Intermolecular CH···O/N H-bonds in the biologically important pairs of natural nucleobases: a thorough quantum-chemical study

References

• Abrescia, N. G., Gonzalez, C., Gouyette, C., & Subrina, J. A. (2004). X-ray and NMR studies of the DNA oligomer d(ATATAT): Hoogsteen base pairing in duplex DNA. Biochemistry, 43, 4092–4100.
   PubMed Web of Science ®Google Scholar
• Abrescia, N. G., Thompson, A., Huynh-Dinh, T., & Subrina, J. A. (2002). Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing. Proceedings of the National Academy of Sciences of the United States of America, 99, 2806–2811.
   PubMed Web of Science ®Google Scholar
• Aishima, J., Gitti, R. K., Noah, J. E., Gan, H. H., Schlick, T., & Wolberger, C. (2002). A Hoogsteen base pair embedded in undistorted B-DNA. Nucleic Acids Research, 30, 5244–5252.
   PubMed Web of Science ®Google Scholar
• Alabugin, I. V., Manoharan, M., Peabody, S., & Weinhold, F. (2003). Electronic basis of improper hydrogen bonding: A subtle balance of hyperconjugation and rehybridization. Journal of the American Chemical Society, 125, 5973–5987.
   PubMed Web of Science ®Google Scholar
• Allerhand, A., & Schleyer, P. V. A. (1963). A survey of C–H groups as proton donors in hydrogen bonding. Journal of the American Chemical Society, 85, 1715–1723.
   Web of Science ®Google Scholar
• Asensio, A., Kobko, N., & Dannenberg, J. J. (2003). Cooperative hydrogen-bonding in adenine–thymine and guanine–cytosine base pairs. Density functional theory and Moller–Plesset molecular orbital study. Journal of Physical Chemistry A, 107, 6441–6443.
   Web of Science ®Google Scholar
• Bacolla, A., & Wells, R. D. (2004). Non-B DNA conformations, genomic rearrangements, and human disease. Journal of Biological Chemistry, 279, 47411–47414.
   PubMed Web of Science ®Google Scholar
• Bader, R. F. W. (1990). Atoms in molecules: A quantum theory. Oxford: Clarendon Press.
   Google Scholar
• Bader, R. F. W. (2009). Bond paths are not chemical bonds. Journal of Physical Chemistry A, 113, 10391–10396.
   PubMed Web of Science ®Google Scholar
• Bader, R. F. W. (2010). Definition of molecular structure: By choice or by appeal to observation? Journal of Physical Chemistry A, 114, 7431–7444.
   PubMed Web of Science ®Google Scholar
• Becke, A. D. (1988). Density-functional exchange-energy approximation with correct asymptotic behaviour. Physical Review A, 38, 3098–3100.
   PubMed Web of Science ®Google Scholar
• Berger, I., Egli, M., & Rich, A. (1996). Inter-strand C–H···O hydrogen bonds stabilizing four-stranded intercalated molecules: Stereoelectronic effects of O4′ in cytosine-rich DNA. Proceedings of the National Academy of Sciences of the United States of America, 93, 12116–12121.
   PubMed Web of Science ®Google Scholar
• Bohnuud, T., Beglov, D., Ngan, C. H., Zerbe, B., Hall, D. R., Brenke, R., Vajda, S., Frank-Kamenetskii, M. D., & Kozakov, D. (2012). Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde. Nucleic Acids Research, 40, 7644–7652.
   PubMed Web of Science ®Google Scholar
• Bondi, A. J. (1964). Van der Waals volumes and radii. Journal of Physical Chemistry, 68, 441–451.
   Web of Science ®Google Scholar
• Borissova, O. F., Shchyolkina, A. K., Chernov, B. K., & Tchurikov, N. A. (1993). Relative stability of AT and GC pairs in parallel DNA duplex formed by a natural sequence. FEBS Letters, 322, 304–306.
   PubMed Web of Science ®Google Scholar
• Boyd, R. J., & Choi, S. (1985). A bond-length-bond-order relationship for intermolecular interactions based on the topological properties of molecular charge distributions. Chemical Physics Letters, 120, 80–85.
   Web of Science ®Google Scholar
• Boyd, R. J., & Choi, S. (1986). Hydrogen bonding between nitriles and hydrogen halides and the topological properties of molecular charge distributions. Chemical Physics Letters, 129, 62–65.
   Web of Science ®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, 553–566.
   Web of Science ®Google Scholar
• Brandhorst, K., & Grunenberg, J. (2008). How strong is it? The interpretation of force and compliance constants as bond strength descriptors. Chemical Society Reviews, 37, 1558–1567.
   PubMed Web of Science ®Google Scholar
• Brandhorst, K., & Grunenberg, J. (2010). Efficient computation of compliance matrices in redundant internal coordinates from Cartesian Hessians for nonstationary points. Journal of Chemical Physics, 132, 184101–184107.
   Web of Science ®Google Scholar
• Brandl, M., Lindauer, K., Meyer, M., & Sühnel, J. (1999). C–H···O and C–H···N interactions in RNA structures. Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), 103, 77–80.
   Google Scholar
• Brandl, M., Meyer, M., & Sühnel, J. (2001). Quantum-chemical analysis of C–H···O and C–H···N interactions in RNA base pairs – H-bond versus anti-H-bond pattern. Journal of Biomolecular Structure and Dynamics, 18, 545–555.
   PubMed Web of Science ®Google Scholar
• Brovarets’, O. O. (2013a). Structurally-energetic properties of the four configurations of the А–Т and G–C DNA base pairs: Comparative quantum-chemical analysis. Ukrainian Biochemical Journal, 85, in press.
   Google Scholar
• Brovarets’, O. O. (2013b). Under what conditions does G–C Watson–Crick DNA base pair acquire all four configurations characteristic for A–T Watson-Crick DNA base pair? Quantum-chemical study. Ukrainian Biochemical Journal, 85, in press.
   Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2010a). How stable are the mutagenic tautomers of DNA bases? Biopolymers and Cell, 26, 72–76.
   Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2010b). Stability of mutagenic tautomers of uracil and its halogen derivatives: The results of quantum-mechanical investigation. Biopolymers and Cell, 26, 295–298.
   Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2010c). Quantum-chemical investigation of the elementary molecular mechanisms of pyrimidine–purine transversions. Ukrainian Biochemical Journal, 82, 57–67.
   PubMedGoogle Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2011a). 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.
   Web of Science ®Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2011b). Intramolecular tautomerization and the conformational variability of some classical mutagens – cytosine derivatives: Quantum chemical study. Biopolymers and Cell, 27, 221–230.
   Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2012). Prototropic tautomerism and basic molecular principles of hypoxanthine mutagenicity: An exhaustive quantum-chemical analysis. Journal of Biomolecular Structure and Dynamics. doi:10.1080/07391102.2012.715041.
   Web of Science ®Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2013). 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 and Dynamics. doi:10.1080/07391102.2012.755795.
   Web of Science ®Google Scholar
• Brovarets’, O. O., Kolomiets’, I. M., & Hovorun, D. M. (2012a). 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.
   Google Scholar
• Brovarets’, O. O., Yurenko, Y. P., Dubey, I. Ya, & Hovorun, D. M. (2012b). Can DNA-binding proteins of replisome tautomerize nucleotide bases? Ab initio model study. Journal of Biomolecular Structure & Dynamics, 29, 1101–1109.
   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.
   Google Scholar
• Brovarets’, O. O., Zhurakivsky, R. O., & Hovorun, D. M. (2013). The physico-chemical ‘anatomy’ of the tautomerisation through the DPT of the biologically important pairs of hypoxanthine with DNA bases: QM and QTAIM perspectives. Journal of Molecular Modelingdoi:10.1007/s00894-012-1720-9.
   Web of Science ®Google Scholar
• Bruce, R. St L., Cooper, M. K., Freeman, H. C., & McGrath, B. G. (1974). Evidence for an intramolecular C–H···N hydrogen bond in (E) -5-methylpyridine-2-carboxaldehyde-2′-pyridylhydrazonetetracarbonylmolybdenum(O) from its crystal structure and proton magnetic resonance spectrum. Inorganic Chemistry, 13, 1032–1037.
   Web of Science ®Google Scholar
• Buckingham, A. D., Del Bene, J. E., & McDowell, S. A. C. (2008). The hydrogen bond. Chemical Physics Letters, 463, 1–10.
   Web of Science ®Google Scholar
• Calhorda, M. J. (2000). Weak hydrogen bonds: Theoretical studies. Chemical Communications. 801–809.
   Web of Science ®Google Scholar
• Carpenter, M. A., Li, M., Rathore, A., Lackey, L., Law, E. K., Land, A. M., … Harris, R. S. (2012). Methylcytosine and normal cytosine deamination by the foreign DNA restriction enzyme APOBEC3A. Journal of Biological Chemistry, 287, 34801–34808.
   PubMed Web of Science ®Google Scholar
• Cerón-Carrasco, J. P., Requena, A., Perpète, E. A., Michaux, C., & Jacquemin, D. (2009). Double proton transfer mechanism in the adenine–uracil base pair and spontaneous mutation in RNA duplex. Chemical Physics Letters, 484, 64–68.
   Web of Science ®Google Scholar
• Chaney, J. D., Goss, C. R., Folting, K., Santarsiero, B. D., & Hollingsworth, M. D. (1996). Formyl C−H···O hydrogen bonding in crystalline bis-formamides? Journal of the American Chemical Society, 118, 9432–9433.
   Web of Science ®Google Scholar
• Cheng, Y.-K., & Pettitt, B. M. (1992). Hoogsteen versus reversed-Hoogsteen base pairing: DNA triple helixes. Journal of the American Chemical Society, 114, 4465–4474.
   Web of Science ®Google Scholar
• Chung, S., & Hippler, M. (2006). Infrared spectroscopy of hydrogen-bonded CHCl3–SO2 in the gas phase. Journal of Chemical Physics, 124, 214316–214323.
   PubMed Web of Science ®Google Scholar
• Ciao, X., & Patel, D. J. (1988). NMR studies of echinomycin bisintercalation complexes with d(A1–C2–G3–T4) and d(T1–C2–G3–A4) duplexes in aqueous solution: Sequence-dependent formation of Hoogsteen Al T4 and Watson–Crick A4 base pairs flanking the bisintercalation site. Biochemistry, 27, 1744–l751.
   PubMed Web of Science ®Google Scholar
• Cleland, W. W., & Kreevoy, M. M. (1994). Low-barrier hydrogen bonds and enzymic catalysis. Science, 264, 1887–1890.
   PubMed Web of Science ®Google Scholar
• Cubero, E., Orozco, M., Hobza, P., & Luque, F. J. (1999a). Hydrogen bond versus anti-hydrogen bond: A comparative analysis based on the electron density topology. Journal of Physical Chemistry A, 103, 6394–6401.
   Web of Science ®Google Scholar
• Cubero, E., Orozco, M., & Luque, F. J. (1999b). Electron density topological analysis of the C–H···O anti-hydrogen bond in the fluoroform–oxirane complex. Chemical Physics Letters, 310, 445–450.
   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.
   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. Journal of Physical Chemistry A, 113, 2233–2235.
   PubMed Web of Science ®Google Scholar
• Deng, J., & Sundaralingam, M. (2000). Synthesis and crystal structure of an octamer RNA r(guguuuac)/r(guaggcac) with G center dot G/U center dot U tandem wobble base pairs: Comparison with other tandem G center dot U pairs. Nucleic Acid Research, 28, 4376–4381.
   PubMed Web of Science ®Google Scholar
• Desiraju, G. R. (1989). Crystal engineering. The design of organic solids. Amsterdam: Elsevier.
   Google Scholar
• Desiraju, G. R. (1991). The C–H···O hydrogen bond in crystals. What is it? Accounts of Chemical Research, 24, 290–296.
   Web of Science ®Google Scholar
• Desiraju, G. R. (1995). Supramolecular synthons in crystal engineering – A new organic synthesis. Angewandte Chemie International Edition, 34, 2311–2327.
   Web of Science ®Google Scholar
• Desiraju, G. R. (2002). Hydrogen bridges in crystal engineering: Interactions without borders. Accounts of Chemical Research, 35, 565–573.
   PubMed Web of Science ®Google Scholar
• Desiraju, G. R., & Steiner, T. (1999). The weak hydrogen bond in structural chemistry and biology. New York, NY: Oxford University Press Inc..
   Google Scholar
• Dong, H., Hua, W., & Li, S. (2007). Estimation on the individual hydrogen-bond strength in molecules with multiple hydrogen bonds. Journal of Physical Chemistry A, 111, 2941–2945.
   PubMed Web of Science ®Google Scholar
• Donohue, J., & Kenneth, N. (1960). Trueblood base pairing in DNA. Journal of Molecular Biology, 2, 363–371.
   PubMed Web of Science ®Google Scholar
• Egli, M., & Gessner, R. V. (1995). Stereoelectronic effects of deoxyribose O4′ on DNA conformation. Proceedings of the National Academy of Sciences of the United States of America, 92, 180–185.
   PubMed Web of Science ®Google Scholar
• Escude, C., Mohammadi, S., Sun, J.-S., Nguyen, C.-H., Bisagni, E., Liquier, J., … Helene, C. (1996). Ligand-induced formation of Hoogsteen-paired parallel DNA. Chemistry & Biology, 3, 57–65.
   PubMedGoogle Scholar
• Espinosa, E., & Molins, E. (2000). Retrieving interaction potentials from the topology of the electron density distribution: The case of hydrogen bonds. Journal of Chemical Physics, 113, 5686–5694.
   Web of 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.
   Web of Science ®Google Scholar
• Fonseca Guerra, C., Bickelhaupt, F. M., Snijders, J. G., & Baerends, E. (1999). The nature of the hydrogen bond in DNA base pairs: The role of charge transfer and resonance assistance. Chemistry – A European Journal, 5, 3581–3594.
   Web of Science ®Google Scholar
• Frank-Kamenetskii, M. D. (2011). DNA breathes Hoogsteen. Artificial DNA: PNA& XNA, 2, 1–3.
   PubMedGoogle Scholar
• Frieden, E. (1975). Non-covalent interactions: Key to biological flexibility and specificity. Journal of Chemical Education, 52, 754–756.
   PubMed Web of Science ®Google Scholar
• 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.
   Web of Science ®Google Scholar
• Frisch, M. J., Pople, J. A., & Binkley, J. S. (1984). Self-consistent molecular orbital methods 25. Supplementary functions for Gaussian basis sets. Journal of Chemical Physics, 80, 3265–3269.
   Web of Science ®Google Scholar
• 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 Inc..
   Google Scholar
• Gerlt, J. A., Kreevoy, M. M., Cleland, W. W., & Frey, P. A. (1997). Understanding enzymic catalysis: The importance of short, strong hydrogen bonds. Chemical Biology, 4, 259–367.
   PubMed Web of Science ®Google Scholar
• Ghosal, G., & Muniyappa, K. (2006). Hoogsteen base-pairing revisited: Resolving a role in normal biological processes and human diseases. Biochemical and Biophysical Research Communications, 343, 1–7.
   PubMed Web of Science ®Google Scholar
• Gilbert, D. E., van der Marel, G. A., van Boom, J. H., & Feigon, J. (1989). Unstable Hoogsteen base pairs adjacent to echinomycin binding sites within a DNA duplex. Proceedings of the National Academy of Sciences of the United States of America, 86, 3006–3010.
   PubMed Web of Science ®Google Scholar
• Gilli, P., Bertolasi, V., Ferretti, V., & Gilli, G. (1994). Evidence for resonance-assisted hydrogen bonding. 4. Covalent nature of the strong homonuclear hydrogen bond. Study of the O–H···O system by crystal structure correlation methods. Journal of the American Chemical Society, 116, 909–915.
   Web of Science ®Google Scholar
• Grabowski, S. J. (2001). Ab initio calculations on conventional and unconventional hydrogen bonds. Study of the hydrogen bond strength. Journal of Physical Chemistry A, 105, 10739–10746.
   Web of Science ®Google Scholar
• Grabowski, S. J. (2004). Hydrogen bonding strength – Measures based on geometric and topological parameters. Journal of Physical Organic Chemistry, 17, 18–31.
   Web of Science ®Google Scholar
• Grabowski, S. J. (2006). Hydrogen bonding – New insights. In J. Leszczynski (Ed.), Series challenges and advances in computational chemistry and physics (p.). New York, NY: Springer.
   Google Scholar
• Grabowski, S. J. (2011). Red- and blue-shifted hydrogen bonds: The bent rule from quantum theory of atoms in molecules perspective. Journal of Physical Chemistry A, 115, 12789–12799.
   PubMed Web of Science ®Google Scholar
• Grunenberg, J. (2004). Direct assessment of interresidue forces in Watson–Crick base pairs using theoretical compliance constants. Journal of the American Chemical Society, 126, 16310–16311.
   PubMed Web of Science ®Google Scholar
• Grunenberg, J., & Barone, G. (2013). Are compliance constants ill-defined descriptors for weak interactions? RSC Advances, 3, 4757–4762.
   Web of Science ®Google Scholar
• Gu, Y., Kar, T., & Scheiner, S. (1999). Fundamental properties of the CH···O interaction: Is it a true hydrogen bond? Journal of the American Chemical Society, 121, 9411–9422.
   Web of Science ®Google Scholar
• Gutowski, M., Van Lenthe, J. H., Verbeek, J., Van Duijneveldt, F. B., & Chalasinski, G. (1986). The basis set superposition error in correlated electronic structure calculations. Chemical Physics Letters, 124, 370–375.
   Web of Science ®Google Scholar
• Hamdani, H. Y., Appasamy, S. D., Willett, P., Artymiuk, P. J., & Firdaus-Raih, M. (2012). NASSAM: A server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules. Nucleic Acids Research, 40, W35–W41.
   PubMed Web of Science ®Google Scholar
• Hariharan, P. C., & Pople, J. A. (1973). The influence of polarization functions on molecular orbital hydrogenation energies. Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), 28, 213–222.
   Web of Science ®Google Scholar
• Harris, V. H., Smith, C. L., Cummins, W. J., Hamilton, A. L., Adams, H., Dickman, M., … Williams, 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.
   PubMed Web of Science ®Google Scholar
• Haschemeyer, A. E. V., & Sobell, H. M. (1963). The crystal structure of an intermolecular nucleoside complex: Adenosine and 5-bromouridine. Proceedings of the National Academy of Sciences of the United States of America, 50, 872–877.
   PubMed Web of Science ®Google Scholar
• Hermann, T., & Westhof, E. (1999). Non-Watson–Crick base pairs in RNA-protein recognition. Chemistry & Biology, 6, R335–R343.
   PubMed Web of Science ®Google Scholar
• Hermansson, K. (2002). Blue-shifting hydrogen bonds. Journal of Physical Chemistry A, 106, 4695–4702.
   Web of Science ®Google Scholar
• Hill-Perkins, M., Jones, M. D., & Karran, P. (1986). Site-specific mutagenesis in vivo by single methylated or deaminated purine bases. Mutation Research, 162, 153–163.
   PubMed Web of Science ®Google Scholar
• Hobza, P., Sponer, J., Cubero, E., Orozco, M., & Luque, F. J. (2000). C–H···O contacts in the adenine···uracil and uracil···uracil nucleic acid base pairs: Nonempirical ab initio study with inclusion of electron correlation effects. Journal of Physical Chemistry B, 104, 6286–6292.
   Web of Science ®Google Scholar
• Hoogsteen, K. (1963). The crystal and molecular structure of a hydrogenbonded complex between 1-methylthymine and 9-methyladenine. Acta Crystallographica, 16, 907–916.
   Web of Science ®Google Scholar
• Hunter, W. N., Brown, T., Anand, N. N., & Kennard, O. (1986). Structure of an adenine·cytosine base pair in DNA and its implications for mismatch repair. Nature, 320, 552–555.
   PubMed Web of Science ®Google Scholar
• Hydrogen-transfer reactions Hynes J. T. Klinman J. P. Limbach H.-H. Schowen R. L. Wiley-VCH Verlag GmbH & Co. KGaA Weinheim 2007
   Google Scholar
• Jeffrey, G. A. (1997). An introduction to hydrogen bonding. New York, NY: Oxford University Press.
   Google Scholar
• Jeffrey, G. A., Maluszynska, H., & Mitra, J. (1985). Hydrogen bonding in nucleosides and nucleotides. International Journal of Biological Macromolecules, 7, 336–348.
   Web of Science ®Google Scholar
• Jeffrey, G. A., & Saenger, W. (1991). Hydrogen bonding in biological structures. Berlin: Springer-Verlag.
   Google Scholar
• Johnson, R. E., Prakash, L., & Prakash, S. (2005). Biochemical evidence for the requirement of Hoogsteen base pairing for replication by human DNA polymerase iota. Proceedings of the National Academy of Sciences of the United States of America, 102, 10466–10471.
   PubMed Web of Science ®Google Scholar
• Jones, C. R., Baruah, P. K., Thompson, A. L., Scheiner, S., & Smith, M. D. (2012). Can a C−H···O interaction be a determinant of conformation? Journal of the American Chemical Society, 134, 12064–12071.
   PubMed Web of Science ®Google Scholar
• Joseph, J., & Jemmis, E. D. (2007). Red-, blue-, or no-shift in hydrogen bonds: A unified explanation. Journal of the American Chemical Society, 129, 4620–4632.
   PubMed Web of Science ®Google Scholar
• Jovin, T. M., Rippe, K., Ramsing, N. B., Klement, R., Elhorst, W., & Voijtiskova, M. (1990). Parallel stranded DNA. In R. H. Sarma, & M. H. Sarma (Eds.), Structure and methods: DNA and RNA (pp. 155–174). New York, NY: Adenine Press, Schenectady.
   Google Scholar
• Kaplan, I. (2006). Intermolecular interactions: Physical picture, computational methods and model potentials (Wiley Series in Theoretical Chemistry). Chichester: John Wiley.
   Google Scholar
• Keith, T. A. (2010). AIMAll (Version 10.07.01). Retrieved from http://www.aim.tkgristmill.com.
   Google Scholar
• Khuu, P., & Ho, P. S. (2009). A rare nucleotide base tautomer in the structure of an asymmetric DNA junction. Biochemistry, 48, 7824–7832.
   PubMed Web of Science ®Google Scholar
• Knop, O., Rankin, K. N., & Boyd, R. J. (2001). Coming to grips with N−H···N bonds. 1. Distance relationships and electron density at the bond critical point. Journal of Physical Chemistry A, 105, 6552–6566.
   Web of Science ®Google Scholar
• Knop, O., Rankin, K. N., & Boyd, R. J. (2003). Coming to grips with N−H···N bonds. 2. Homocorrelations between parameters deriving from the electron density at the bond critical point. Journal of Physical Chemistry A, 107, 272–284.
   Web of Science ®Google Scholar
• Koch, U., & Popelier, P. L. A. (1995). Characterization of CH–O hydrogen bonds on the basis of the charge density. Journal of Physical Chemistry, 99, 9747–9754.
   Web of Science ®Google Scholar
• Kollman, P. A. (1977). Noncovalent interaction. Accounts of Chemical Research, 10, 365–371.
   Web of Science ®Google Scholar
• Krishnan, R., Binkley, J. S., Seeger, R., & Pople, J. A. (1980). Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions. Journal of Chemical Physics, 72, 650–654.
   Web of Science ®Google Scholar
• Kryachko, E. S. (2006). Hydrogen bonding – New insights. Dordrecht: Springer.
   Google Scholar
• Kryachko, E. S. (2010). Three computational mise-en-scènes of red- and blue-shifted hydrogen bonding motifs: Concept of negative intramolecular coupling. What else? International Journal of Quantum Chemistry, 110, 104–119.
   Web of Science ®Google Scholar
• Lee, J. C., & Gutell, R. R. (2004). Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs. Journal of Molecular Biology, 344, 1225–1249.
   PubMed Web of Science ®Google Scholar
• 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: Condensed Matter and Materials Physics, 37, 785–789.
   PubMed Web of Science ®Google Scholar
• Lehn, J.-M. (1995). Supramolecular chemistry. Weinheim: Verlag-Chemie.
   Google Scholar
• Lemieux, A., & Major, F. (2002). RNA canonical and non-canonical base pairing types: A recognition method and complete repertoire. Nucleic Acids Research, 30, 4250–4263.
   PubMed Web of Science ®Google Scholar
• Leonard, G. A., McAuley-Hecht, K., Brown, T., & Hunter, W. N. (1995). Do C–H···O hydrogen bonds contribute to the stability of nucleic acid base pairs? Acta Crystallographica, Section D: Biological Crystallography, 51, 136–139.
   PubMed Web of Science ®Google Scholar
• Leontis, N. B., Stombaugh, J., & Westhof, E. (2002). The non-Watson–Crick base pairs and their associated isostericity matrices. Nucleic Acid Research, 30, 3497–3531.
   PubMed Web of Science ®Google Scholar
• Leontis, N. B., & Westhof, E. (1998). Conserved geometrical base-pairing patterns in RNA. Quarterly Reviews of Biophysics, 31, 399–455.
   PubMed Web of Science ®Google Scholar
• Leontis, N. B., & Westhof, E. (2001). Geometric nomenclature and classification of RNA base pairs. RNA, 7, 499–512.
   PubMed Web of Science ®Google Scholar
• Lescoute, A., Leontis, N. B., Massire, C., & Westhof, E. (2005). Recurrent structural RNA motifs, isostericity matrices and sequence alignments. Nucleic Acid Research, 33, 2395–2409.
   PubMed Web of Science ®Google Scholar
• Lindahl, T. (1993). Instability and decay of the primary structure of DNA. Nature, 362, 709–715.
   PubMed Web of Science ®Google Scholar
• Liu, K., Miles, T. H., Frazier, J., & Sasisekharan, V. (1993). A novel DNA duplex. A parallel-stranded DNA helix with Hoogsteen base pairing. Biochemistry, 32, 11802–11809.
   PubMed Web of Science ®Google Scholar
• Löwdin, P.-O. (1963). Proton tunneling in DNA and its biological implications. Reviews of Modern Physics, 35, 724–732.
   Web of Science ®Google Scholar
• 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 (pp. 213–360). New York, NY: Academic Press.
   Google Scholar
• Mandel-Gutfreund, Y., Margalit, H., Jernigan, R. L., & Zhurkin, V. B. (1998). A role for CH–O interactions in protein-DNA recognition. Journal of Molecular Biology, 277, 1129–1140.
   PubMed Web of Science ®Google Scholar
• 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.
   Web of Science ®Google Scholar
• Matsuura, H., Yoshida, H., Hieda, M., Yamanaka, S. Y., Harada, T., Shinya, K., & Ohno, K. (2003). Experimental evidence for intramolecular blue-shifting C–H···O hydrogen bonding by matrix-isolation infrared spectroscopy. Journal of the American Chemical Society, 125, 13910–13911.
   PubMed Web of Science ®Google Scholar
• 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. Journal of Physical Chemistry B, 110, 563–578.
   PubMed Web of Science ®Google Scholar
• Mishchuk, Ya 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.
   Web of Science ®Google Scholar
• Mizuno, K., Ochi, T., & Shindo, Y. (1998). Hydrophobic hydration of acetone probed by nuclear magnetic resonance and infrared: Evidence for the interaction C–H···OH2. Journal of Chemical Physics, 109, 9502–9507.
   Web of Science ®Google Scholar
• Nagaswamy, U., Voss, N., Zhang, Z., & Fox, G. E. (2000). Database of non-canonical base pairs found in known RNA structures. Nucleic Acids Research, 28, 375–376.
   PubMed Web of Science ®Google Scholar
• Nair, D. T., Johnson, R. E., Prakash, S., Prakash, L., & Aggarwal, A. K. (2004). Replication by human DNA polymerase-ι occurs by Hoogsteen base pairing. Nature, 430, 377–380.
   PubMed Web of Science ®Google Scholar
• Nair, D. T., Johnson, R. E., Prakash, S., Prakash, L., & Aggarwal, A. K. (2005). Human DNA polymerase iota incorporates dCTP opposite template G via a GC+ Hoogsteen base pair. Structure, 13, 1569–1577.
   PubMed Web of Science ®Google Scholar
• Neidle, S. (2008). Principles of nucleic acid structure. Amsterdam: Elsevier.
   Google Scholar
• Nikolova, E. N., Goh, G. B., Brooks, C. L., III, & Al-Hashimi, H. M. (2013). Characterizing the protonation state of cytosine in transient G•C Hoogsteen base pairs in duplex DNA. Journal of the American Chemical Society, 135, 6766–6769. doi:10.1021/ja400994e.
   PubMed Web of Science ®Google Scholar
• Nikolova, E. N., Kim, E., Wise, A. A., O’Brien, P. J., Andricioaei, I., & Al-Hashimi, H. M. (2011). Transient Hoogsteen base pairs in canonical duplex DNA. Nature, 470, 498–502.
   PubMed Web of Science ®Google Scholar
• Novoa, J. J., Lafuente, P., & Mota, F. (1998). Are non-linear C–H···O contacts hydrogen bonds or van der Waals interactions? Establishing the limits between hydrogen bonds and van der Waals interactions. Chemical Physics Letters, 290, 519–525.
   Web of Science ®Google Scholar
• Olson, W. K., Esguerra, M., Xin, Y., & Lu, X. J. (2009). New information content in RNA base pairing deduced from quantitative analysis of high-resolution structures. Methods, 47, 177–186.
   PubMed Web of Science ®Google Scholar
• Otto, C., Thomas, G. A., Rippe, K., Jovin, T. M., & Pelicolas, W. L. (1991). The hydrogen-bonding structure in parallel-stranded duplex DNA is reverse Watson–Crick. Biochemistry, 30, 3062–3069.
   PubMed Web of Science ®Google Scholar
• Pan, B., Ban, C., Wahl, M. C., & Sundaralingam, M. (1997). Crystal structure of d(GCGCGCG) with 5′-overhang G residues. Biophysical Journal, 73, 1553–1561.
   PubMed Web of Science ®Google Scholar
• Panigrahi, S., Pal, R., & Bhattacharyya, D. (2011). Structure and energy of non-canonical basepairs: Comparison of various computational chemistry methods with crystallographic ensembles. Journal of Biomolecular Structure and Dynamics, 29, 541–556.
   PubMed Web of Science ®Google Scholar
• Parr, R. G., & Yang, W. (1989). Density-functional theory of atoms and molecules. Oxford: Oxford University Press.
   Google Scholar
• Parthasarathi, R., Amutha, R., Subramanian, V., Nair, B. U., & Ramasami, T. (2004). Bader’s and reactivity descriptors’ analysis of DNA base pairs. Journal of Physical Chemistry A, 108, 3817–3828.
   Web of Science ®Google Scholar
• Parvathy, V. R., Bhaumik, S. R., Chary, K. V., Govil, G., Liu, K., Howard, F. B., & Miles, H. T. (2002). NMR structure of a parallel-stranded DNA duplex at atomic resolution. Nucleic Acids Research, 30, 1500–1511.
   PubMed Web of Science ®Google Scholar
• Patel, D. J., Phan, A. T., & Kuryavyi, V. (2007). Human telomere, oncogenic promoter and 5′-UTR G-quadruplexes: Diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Research, 35, 7429–7455.
   PubMed Web of Science ®Google Scholar
• Patikoglou, G. A., Kim, J. L., Sun, L., Yang, S. H., Kodadek, T., & Burley, S. K. (1999). TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes & Development, 13, 3217–3230.
   PubMed Web of Science ®Google Scholar
• Pelmenschikov, A., Hovorun, D. M., Shishkin, O. V., & Leszczynski, J. (2000). A density functional theory study of vibrational coupling between ribose and base rings of nucleic acids with ribosyl guanosine as a model system. Journal of Chemical Physics, 113, 5986–5990.
   Web of Science ®Google Scholar
• Perrin, C. L., & Nielson, J. B. (1997). ‘Strong’ hydrogen bonds in chemistry and biology. Annual Review of Physical Chemistry, 48, 511–544.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Ponomareva, A. G., Yurenko, Ye 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.
   PubMed Web of Science ®Google Scholar
• Ponomareva, A. G., Yurenko, Ye P., Zhurakivsky, R. O., van Mourik, T., & Hovorun, D. M. (2013a). Conformational landscape of the nucleoside reverse transcriptase inhibitor d4T: A comprehensive quantum-chemical approach. Current Physical Chemistry, 3, 83–92.
   Google Scholar
• Ponomareva, A. G., Yurenko, Ye. P., Zhurakivsky, R. O., van Mourik, T., & Hovorun, D. M. (2013b). Structural and energetic properties of the potential HIV-1 reverse transcriptase inhibitors d4A and d4G: A comprehensive theoretical investigation, Journal of Biomolecular Structure & Dynamics, in press.
   Google Scholar
• Pranav, R. S., & Wategaonkar, S. (2010). Blue shifted hydrogen bond in 3-methylindole CHX3 complexes (X = Cl, F). Physical Chemistry Chemical Physics, 12, 6650–6659.
   PubMed Web of Science ®Google Scholar
• Quigley, G. J., Ughetto, G., van der Marel, G. A., van Boom, J. H., Wang, A. H.-J., & Rich, A. (1986). Non-Watson–Crick G C and A T base pairs in a DNA-antibiotic complex. Science, 232, 1255–1258.
   PubMed Web of Science ®Google Scholar
• Quinn, J. R., Zimmerman, S. C., Del Bene, J. E., & Shavitt, L. (2007). Does the AT or GC base-pair possess enhanced stability? Quantifying the effects of CH···O interactions and secondary interactions on base-pair stability using a phenomenological analysis and ab initio calculations. Journal of the American Chemical Society, 129, 934–941.
   PubMed Web of Science ®Google Scholar
• Rice, P. A., Yang, S., Mizuuchi, K., & Nash, H. A. (1996). Crystal structure of an IHF–DNA complex: A protein-induced DNA U-turn. Cell, 87, 1295–1306.
   PubMed Web of Science ®Google Scholar
• Roy, A., Panigrahi, S., Bhattacharyya, M., & Bhattacharyya, D. (2008). Structure, stability, and dynamics of canonical and noncanonical base pairs: Quantum chemical studies. Journal of Physical Chemistry B, 112, 3786–3796.
   PubMed Web of Science ®Google Scholar
• Saenger, W. (1984). Principles of nucleic acid structure. New York, NY: Springer-Verlag.
   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.
   Web of Science ®Google Scholar
• 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. Journal of Physical Chemistry B, 114, 1454–1461.
   Web of Science ®Google Scholar
• Scheiner, S., Grabowski, S. T., & Kar, T. (2001). Influence of hybridization and substitution on the properties of the CH···O hydrogen bond. Journal of Physical Chemistry A, 105, 10607–10612.
   Web of Science ®Google Scholar
• Scheiner, S., & Kar, T. (2002). Red- versus blue-shifting hydrogen bonds: Are there fundamental distinctions? Journal of Physical Chemistry A, 106, 1784–1789.
   Web of Science ®Google Scholar
• Scheiner, S., & Kar, T. (2008). Spectroscopic and structural signature of the CH–O hydrogen bond. Journal of Physical Chemistry A, 112, 11854–11860.
   PubMed Web of Science ®Google Scholar
• Schuster, P., Zundel, G., & Sandorfy, C. (1976). The hydrogen bond. Structure and spectroscopy. Amsterdam: North-Holland.
   Google Scholar
• Seaman, F. C., & Hurley, L. (1993). Interstrand cross-linking by bizelesin produces a Watson–Crick to Hoogsteen base-pairing transition region in d(CGTAATTACC). Biochemistry, 32, 12577–l2585.
   PubMed Web of Science ®Google Scholar
• 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.
   Web of Science ®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, 15–21.
   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, 245–251.
   Web of Science ®Google Scholar
• 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 Modeling (Theoretica Chimica Acta), 74, 101–110.
   Google Scholar
• Starikov, E. B., & Steiner, T. (1997). Computational support for the suggested contribution of C–H···O=C interactions to the stability of nucleic acid base pairs. Acta Crystallographica, Section D: Biological Crystallography, 53, 345–347.
   PubMedGoogle Scholar
• Steiner, T. (1997). Unrolling the hydrogen bond properties of C−H···O interactions. Chemical Communications. 727–734.
   Web of Science ®Google Scholar
• Steiner, T. (1999). Not all short C–H···O contacts are hydrogen bonds: The prototypical example of contacts to C=O–H. Chemical Communications. 313–314.
   Web of Science ®Google Scholar
• Steiner, T., & Saenger, W. (1992). Geometry of C–H···O hydrogen bonds in carbohydrate crystal structures. Analysis of neutron diffraction data. Journal of the American Chemical Society, 114, 10146–10154.
   Web of Science ®Google Scholar
• Steiner, T., & Saenger, W. (1993). Role of C–H···O hydrogen bonds in the coordination of water molecules. Analysis of neutron diffraction data. Journal of the American Chemical Society, 115, 4540–4547.
   Web of Science ®Google Scholar
• Strobel, A. A., Ortoleva-Donnelly, L., Ryder, S. P., Cate, J. H., & Moncoeur, E. (1998). Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site. Nature: Structural Biology, 5, 60–66.
   PubMedGoogle Scholar
• Sühnel, J. (2002). Beyond nucleic acid base pairs: From triads to heptads. Biopolymers, 61, 32–51.
   Web of Science ®Google Scholar
• Sutor, D. J. (1962). The C–H···O hydrogen bonds in crystals. Nature, 195, 68–69.
   Web of Science ®Google Scholar
• Sutor, D. J. (1963). Evidence for the existence of C–H···O hydrogen bonds in crystals. Journal of the Chemical Society. 1105–1110.
   Web of Science ®Google Scholar
• Szatyłowicz, H., & Sadlej-Sosnowska, N. (2010). Characterizing the strength of individual hydrogen bonds in DNA base pairs. Journal of Chemical Information and Modeling, 50, 2151–2161.
   PubMed Web of Science ®Google Scholar
• Taylor, R., & Kennard, O. (1982). Crystallographic evidence for the existence of C–H···O, C–H···N and C–H···Cl hydrogen bonds. Journal of the American Chemical Society, 104, 5063–5070.
   Web of Science ®Google Scholar
• Tchurikov, N. A., Chernov, B. K., Golova, Y. B., & Nechipurenko, Y. D. (1989). Parallel DNA: Generation of a duplex between two Drosophila sequences in vitro. FEBS Letters, 257, 415–418.
   PubMed Web of Science ®Google Scholar
• Tchurikov, N. A., Chistyakova, L. G., Zavilgelsky, G. B., Manukhov, I. V., Chernov, B. K., & Golova, Y. B. (2000). Gene-specific silencing by expression of parallel complementary RNA in Escherichia coli. Journal of Biological Chemistry, 275, 26523–26529.
   PubMed Web of Science ®Google Scholar
• Tchurikov, N. A., Shchyolkina, A. K., Borissova, O. F., & Chernov, B. K. (1992). Southern molecular hybridization experiments with parallel complementary DNA probes. FEBS Letters, 297, 233–236.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed 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.
   PubMed Web of Science ®Google Scholar
• Voet, D., & Rich, A. (1970). The crystal structures of purines, pyrimidines and their intermolecular complexes. Progress in Nucleic Acid Research & Molecular Biology, 10, 183–265.
   PubMedGoogle Scholar
• Wahl, M. C., Rao, S. T., & Sundaralingam, M. (1996). The structure of r(UUCGCG) has a 5′-UU-overhang exhibiting Hoogsteen-like trans U–U base pairs. Nature Structural Biology, 3, 24–31.
   PubMedGoogle Scholar
• Wahl, M. C., & Sundaralingam, M. (1997). C–H···O hydrogen bonding in biology. Trends in Biochemical Sciences, 22, 97–102.
   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 of the United States of America, 124, 17644–17648.
   Web of Science ®Google Scholar
• Warshel, A., Papazyan, A., & Kollman, P. A. (1995). On low-barrier hydrogen bonds and enzyme catalysis. Science, 269, 102–106.
   PubMed Web of Science ®Google Scholar
• Watson, J. D., & Crick, F. H. C. (1953a). Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature, 171, 737–738.
   PubMed Web of Science ®Google Scholar
• Watson, J. D., & Crick, F. H. C. (1953b). Genetical implications of the structure of deoxyribonucleic acid. Nature, 171, 964–967.
   PubMed Web of Science ®Google Scholar
• Weinhold, F., & Klein, R. A. (2012). What is a hydrogen bond? Mutually consistent theoretical and experimental criteria for characterizing H-bonding interactions. Molecular Physics, 110, 565–579.
   Web of Science ®Google Scholar
• Weinhold, F., & Landis, C. (2005). Valency and bonding. A natural bond orbital donor-acceptor perspective. Cambridge: Cambridge University Press.
   Google Scholar
• Wöhnert, J., Dingley, A. J., Stoldt, M., Görlach, M., Grzesiek, S., & Brown, L. R. (1999). Direct identification of NH···N hydrogen bonds in non-canonical base pairs of RNA by NMR spectroscopy. Nucleic Acid Research, 27, 3104–3110.
   PubMed Web of Science ®Google Scholar
• Xin, Y., & Olson, W. K. (2009). BPS: A database of RNA base-pair structures. Nucleic Acids Research, 37, D83–D88.
   PubMed Web of Science ®Google Scholar
• Yurenko, Y. P., Zhurakivsky, R. O., Ghomi, M., Samijlenko, S. P., & Hovorun, D. M. (2007a). Comprehensive conformational analysis of the nucleoside analogue 2′-β-deoxy-6-azacytidine by DFT and MP2 calculations. Journal of Physical Chemistry B, 111, 6263–6271.
   PubMed Web of Science ®Google Scholar
• Yurenko, Y. P., Zhurakivsky, R. O., Ghomi, M., Samijlenko, S. P., & Hovorun, D. M. (2007b). How many conformers determine the thymidine low-temperature matrix infrared spectrum? DFT and MP2 quantum chemical study. Journal of Physical Chemistry B, 111, 9655–9663.
   PubMed Web of Science ®Google Scholar
• Yurenko, Y. P., Zhurakivsky, R. O., Ghomi, M., Samijlenko, S. P., & Hovorun, D. M. (2007c). The whole of intramolecular H-bonding in the isolated DNA nucleoside thymidine: AIM electron density topological study. Chemical Physics Letters, 447, 140–146.
   Web of Science ®Google Scholar
• Yurenko, Y. P., Zhurakivsky, R. O., Ghomi, M., Samijlenko, S. P., & Hovorun, D. M. (2008). Ab initio comprehensive conformational analysis of 2′-deoxyuridine, the biologically significant DNA minor nucleoside, and reconstruction of its low-temperature matrix infrared spectrum. Journal of Physical Chemistry B, 112, 1240–1250.
   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 and Dynamics, 29, 51–65.
   PubMed Web of Science ®Google Scholar
• Zagryadskaya, E. I., Doyon, F. R., & Steinberg, S. V. (2003). Importance of the reverse Hoogsteen base pair 54–58 for tRNA function. Nucleic Acids Research, 31, 3946–3953.
   PubMed Web of Science ®Google Scholar
• Zhou, P.-P., & Qiu, W.-Y. (2009). Red-shifted hydrogen bonds and blue-shifted van der Waals contact in the standard Watson–Crick adenine–thymine base pair. Journal of Physical Chemistry A, 113, 10306–10320.
   PubMed Web of Science ®Google Scholar
• Zundel, G. (2000). Hydrogen bonds with large proton polarizability and proton transfer processes in electrochemistry and biology. In I. Prigogine, & S. A. Rice (Eds.), Advances in chemical physics (pp. 1–217). New York, NY: Wiley.
   Google Scholar