10.1021/jp057275r
   PubMed Web of Science ®Google Scholar
• Fonseca Guerra, C., Bickelhaupt, F. M., Snijders, J. G., & Baerends, E. J. (2000). Hydrogen bonding in DNA base pairs: Reconciliation of theory and experiment. Journal of the American Chemical Society, 122, 4117–4128.10.1021/ja993262d
   Web of Science ®Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., ... Fox, D. J. (2009). Gaussian 09 (Revision A.02). Wallingford, CT: Gaussian.
   Google Scholar
• Gálvez, O., Gómez, P. C., & Pacios, L. F. (2003). Variation with the intermolecular distance of properties dependent on the electron density in cyclic dimers with two hydrogen bonds. The Journal of Chemical Physics, 118, 4878–4895.10.1063/1.1545678
   Web of Science ®Google Scholar
• Glendening, E. D., Reed, A. E., Carpenter, J. E., & Weinhold, F. (1998). NBO Version 3.1.
   Google Scholar
• Goodman, M. F. (1995). Mutations caught in the act. Nature, 378, 237–238.10.1038/378237a0
   PubMed Web of Science ®Google Scholar
• Grabowski, S. J. (2006). Hydrogen bonding – New insights. Dordrecht: Springer Science & Business Media.
   Google Scholar
• Grabowski, S. J., Sokalski, W. A., & Leszczynski, J. (2005). How short can the H···H intermolecular contact be? New findings that reveal the covalent nature of extremely strong interactions. The Journal of Physical Chemistry A, 109, 4331–4341.10.1021/jp0444215
   PubMed Web of Science ®Google Scholar
• Guckian, K. M., Krugh, T. R., & Kool, E. T. (2000). Solution structure of a nonpolar, non-hydrogen-bonded base pair surrogate in DNA. Journal of the American Chemical Society, 122, 6841–6847.10.1021/ja994164v
   PubMed Web of Science ®Google Scholar
• Halder, A., Halder, S., Bhattacharyya, D., & Mitra, A. (2014). Feasibility of occurrence of different types of protonated base pairs in RNA: A quantum chemical study. Physical Chemistry Chemical Physics, 16, 18383–18396.10.1039/C4CP02541E
   PubMed Web of Science ®Google Scholar
• Harris, V. H., Smith, C. L., Jonathan Cummins, W. J., Hamilton, A. L., Adams, H., Dickman, M., ... Hornby, D. M. (2003). The effect of tautomeric constant on the specificity of nucleotide incorporation during dna replication: Support for the rare tautomer hypothesis of substitution mutagenesis. Journal of Molecular Biology, 326, 1389–1401.10.1016/S0022-2836(03)00051-2
   PubMed Web of Science ®Google Scholar
• Hertwig, R. H., & Koch, W. (1995). On the accuracy of density functionals and their basis set dependence: An extensive study on the main group homonuclear diatomic molecules Li2 to Br2. Journal of Computational Chemistry, 16, 576–585.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• 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
   Web of Science ®Google Scholar
• Jissy, A. K., & Datta, A. (2014). Design and applications of noncanonical dna base pairs. The Journal of Physical Chemistry Letters, 5, 154–166.10.1021/jz402352d
   PubMed Web of Science ®Google Scholar
• Kannappan, V., Suganthi, S., & Sathyanarayanamoorthi, V. (2014). Polarizable continuum model solvation analysis of certain 5-substituted isoquinoline derivatives. Journal of Molecular Liquids, 199, 123–127.10.1016/j.molliq.2014.08.020
   Web of Science ®Google Scholar
• Lazzereti, P. (2000). Ring currents. In J. W. Emsley, J. Feeney, & L. H. Sutcliffe (Eds.), Progress in nuclear magnetic resonance spectroscopy (Vol. 36, pp. 1–88). Amsterdam: Elsevier.
   Google Scholar
• Lazzeretti, P. (2004). Assessment of aromaticity via molecular response properties. Physical Chemistry Chemical Physics, 6, 217–223.10.1039/b311178d
   Web of Science ®Google Scholar
• Leszczynski, J. (Ed.). (1995). Liquid state quantum chemistry in computational chemistry: Review of current trends. Singapore: World Scientific.
   Google Scholar
• Leulliot, N., Ghomi, M., Scalmani, G., & Berthier, G. (1999). Ground state properties of the nucleic acid constituents studied by density functional calculations. I. Conformational features of ribose, dimethyl phosphate, uridine, cytidine, 5′-Methyl phosphate−uridine, and 3′-methyl phosphate−uridine. The Journal of Physical Chemistry A, 103, 8716–8724.10.1021/jp9915634
   Web of Science ®Google Scholar
• Lippert, B., & Gupta, D. (2009). Promotion of rare nucleobase tautomers by metal binding. Dalton Transactions, 4619–4634.10.1039/b823087k
   PubMed Web of Science ®Google Scholar
• Marian, C., Nolting, D., & Weinkauf, R. (2005). The electronic spectrum of protonated adenine: Theory and experiment. Physical Chemistry Chemical Physics, 7, 3306–3316.10.1039/b507422c
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Mennucci, B. (2012). Polarizable continuum model. Wiley Interdisciplinary Reviews: Computational Molecular Science, 2, 386–404.10.1002/wcms.v2.3
   Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Paragi, G., Szájli, E., Bogár, F., Kovács, L., Guerra, C., & Bickelhaupt, F. M. (2008). Hydrogen bonding of 3- and 5-methyl-6-aminouracil with natural DNA bases. New Journal of Chemistry, 32, 1981–1987.10.1039/b803593h
   Web of Science ®Google Scholar
• Ponomareva, A. G., Yurenko, Y. P., Zhurakivsky, R. O., Mourik, T. V., & Hovorun, D. M. (2014). Structural and energetic properties of the potential HIV-1 reverse transcriptase inhibitors d4A and d4G: A comprehensive theoretical investigation. Journal of Biomolecular Structure and Dynamics, 32, 730–740.10.1080/07391102.2013.789401
   PubMed Web of Science ®Google Scholar
• Popelier, P. (2000). Chemical modelling. New York, NY: Prentice Hall.10.1039/1472-0965
   Google Scholar
• Rajabi, K., Theel, K., Gillis, E. A. L., Beran, G., & Fridgen, T. D. (2009). The structure of the protonated adenine dimer by infrared multiple photon dissociation spectroscopy and electronic structure calculations. The Journal of Physical Chemistry A, 113, 8099–8107.10.1021/jp9033062
   PubMed Web of Science ®Google Scholar
• Reed, A. E., Curtiss, L. A., & Weinhold, F. (1988). Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chemical Reviews, 88, 899–926.10.1021/cr00088a005
   Web of Science ®Google Scholar
• Rohrer, G. S. (2001). Structure and bonding in crystalline materials. Cambridge: Cambridge University Press.
