How proton transfer affects the helical parameters in DNA:DNA microhelices

References

• Alcolea Palafox, M. (2017). Computational chemistry applied to vibrational spectroscopy: A tool for characterization of nucleic acid bases and some of their 5-substituted derivatives. In P. Ramasami (Ed.), Computational sciences (Book) (Vol. 5, pp. 117–151). Walter de Gruyter, Inc.
   Google Scholar
• Alcolea Palafox, M. (2019). Effect of the sulfur atom on S2 and S4 positions of the uracil ring in different DNA:RNA hybrid microhelixes with three nucleotide base pairs. Biopolymers, 110(3), e23247. https://doi.org/10.1002/bip.23247
   PubMed Web of Science ®Google Scholar
• Alcolea Palafox, M., Franklin Benial, A. M., & Rastogi, V. K. (2019). Biomolecules of 2-thiouracil, 4-thiouracil and 2,4-dithiouracil: A DFT study of the hydration, molecular docking and effect in DNA:RNA microhelices. International Journal of Molecular Sciences, 20(14), 3477–3507. https://doi.org/10.3390/ijms20143477
   PubMed Web of Science ®Google Scholar
• Alcolea Palafox, M., & Iza, N. (2010). Tautomerism of the Natural Thymidine Nucleoside and the antiviral analogue D4T. Structure and influence of an aqueous environment using MP2 and DFT methods. Physical Chemistry Chemical Physics, 12(4), 881–893. https://doi.org/10.1039/b915566j
   PubMed Web of Science ®Google Scholar
• Alcolea Palafox, M., Iza, N., de la Fuente, M., & Navarro, R. (2009). Simulation of the first hydration shell of nucleosides D4T and Thymidine: Structures obtained using MP2 and DFT methods. The Journal of Physical Chemistry B, 113(8), 2458–2476. https://doi.org/10.1021/jp806684v
   PubMed Web of Science ®Google Scholar
• 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(5), 1862–1867. https://doi.org/10.1073/pnas.1012825108
   PubMed Web of Science ®Google Scholar
• Bloomfield, V. A., Crothers, D. M., & Tinoco, I., Jr. (2000). Nucleic acids: Structures, properties and functions. University Science Books.
   Google Scholar
• 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(4), 553–566. https://doi.org/10.1080/00268977000101561
   Web of Science ®Google Scholar
• Brovarets, O. O., & Hovorun, D. M. (2010). How stable are the mutagenic tautomers of DNA bases? Biopolymers and Cell, 26(1), 72–76. https://doi.org/10.7124/bc.000147
   Google Scholar
• Brovarets', O. O., & Hovorun, D. M. (2013). Atomistic understanding of the C·T mismatched DNA base pair tautomerization via the DPT: QM and QTAIM computational approaches. Journal of Computational Chemistry, 34(30), 2577–2590. https://doi.org/10.1002/jcc.23412
   PubMed Web of Science ®Google Scholar
• Brovarets', O. O., & Hovorun, D. M. (2014a). DPT tautomerisation of the G·A(syn) and A*·G*(syn) DNA mismatches: A QM/QTAIM combined atomistic investigation. Physical Chemistry Chemical Physics, 16(19), 9074–9085. https://doi.org/10.1039/c4cp00488d
   PubMed Web of Science ®Google Scholar
• Brovarets', O. O., & Hovorun, D. M. (2014b). How does the long G·G* Watson–Crick DNA base mispair comprising keto and enol tautomers of the guanine tautomerise? The results of a QM/QTAIM investigation. Physical Chemistry Chemical Physics, 16(30), 15886–15899. https://doi.org/10.1039/c4cp01241k
   PubMed Web of Science ®Google Scholar
• Brovarets', O. O., & Hovorun, D. M. (2015a). 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(5), 925–945. https://doi.org/10.1080/07391102.2014.924879
   PubMed Web of Science ®Google Scholar
• Brovarets', O. O., & Hovorun, D. M. (2015b). Proton tunneling in the A·T Watson–Crick DNA base pair: Myth or reality? Journal of Biomolecular Structure & Dynamics, 33(12), 2716–2720. https://doi.org/10.1080/07391102.2015.1092886
   PubMed Web of Science ®Google Scholar
• Brovarets', O. O., & Hovorun, D. M. (2015c). Tautomeric transition between wobble А·С DNA base mispair and Watson–Crick-like A·C* mismatch: Microstructural mechanism and biological significance. Physical Chemistry Chemical Physics, 17(23), 15103–15110. https://doi.org/10.1039/C5CP01568E
   PubMed Web of Science ®Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2015d). Novel physico-chemical mechanism of the mutagenic tautomerisation of the Watson–Crick-like A· G and C· T DNA base mispairs: A quantum-chemical picture. RSC Advances, 5(81), 66318–66333. https://doi.org/10.1039/C5RA11773A
   Web of Science ®Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2015e). New structural hypostases of the AT and GC Watson–Crick DNA base pairs caused by their mutagenic tautomerisation in a wobble manner: A QM/QTAIM prediction. RSC Advances, 5(121), 99594–99605. https://doi.org/10.1039/C5RA19971A
   Web of Science ®Google Scholar
• 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 Tomofumi Tada (Ed.), Quantum chemistry-molecules for innovations (Chapter 4, pp. 59–102). InTech Europe. https://doi.org/10.5772/35743
   Google Scholar
• Brovarets', O. O., Oliynyk, T. A., & Hovorun, D. M. (2019). Novel tautomerisation mechanisms of the biologically important conformers of the reverse Löwdin, Hoogsteen, and reverse Hoogsteen G*·C* DNA base pairs via proton transfer: A quantum-mechanical survey. Frontiers in Chemistry, 7, 597, 1-25. https://doi.org/10.3389/fchem.2019.00597
   PubMed Web of Science ®Google Scholar
• Brovarets', O. O., Tsiupa, K. S., Dinets, A., & Hovorun, D. M. (2018). Unexpected routes of the mutagenic tautomerization of the T nucleobase in the classical A·T DNA base pairs: A QM/QTAIM comprehensive view. Frontiers in Chemistry, 6, 532. https://doi.org/10.3389/fchem.2018.00532
   PubMed Web of Science ®Google Scholar
• Brovarets', O. O., Tsiupa, K. S., & Hovorun, D. M. (2018). Novel pathway for mutagenic tautomerization of classical А·Т DNA base pairs via sequential proton transfer through quasi-orthogonal transition states: A QM/QTAIM investigation. PLoS One, 13(6), e0199044. https://doi.org/10.1371/journal.pone.0199044
   PubMed Web of Science ®Google Scholar
• Brovarets’, O. O., Zhurakivsky, R. O., & Hovorun, D. M. (2014a). 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. https://doi.org/10.1016/j.cplett.2013.12.034
   Web of Science ®Google Scholar
• Brovarets', O. O., Zhurakivsky, R. O., & Hovorun, D. M. (2014b). Is the DPT tautomerization of the long A·G Watson–Crick DNA base mispair a source of the adenine and guanine mutagenic tautomers? A QM and QTAIM response to the biologically important question. Journal of Computational Chemistry, 35(6), 451–466. https://doi.org/10.1002/jcc.23515
   PubMed Web of Science ®Google Scholar
• Chahinian, M., Seba, H. B., & Ancian, B. (1998). Hydration structure of uracil as studied by 1D and 2D heteronuclear Overhauser spectroscopy: Evidence for the formation of a trihydrate in the first salvation. Chemical Physics Letters, 285(5–6), 337–345. https://doi.org/10.1016/S0009-2614(98)00109-2
   Web of Science ®Google Scholar
• Churchill, C. D. M., & Wetmore, S. D. (2011). Developing a computational model that accurately reproduces the structural features of a dinucleoside monophosphate unit within B-DNA. Physical Chemistry Chemical Physics, 13(36), 16373–16383. https://doi.org/10.1039/c1cp21689a
   PubMed Web of Science ®Google Scholar
• Cognet, J. A. H., Gabarro-Arpa, J., Le Bret, M., van der Marel, G. A., van Boom, J. H., & Fazakerley, G. V. (1991). Solution conformation of an oligonucleotide containing a G.G mismatch determined by nuclear magnetic resonance and molecular mechanics. Nucleic Acids Research, 19(24), 6771–6779. https://doi.org/10.1093/nar/19.24.6771
   PubMed Web of Science ®Google Scholar
• Danilov, V. I., Anisimov, V. M., Kurita, N., & Hovorun, D. M. (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(4–6), 285–293. https://doi.org/10.1016/j.cplett.2005.06.123
   Web of Science ®Google Scholar
• 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(11), 2233–2235. https://doi.org/10.1021/jp811007j
   PubMed Web of Science ®Google Scholar
• Danilov, V. I., van Mourik, T., & Poltev, V. I. (2006). Modeling of the ‘hydration shell’ of uracil and thymine in small water clusters by DFT and MP2 methods. Chemical Physics Letters, 429(1–3), 255–260. https://doi.org/10.1016/j.cplett.2006.08.035
   Web of Science ®Google Scholar
• Dickerson, R. E. (1989). Definitions and nomenclature of nucleic acid structure components. Nucleic Acids Research, 17(5), 1797–1803. https://doi.org/10.1093/nar/17.5.1797
   PubMed Web of Science ®Google Scholar
• Diekmann, S. (1989). Definitions and nomenclature of nucleic acid structure parameters. Journal of Molecular Biology, 205(4), 787–791. https://doi.org/10.1016/0022-2836(89)90324-0
   PubMed Web of Science ®Google Scholar
• Fogarasi, G. (2008). Water-mediated tautomerization of cytosine to the rare imino form: An ab initio dynamics study. Chemical Physics, 349(1–3), 204–209. https://doi.org/10.1016/j.chemphys.2008.02.016
   Web of Science ®Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Petersson, G. A., Nakatsuji, H., Li, X., Caricato, M., Marenich, A. V., Bloino, J., Janesko, B. G., Gomperts, R., Mennucci, B., Hratchian, H. P., Ortiz, J. V., ... & Fox, D. J. (2019). Gaussian 16, revision C.01. Gaussian, Inc.
   Google Scholar
• 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(10), 4311–4317. https://doi.org/10.1039/c0cp02177f
   PubMed Web of Science ®Google Scholar
• Gould, I. R., Burton, N. A., Hall, R. J., & Hillier, I. H. (1995). Tautomerism in uracil, cytosine and guanine: A comparison of electron correlation predicted by ab initio and density functional theory methods. Journal of Molecular Structure: THEOCHEM, 331(1–2), 147–154. https://doi.org/10.1016/0166-1280(94)03887-Q
   Web of Science ®Google Scholar
• Hendricks, J. H., Lyapustina, S. A., Clercq, H. L., & Bowen, K. H. (1998). The dipole bound-to-covalent anion transformation in uracil. Journal of Chemical Physics, 108(1), 8–11. https://doi.org/10.1063/1.475360
   Web of Science ®Google Scholar
• Heuberger, B. D., Pal, A., Del Frate, F., Topkar, V. V., & Szostak, J. W. (2015). Replacing uridine with 2-thiouridine enhances the rate and fidelity of nonenzymatic RNA primer extension. Journal of the American Chemical Society, 137(7), 2769–2775. https://doi.org/10.1021/jacs.5b00445
   PubMed Web of Science ®Google Scholar
• Hu, X., Li, H., Liang, W., & Han, S. (2005). Systematic study of the tautomerism of uracil induced by proton transfer. Exploration of water stabilization and mutagenicity. The Journal of Physical Chemistry B, 109(12), 5935–5944. https://doi.org/10.1021/jp044665p
   PubMed Web of Science ®Google Scholar
• Hunter, R. S., & van Mourik, T. (2012). DNA base stacking: The stacked uracil/uracil and thymine/thymine minima. Journal of Computational Chemistry, 33(27), 2161–2172. https://doi.org/10.1002/jcc.23052
   PubMed Web of Science ®Google Scholar
• Karabıyık, H., Sevinçek, R., & Karabıyık, H. (2014). π-Cooperativity effect on the base stacking interactions in DNA: Is there a novel stabilization factor coupled with base pairing H-bonds? Physical Chemistry Chemical Physics, 16(29), 15527–15538. https://doi.org/10.1039/c4cp00997e
   PubMed Web of Science ®Google Scholar
• Kim, H.-S., Ahn, D.-S., Chung, S.-Y., Kim, S. K., & Lee, S. (2007). Tautomerization of adenine facilitated by water: Computational study of microsolvation. The Journal of Physical Chemistry A, 111(32), 8007–8012. https://doi.org/10.1021/jp074229d
   PubMed Web of Science ®Google Scholar
• Lavery, R., Moakher, M., Maddocks, J. H., Petkeviciute, D., & Zakrzewska, K. (2009). Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Research, 37(17), 5917–5929. https://doi.org/10.1093/nar/gkp608
   PubMed Web of Science ®Google Scholar
• Leslie, A. G. W., Arnott, S., Chandrasekaran, R., & Ratliff, R. L. (1980). Polymorphism of DNA double helices. Journal of Molecular Biology, 143(1), 49–72. https://doi.org/10.1016/0022-2836(80)90124-2
   PubMed Web of Science ®Google Scholar
• Löwdin, P. O. (1963). Proton tunneling in DNA and its biological implications. Reviews of Modern Physics, 35(3), 724–732. https://doi.org/10.1103/RevModPhys.35.724
   Web of Science ®Google Scholar
• Maehigashi, T., Hsiao, C., Woods, K. K., Moulaei, T., Hud, N. V., & Williams, L. D. (2012). B-DNA structure is intrinsically polymorphic: Even at the level of base pair positions. Nucleic Acids Research, 40(8), 3714–3722. https://doi.org/10.1093/nar/gkr1168
   PubMed Web of Science ®Google Scholar
• Mentel, Ł. M., & Baerends, E. J. (2014). Can the counterpoise correction for basis set superposition effect be justified? Journal of Chemical Theory and Computation, 10(1), 252–267. https://doi.org/10.1021/ct400990u
   PubMed Web of Science ®Google Scholar
• Mohamed, T. A., Shabaan, I. A., Zoghaib, W. M., Husband, J., Farag, R. S., & Alajhaz, A. E. N. M. A. (2009). Tautomerism, normal coordinate analysis, vibrational assignments, calculated IR, Raman and NMR spectra of adenine. Journal of Molecular Structure, 938(1–3), 263–276. https://doi.org/10.1016/j.molstruc.2009.09.040
   Web of Science ®Google Scholar
• Mohammadi, M., & Ramazani, S. (2016). Theoretical kinetics study of thymine tautomerism and interaction of Na+ with its tautomers. Molecular Physics, 114(22), 3356–3374. https://doi.org/10.1080/00268976.2016.1232845
   Web of Science ®Google Scholar
• van Mourik, T. (2009). Comment on ‘To stack or not to stack: Performance of a new density functional for the uracil and thymine dimers’ [Chem. Phys. Lett. 459 (2008) 164]. Chemical Physics Letters, 473(1–3), 206–208. https://doi.org/10.1016/j.cplett.2009.03.050
   Web of Science ®Google Scholar
• Neidle, S. (2008). Principles of nucleic acid structure. In The building-blocks of DNA and RNA (Chapter 2). Elsevier.
   Google Scholar
• Podolyan, Y., Gorb, L., & Leszczynski, J. (2003). Ab initio study of the prototropic tautomerism of cytosine and guanine and their contribution to spontaneous point mutations. International Journal of Molecular Sciences, 4(7), 410–421. https://doi.org/10.3390/i4070410
   Web of Science ®Google Scholar
• Rejnek, J., Hanus, M., Kabelác, M., Ryjácek, F., & Hobza, P. (2005). Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution. Part 4. Uracil and thymine. Physical Chemistry Chemical Physics, 7(9), 2006–2017. https://doi.org/10.1039/b501499a
   PubMed Web of Science ®Google Scholar
• Riley, K. E., & Hobza, P. (2011). Noncovalent interactions in biochemistry. WIREs Computational Molecular Science, 1(1), 3–17. https://doi.org/10.1002/wcms.8
   Google Scholar
• Riley, K. E., Pitonák, M., Jurecka, P., & Hobza, P. (2010). Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories. Chemical Reviews, 110(9), 5023–5063. https://doi.org/10.1021/cr1000173
   PubMed Web of Science ®Google Scholar
• Saenger, W. (1984). Principles in nucleic acid structure. Springer Verlag Publishers.
   Google Scholar
• Shishkin, O. V., Pelmenschikov, A., Hovorun, D. M., & Leszczynski, J. (2000a). Theoretical analysis of low-lying vibrational modes of free canonical 2-deoxyribonucleosides. Chemical Physics, 260(3), 317–325. https://doi.org/10.1016/S0301-0104(00)00251-2
   Web of Science ®Google Scholar
• Shishkin, O. V., Pelmenschikov, A., Hovorun, D. M., & Leszczynski, J. (2000b). Molecular structure of free canonical 2′-deoxyribonucleosides: A density functional study. Journal of Molecular Structure, 526(1–3), 329–341. https://doi.org/10.1016/S0022-2860(00)00497-X
   Google Scholar
• Shishkin, O. V., Sponer, J., & Hobza, P. (1999). Intramolecular flexibility of DNA bases in adenine-thymine and guanine-cytosine Watson–Crick base pairs. Journal of Molecular Structure, 477(1–3), 15–21. https://doi.org/10.1016/S0022-2860(98)00603-6
   Web of Science ®Google Scholar
• 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(1–3), 245–251. https://doi.org/10.1016/S0166-1280(00)00681-3
   Google Scholar
• Srivastava, R. (2019). The role of proton transfer on mutations. Frontiers in Chemistry, 7(536), 1–17. https://doi.org/10.3389/fchem.2019.00536
   PubMedGoogle 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 of the United States of America, 108(43), 17644–17648. https://doi.org/10.1073/pnas.1114496108
   PubMed Web of Science ®Google Scholar
• Yokoyama, S., Watanabe, T., Murao, K., Ishikura, H., Yamaizumi, Z., Nishimura, S., & Miyazawa, T. (1985). Molecular mechanism of codon recognition by tRNA species with modified uridine in the first position of the anticodon. Proceedings of the National Academy of Sciences of the United States of America, 82(15), 4905–4909. https://doi.org/10.1073/pnas.82.15.4905
   PubMed Web of Science ®Google Scholar
• Yurenko, Y. P., Novotný, J., Nikolaienko, T. Y., & Marek, R. (2016). Nucleotides containing variously modified sugars: Energetics, structure, and mechanical properties. Physical Chemistry Chemical Physics, 18(3), 1615–1628. https://doi.org/10.1039/c5cp05478h
   PubMed 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 & Dynamics, 29(1), 51–65. https://doi.org/10.1080/07391102.2011.10507374
   PubMed Web of Science ®Google Scholar
• Zhao, Y., & Truhlar, D. G. (2008a). Density functionals with broad applicability in chemistry. Accounts of Chemical Research, 41(2), 157–167. https://doi.org/10.1021/ar700111a
   PubMed Web of Science ®Google Scholar
• Zhao, Y., & Truhlar, D. G. (2008b). The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: Two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theoretical Chemistry Accounts, 120(1–3), 215–241. https://doi.org/10.1007/s00214-007-0310-x
   Web of Science ®Google Scholar
• Zhurkin, V. B., Lysov, Y. P., & Ivanov, V. I. (1975). Computer analysis of conformational possibilities of double-helical DNA. FEBS Letters, 59(1), 44–47. https://doi.org/10.1016/0014-5793(75)80337-1
   PubMed Web of Science ®Google Scholar
• Zubatiuk, T. A., Shishkin, O. V., Gorb, L., Hovorun, D. M., & Leszczynski, J. (2013). B-DNA characteristics are preserved in double stranded. d(A)3·d(T)3 and d(G)3·d(C)3 mini-helixes: Conclusions from DFT/M06-2X study. Physical Chemistry Chemical Physics, 15(41), 18155–18166. https://doi.org/10.1039/c3cp51584b
   PubMed Web of Science ®Google Scholar