   Google Scholar
• Roohi, H., & Bagheri, S. (2013). Effect of axial strain on structural and electronic properties of zig-zag type of boron nitride nanotube (BNNT): A quantum chemical study. Structural Chemistry, 24, 409–420.10.1007/s11224-012-0088-x
   Web of Science ®Google Scholar
• Rozas, I., Alkorta, I., & Elguero, J. (2000). Behavior of ylides containing N, O, and C atoms as hydrogen bond acceptors. Journal of the American Chemical Society, 122, 11154–11161.10.1021/ja0017864
   Web of Science ®Google Scholar
• Russo, N., Toscano, M., Grand, A., & Jolibois, F. (1998). Protonation of thymine, cytosine, adenine, and guanine DNA nucleic acid bases: Theoretical investigation into the framework of density functional theory. Journal of Computational Chemistry, 19, 989–1000.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Samijlenko, S. P., Krechkivska, O. M., Kosach, D. A., & Hovorun, D. M. (2004). Transitions to high tautomeric states can be induced in adenine by interactions with carboxylate and sodium ions: DFT calculation data. Journal of Molecular Structure, 708, 97–104.10.1016/j.molstruc.2004.05.034
   Web of Science ®Google Scholar
• Schreiber, M., & González, L. (2007). Structure and bonding of Ag(I)-DNA base complexes and Ag(I)-adenine-cytosine mispairs: An ab Initio study. Journal of Computational Chemistry, 28, 2299–2308.10.1002/jcc.v28:14
   PubMed Web of Science ®Google Scholar
• Shukla, M. K., & Leszczynski, J. (2000). A DFT investigation on effects of hydration on the tautomeric equilibria of hypoxanthine. Journal of Molecular Structure: THEOCHEM, 529, 99–112.10.1016/S0166-1280(00)00536-4
   Web of Science ®Google Scholar
• Sinden, R. R. (1994). DNA structure and function. San Diego, CA: Academic Press.
   Google Scholar
• Šponer, J., & Hobza, P. (2003). Molecular interactions of nucleic acid bases. A review of quantum-chemical studies. Collection of Czechoslovak Chemical Communications, 68, 2231–2282.
   Web of Science ®Google Scholar
• Tomasi, J., Mennucci, B., & Cammi, R. (2005). Quantum mechanical continuum solvation models. Chemical Reviews, 105, 2999–3094.10.1021/cr9904009
   PubMed Web of Science ®Google Scholar
• Tomasi, J., & Persico, M. (1994). Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent. Chemical Reviews, 94, 2027–2094.10.1021/cr00031a013
   Web of Science ®Google Scholar
• Topal, M. D., & Fresco, J. R. (1976). Complementary base pairing and the origin of substitution mutations. Nature, 263, 285–289.10.1038/263285a0
   PubMed Web of Science ®Google Scholar
• van Zundert, G. C. P., Jaeqx, S., Berden, G., Bakker, J. M., Kleinermanns, K., Oomens, J., & Rijs, A. M. (2011). IR spectroscopy of isolated neutral and protonated adenine and 9-methyladenine. ChemPhysChem, 12, 1921–1927.10.1002/cphc.201100133
   PubMed Web of Science ®Google Scholar
• von Ragué Schleyer, P., Manoharan, M., Wang, Z. X., Kiran, B., Jiao, H. J., Puchta, R., & van Eikema Hommes, N. J. R. V. E. (2001). Dissected nucleus-independent chemical shift analysis of π-aromaticity and antiaromaticity. Organic Letters, 3, 2465–2468.10.1021/ol016217v
   PubMed Web of Science ®Google Scholar
• 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, 108, 17644–17648.10.1073/pnas.1114496108
   PubMed Web of Science ®Google Scholar
• Watson, J. D., & Crick, F. H. C. (1953). Genetical implications of the structure of deoxyribonucleic acid. Nature, 171, 964–967.10.1038/171964b0
   PubMed Web of Science ®Google Scholar
• Wiberg, K. B. (2004). Basis set effects on calculated geometries: 6-311++G** vs. aug-cc-pVDZ. Journal of Computational Chemistry, 25, 1342–1346.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Wilcox, J. L., Ahluwalia, A. K., & Bevilacqua, P. C. (2011). Charged nucleobases and their potential for RNA catalysis. Accounts of Chemical Research, 44, 1270–1279.10.1021/ar2000452
   PubMed Web of Science ®Google Scholar
• Wolinski, K., Hinton, J. F., & Pulay, P. (1990). Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations. Journal of the American Chemical Society, 112, 8251–8260.10.1021/ja00179a005
   Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar