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Handbook of Computational Chemistry pp 1257–1275Cite as

Computational Modeling of DNA and RNA Fragments

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Abstract

A comprehensive analysis of the benefits and pitfalls of quantum chemical methods used to determine the structures, properties, and functions of DNA and RNA fragments is presented. Main emphasis is given to the application of different ab initio quantum chemical methods. An overview of computations reveals that quantum chemical methods provide an important means to investigate structures and interactions in nucleic acids. However, judicious selection of computational approach is necessary, depending upon the nature of the problem under investigation.

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References

  • Ban, N., Nissen, P., Hansen, J., Moore, P. B., & Steitz, T. A. (2000). The complete atomic structure of the large ribosomal subunit at 2.4 Angstrom resolution. Science, 289, 905.

    Article  CAS  Google Scholar 

  • Banáš, P., Jurecka, P., Walter, N. G., Šponer, J., & Otyepka, M. (2009). Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM. Methods, 49, 202.

    Article  Google Scholar 

  • Barbatti, M., Aquino, A. J. A., Szymczak, J. J., Nachtigallova, D., Hobza, P., & Lischka, H. (2010). Relaxation mechanisms of UV-photoexcited DNA and RNA nucleobases. Proceedings of the National Academy of Sciences of the United States of America, 107, 21453.

    Article  CAS  Google Scholar 

  • Bisgaard, C. Z., Satzger, H., Ullrich, S., & Stolow, A. (2009). Excited-state dynamics of isolated DNA bases: A case study of adenine. ChemPhysChem, 10, 101.

    Article  CAS  Google Scholar 

  • Boudaffa, B., Cloutier, P., Haunting, D., Huels, M. A., & Sanche, L. (2000). Resonant formation of DNA strand breaks by low-energy (3 to 20 eV) electrons. Science, 287, 1658.

    Article  Google Scholar 

  • Calladine, C. R. (1982). Mechanics of sequence-dependent stacking of bases in B-DNA. Journal of Molecular Biology, 25, 343.

    Article  Google Scholar 

  • Chen, H., & Li, S. (2006). Theoretical study on the excitation energies of six tautomers of guanine: Evidence for the assignment of the rare tautomers. The Journal of Physical Chemistry A, 110, 12360.

    Article  CAS  Google Scholar 

  • Chen, G., & Turner, D. H. (2006). Consecutive GA pairs stabilize medium-size RNA internal loops. Biochemistry, 45, 4025.

    Article  CAS  Google Scholar 

  • Chen, L., Cai, L., Zhang, X., & Rich, A. (1994). Crystal structure of a four-stranded intercalated DNA: d(C4). Biochemistry, 33, 13540.

    Article  CAS  Google Scholar 

  • Choi, M. Y., & Miller, R. E. (2006). Four tautomers of isolated guanine from infrared laser spectroscopy in helium nanodroplets. Journal of the American Chemical Society, 128, 7320.

    Article  CAS  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.

    Article  CAS  Google Scholar 

  • Crespo-Hernandez, C. E., Arce, R., Ishikawa, Y., Gorb, L., Leszczynski, J., & Close, D. M. (2004). Ab initio ionization energy thresholds of DNA and RNA bases in gas phase and in aqueous solution. The Journal of Physical Chemistry A, 108, 6373.

    Article  CAS  Google Scholar 

  • de Vries, M. S., & Hobza, P. (2007). Gas-phase spectroscopy of molecular building blocks. Annual Review of Physical Chemistry, 58, 585.

    Article  Google Scholar 

  • Dickerson, R. E., & Drew, H. R. (1981). Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. Journal of Molecular Biology, 15, 761.

    Article  Google Scholar 

  • Dong, F., & Miller, R. E. (2002). Vibrational transition moment angles in isolated biomolecules: A structural tool. Science, 298, 1227.

    Article  CAS  Google Scholar 

  • Elstner, M., Hobza, P., Frauenheim, T., Suhai, S., & Efthimios, K. (2001). Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment. Journal of Chemical Physics, 114, 5149.

    Article  CAS  Google Scholar 

  • Fire, A., Xu, S. Q., Montgomery, M. K., Kostas, S. A., Driver, S. E., & Mello, C. C. (1998). Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 391, 806.

    Article  CAS  Google Scholar 

  • Gehring, K., Leroy, J.-L., & Gueron, M. (1993). A tetrameric DNA structure with protonated cytosine-cytosine base pairs. Nature, 363, 561.

    Article  CAS  Google Scholar 

  • Glaser, R., Hodgen, B., Farrelly, D., & Mckee, E. (2007). Adenine synthesis in interstellar space: Mechanisms of prebiotic pyrimidine-ring formation of monocyclic HCN-pentamers. Astrobiology, 7, 455.

    Article  CAS  Google Scholar 

  • Gorb, L., Kaczmarek, A., Gorb, A., Sadlej, A. J., & Leszczynski, J. (2005). Thermodynamics and kinetics of intramolecular proton transfer in guanine. Post Hartree-Fock study. Journal of Physical Chemistry B, 109, 13770.

    Article  CAS  Google Scholar 

  • Grimme, S. (2004). Accurate description of van der Waals complexes by density functional theory including empirical corrections. Journal of Computational Chemistry, 25, 1463.

    Article  CAS  Google Scholar 

  • Gu, J., Wang, J., Rak, J., & Leszczynski, J. (2007). Findings on the electron-attachment-induced abasic site in a DNA double helix. Angewandte Chemie, 119, 3549.

    Article  Google Scholar 

  • Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N., & Altman, S. (1983). The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell, 35, 849.

    Article  CAS  Google Scholar 

  • Halkier, A., Helgaker, T., Jorgensen, P., Klopper, W., & Olsen, J. (1999). Basis-set convergence of the energy in molecular Hartree-Fock calculations. Chemical Physics Letters, 302, 437.

    Article  CAS  Google Scholar 

  • Harpe, K. de La & Kohler, B. (2011). Observation of long-lived excited states in DNA oligonucleotides with significant base sequence disorder. The Journal of Physical Chemistry Letters, 2, 133.

    Article  Google Scholar 

  • Heßelmann, A., Jansen, G., & Schütz, M. (2005). Density-functional theory-symmetry-adapted intermolecular perturbation theory with density fitting: A new efficient method to study intermolecular interaction energies. Journal of Chemical Physics, 122, 014103.

    Article  Google Scholar 

  • Hobza, P., & Sponer, J. (1998). Significant structural deformation of nucleic acid bases in stacked base pairs: An ab initio study beyond Hartree-Fock. Chemical Physics Letters, 288, 7.

    Article  CAS  Google Scholar 

  • Hobza, P., & Sponer, J. (1999). Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations. Chemical Review, 99, 3247.

    Article  CAS  Google Scholar 

  • Hobza, P., Sponer, J., & Reschel, T. (1995). Density-functional theory and molecular clusters. Journal of Computational Chemistry, 16, 1315.

    Article  CAS  Google Scholar 

  • Ishii, K., Tajima, A., Taketsugu, T., & Yamashita, K. (2006). Theoretical elucidation of the unusually high [HNC]/[HCN] abundance ratio in interstellar space: Two-dimensional and two-state quantum wave packet dynamics study on the branching ratio of the dissociative recombination reaction HCNH+ + e − → HNC/HCN + H. The Astrophysical Journal, 636, 927.

    Article  CAS  Google Scholar 

  • Jeziorski, B., Moszynski, R., & Szalewicz, K. (1994). Perturbation theory approach to intermolecular potential energy surfaces of van der Waals complexes. Chemical Review, 94, 1887.

    Article  CAS  Google Scholar 

  • Jurecka, P., Cerny, J., Hobza, P., & Salahub, D. R. (2007). Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations. Journal of Computational Chemistry, 28, 555.

    Article  CAS  Google Scholar 

  • Kabelác, M., & Hobza, P. (2001). At nonzero temperatures, stacked structures of methylated nucleic acid base pairs and microhydrated nonmethylated nucleic acid base pairs are favored over planar hydrogen-bonded structures: A molecular dynamics simulations study. Chemistry – A European Journal, 7, 2067.

    Article  Google Scholar 

  • Kohler, B. (2010). Nonradiative decay mechanisms in DNA model systems. The Journal of Physical Chemistry Letters, 1, 2047.

    Article  CAS  Google Scholar 

  • Kopitz, H., Zivkovic, A., Engels, J. W., & Gohlke, H. (2008). Determinants of the unexpected stability of RNA fluorobenzene self pairs. ChemBioChem, 9, 2619.

    Article  CAS  Google Scholar 

  • Kristyán, S., & Pulay, P. (1994). Can (semi)local density functional theory account for the London dispersion forces? Chemical Physics Letters, 229, 175.

    Article  Google Scholar 

  • Kruger, K., Grabowski, P. J., Zaug, A. J., Sands, J., Gottschling, D. E., & Cech, T. R. (1982). Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell, 31, 147.

    Article  CAS  Google Scholar 

  • Kumar, A., & Sevilla, M. D. (2007). Low-energy electron attachment to 5′-thymidine monophosphate: Modeling single strand breaks through dissociative electron attachment. Journal of Physical Chemistry B, 111, 5464.

    Article  CAS  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.

    Article  CAS  Google Scholar 

  • Leszczynski, J. (1992). Are the amino groups in the nucleic acid bases coplanar with the molecular rings? Ab Initio HF/631G∗ and MP2/631G∗ Studies. International Journal of Quantum Chemistry: Quantum Biology Symposium, 19, 43.

    Article  CAS  Google Scholar 

  • Leszczynski, J. (2000). Isolated, solvated, and complexed nucleic acid bases: Structures and properties. In M. Hargittai & I. Hargittai (Eds.), Advances in molecular structure research (Vol. 6, p. 209). Stamford, CT: JAI Press.

    Google Scholar 

  • Lin, J., Yu, C., Peng, S., Akiyama, I., Li, K., Lee, L. K., & LeBreton, P. R. (1980). Ultraviolet photoelectron studies of the ground-state electronic structure and gas-phase tautomerism of purine and adenine. Journal of the American Chemical Society, 102, 4627.

    Article  CAS  Google Scholar 

  • Marian, C. M. (2007). The guanine tautomer puzzle: Quantum chemical investigation of ground and excited states. The Journal of Physical Chemistry A, 111, 1545.

    Article  CAS  Google Scholar 

  • Matthews, C. N. (1997). Hydrogen cyanide polymers from the impact of Comet P/Shoemaker/Levy 9 on Jupiter. Advance in Space Research, 19, 1087.

    Article  CAS  Google Scholar 

  • McMullan, R. K., Benci, P., & Craven, B. M. (1980). The neutron crystal structure of 9-methyladenine at 126 K. Acta Crystallographica Section B, 36, 1424.

    Article  Google Scholar 

  • Middleton, C. T., de La Harpe, K., Su, C., Law, Y. K., Crespo-Hernandez, C. E., & Kohler. B. (2009). DNA excited-state dynamics: From single bases to the double helix. Annual Review of Physical Chemistry, 60, 217.

    Article  CAS  Google Scholar 

  • Miller, S. L., & Urey, H. C. (1959). Organic compound synthesis on the primitive earth. Science, 130, 245.

    Article  CAS  Google Scholar 

  • Mix, L. J. (2006). The astrobiology primer: An outline of general knowledge - version 1, 2006. Astrobiology, 6, 735.

    Article  Google Scholar 

  • Mons, M., Dimicoli, I., Piuzzi, F., Tardivel, B., & Elhanine, M. (2002). Tautomerism of the DNA base guanine and its methylated derivatives as studied by gas-phase infrared and ultraviolet spectroscopy. The Journal of Physical Chemistry A, 106, 5088.

    Article  CAS  Google Scholar 

  • Mons, M., Piuzzi, F., Dimicoli, I., Gorb, L., & Leszczynki, J. (2006). Near-UV resonant two-photon ionization spectroscopy of gas phase guanine: Evidence for the observation of three rare tautomers. The Journal of Physical Chemistry A, 110, 10921.

    Article  CAS  Google Scholar 

  • Morgado, C. A., Jurecka, P., Svozil, D., Hobza, P., & Šponer, J. (2009). Balance of attraction and repulsion in nucleic-acid base stacking: CCSD(T)/complete-basis-set-limit calculations on uracil dimer and a comparison with the force-field description. Journal of Chemical Theory and Computation, 5, 1524.

    Article  CAS  Google Scholar 

  • Nir, E., Janzen, Ch., Imhof, P., Kleinermanns, K., & de Vries, M. S. (2001). Guanine tautomerism revealed by UV–UV and IR–UV hole burning spectroscopy. Journal of Chemical Physics, 115, 4604.

    Article  CAS  Google Scholar 

  • Ponnamperuma, C., Lemmon, R. M., Mariner, R., & Calvin, M. (1963). Formation of adenine by electron irradiation of methane, ammonia, and water. Proceedings of the National Academy of Sciences of the United States of America, 49, 7p. 37.

    Google Scholar 

  • Réblová, K., Spackova, N., Štefl, R., Csaszar, K., Koa, J., Leontis, N. B., & Šponer, J. (2003). Non-Watson-Crick base pairing and hydration in RNA motifs: Molecular dynamics of 5S rRNA Loop E. Biophysical Journal, 84, 3564.

    Article  Google Scholar 

  • Serrano-Andres, L., & Merchan, M. (2009). Are the five natural DNA/RNA base monomers a good choice from natural selection? Journal of Photochemistry and Photobiology C: Photochemistry Reviews, 10, 21.

    Article  CAS  Google Scholar 

  • Sheina, G. G., Stepanian, S. G., Radchenko, E. D., & Blagoi, Yu. P. (1987). IR spectra of guanine and hypoxanthine isolated molecules. Journal of Molecular Structure, 158, 275.

    Article  CAS  Google Scholar 

  • Shukla, M. K., & Leszczynski, J. (2007). Electronic spectra, excited state structures and interactions of nucleic acid bases and base assemblies. Journal of Biomolecular Structure & Dynamics, 25, 93.

    Article  CAS  Google Scholar 

  • Shukla, M. K., & Leszczynski, J. (Eds.). (2008). In J. Leszczynski (Ed.), Computational study of UV-induced excitations of DNA fragments. Radiation induced molecular phenomena in nucleic acids, Challenges and advances in computational chemistry and physics (Vol. 5). Dordrecht: Springer Science+Business Media B.V.

    Google Scholar 

  • Siegfried, N. A., Metzger, S. L., & Bevilacqua, P. C. (2007). Folding cooperativity in RNA and DNA is dependent on position in the helix. Biochemistry, 46, 172.

    Article  CAS  Google Scholar 

  • Smith, I. W. M., Talbi, D., & Herbst, E. (2001). The production of HCN dimer and more complex oligomers in dense interstellar clouds. Astronomy & Astrophysics, 369, 611.

    Article  CAS  Google Scholar 

  • Soliva, R., Laughton, C. A., Luque, F. J., & Orozco, M. (1998). Molecular dynamics simulations in aqueous solution of triple helices containing d(G.C.C) trios. Journal of the American Chemical Society, 120, 11226.

    Article  CAS  Google Scholar 

  • Solomun, T., Seitz, H., & Sturm, H. (2009). DNA damage by low-energy electron impact: Dependence on guanine content. Journal of Physical Chemistry B, 113, 11557.

    Article  CAS  Google Scholar 

  • Spackova, N., Berger, I., Egli, M., & Sponer, J. (1998). Molecular dynamics of hemiprotonated intercalated four-stranded i-DNA: Stable trajectories on a nanosecond scale. Journal of the American Chemical Society, 120, 6147.

    Article  CAS  Google Scholar 

  • Sponer, J., & Hobza, P. (1994). Bifurcated hydrogen bonds in DNA crystal structures. An ab initio quantum chemical study. Journal of the American Chemical Society, 116, 709.

    Article  CAS  Google Scholar 

  • Sponer, J., & Kypr, J. (1991). Different intrastrand and interstrand contributions to stacking account for roll variations at the alternating purine-pyrimidine sequences in A-DNA and A-RNA. Journal of Molecular Biology, 221, 761.

    Article  CAS  Google Scholar 

  • Sponer, J., & Kypr, J. (1993). Theoretical analysis of the base stacking in DNA: choice of the force field and a comparison with the oligonucleotide crystal structures. Journal of Biomolecular Structure & Dynamics, 11, 277.

    Article  CAS  Google Scholar 

  • Sponer, J., Leszczynski, J., & Hobza, P. (1996a). Structures and energies of hydrogen-bonded DNA base pairs. A nonempirical study with inclusion of electron correlation. The Journal of Physical Chemistry, 100, 1965.

    Article  CAS  Google Scholar 

  • Sponer, J., Leszczynski, J., & Hobza, P. (1996b). On the nature of nucleic acid base stacking. Nonempirical ab initio and empirical potential characterization of 10 stacked base pairs. Comparison of stacked and H-bonded base pairs. The Journal of Physical Chemistry, 100, 5590.

    Article  CAS  Google Scholar 

  • Sponer, J., Leszczynski, J., Vetterl, V., & Hobza, P. (1996c). Base stacking and hydrogen bonding in protonated cytosine dimer: The role of molecular ion-dipole and induction interactions. Journal of Biomolecular Structure & Dynamics, 13, 695.

    Article  CAS  Google Scholar 

  • Sponer, J., Gabb, H. A., Leszczynski, J., & Hobza, P. (1997). Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA. A quantum-chemical study. Biophysical Journal, 73, 76.

    Article  CAS  Google Scholar 

  • Sponer, J., Mokdad, A., Sponer, J. E., Spackova, N., Leszczynski, J., & Leontis, N. B. (2003). Unique tertiary and neighbor interactions determine conservation patterns of Cis Watson-Crick A/G base-pairs. Journal of Molecular Biology, 330, 967.

    Article  CAS  Google Scholar 

  • Sponer, J., Jurecka, P., & Hobza, P. (2004). Accurate interaction energies of hydrogen-bonded nucleic acid base pairs. Journal of the American Chemical Society, 126, 10142.

    Article  CAS  Google Scholar 

  • Sponer, J. E., Leszczynski, J., Sychrovský, V., & Šponer, J. (2005a). The sugar edge/sugar edge base pairs in RNA. Stabilities and structures from quantum chemical calculations. Journal of Physical Chemistry B, 109, 18680.

    Article  CAS  Google Scholar 

  • Sponer, J. E., Spackova, N., Leszczynski, J., & Šponer, J. (2005b). Principles of RNA base pairing: Structures and energies of the trans Watson-Crick/sugar edge base pairs. Journal of Physical Chemistry B, 109, 11399.

    Article  CAS  Google Scholar 

  • Sponer, J., Jurecka, P., Marchan, I., Luque, F. J., Orozco, M., & Hobza, P. (2006). Nature of base stacking. Reference quantum chemical stacking energies in ten unique B-DNA base pair steps. Chemistry – A European Journal, 12, 2854.

    Google Scholar 

  • Sponer, J. E., Réblová, K., Mokdad, A., Sychrovský, V., Leszczynski, J., & Šponer, J. (2007). Leading RNA tertiary interactions: Structures, energies, and water insertion of A-minor and P-interactions. A quantum chemical view. Journal of Physical Chemistry B, 111, 9153 and references cited therein.

    Google Scholar 

  • Sponer, J., Riley, K. E., & Hobza, P. (2008). Nature and magnitude of aromatic stacking of nucleic acid bases. Physical Chemistry Chemical Physics, 10, 2595.

    Article  CAS  Google Scholar 

  • Sponer, J., Zgarbova, M., Jurecka, P., Riley, K. E., Sponer, J. E., & Hobza, P. (2009). Reference quantum chemical calculations on RNA base pairs directly involving the 2′-OH group of ribose. Journal of Chemical Theory and Computation, 5, 1166.

    Article  CAS  Google Scholar 

  • Sponer, J., Sponer, J. E., Petrov, A. I., & Leontis, N. B. (2010). Quantum chemical studies of nucleic acids can we construct a bridge to the RNA structural biology and bioinformatics communities? Journal of Physical Chemistry B, 114, 15723.

    Article  CAS  Google Scholar 

  • Stombaugh, J., Zirbel, C. L., Westhof, E., & Leontis, N. B. (2009). Frequency and isostericity of RNA base pairs. Nucleic Acid Research, 37, 2294.

    Article  CAS  Google Scholar 

  • Suzuki, M., Amano, N., Kakinuma, J., & Tateno, M. (1997). Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA. Journal of Molecular Biology, 274, 421.

    Article  CAS  Google Scholar 

  • Svozil, D., Hobza, P., & Sponer, J. (2010). Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations? The Journal of Physical Chemistry B, 114, 1191.

    Google Scholar 

  • Szalewicz, K., & Jeziorski, B. (1998). Comment on “On the importance of the fragment relaxation energy terms in the estimation of the basis set superposition error correction to the intermolecular interaction energy” [Journal of Chemical Physics, 104, 8821 (1996)]. Journal of Chemical Physics, 109, 1198.

    Article  CAS  Google Scholar 

  • Tennekes, P. P., Harju, J., Juvela, M., & Toth, L. V. (2006). HCN and HNC mapping of the protostellar core Chamaeleon-MMS1. Astronomy & Astrophysics, 456, 1037.

    Article  CAS  Google Scholar 

  • Vlieghe, D., Sponer, J., & Van Meervelt, L. (1999). Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode. Biochemistry, 38, 16443.

    Article  CAS  Google Scholar 

  • Wimberly, B. T., Brodersen, D. E., Clemons, W. M., Jr., Morgan-Warren, R. J., Carter, A. P., Vonrhein, C., Hartsch, T., & Ramakrishnan, V. (2000). Structure of the 30S ribosomal subunit. Nature, 407, 327.

    Article  CAS  Google Scholar 

  • Wing, R., Drew, H., Takano, T., Broka, C., Tanaka, S., Itakura, K., & Dickerson, R. E. (1980). Crystal structure analysis of a complete turn of B-DNA. Nature, 287, 755.

    Article  CAS  Google Scholar 

  • Yamazaki, S., Domcke, W., & Sobolewski, A. (2008). Nonradiative decay mechanisms of the biologically relevant tautomer of guanine. The Journal of Physical Chemistry A, 112, 11965.

    Article  CAS  Google Scholar 

  • Yanagi, K., Prive, G. G., & Dickerson, R. E. (1991). Analysis of local helix geometry in three B-DNA decamers and eight dodecamers. Journal of Molecular Biology, 217, 201.

    Article  CAS  Google Scholar 

  • Yildirim, I., & Turner, D. H. (2005). RNA challenges for computational chemists. Biochemistry, 44, 13225.

    Article  CAS  Google Scholar 

  • Yildirim, I., Stern, H. A., Sponer, J., Spackova, N., & Turner, D. H. (2009). Effects of restrained sampling space and nonplanar amino groups on free-energy predictions for RNA with imino and sheared tandem GA base Pairs. Flanked by GC, CG, iGiC or iCIG base pairs. Journal of Chemical Theory and Computation, 5, 2088.

    Google Scholar 

  • Zhao, Y., & Truhlar, D. G. (2008). Density functionals with broad applicability in chemistry. Accounts of Chemical Research, 41, 157.

    Article  CAS  Google Scholar 

  • Zhou, J., Kostko, O., Nicolas, C., Tang, X., Belau, L., de Vries, M. S., & Ahmed, M. (2009). Experimental observation of guanine tautomers with VUV photoionization. The Journal of Physical Chemistry A, 113, 4829.

    Article  CAS  Google Scholar 

  • Zirbel, C. L., Sponer, J. E., Sponer, J., Stombaugh, J., & Leontis, N. B. (2009). Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acid Research, 37, 4898.

    Article  CAS  Google Scholar 

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Acknowledgments

JS acknowledges the support from the Grant Agency of the Academy of Sciences of the Czech Republic grant IAA400040802, Grant Agency of the Czech Republic grant 203/09/1476, Ministry of Education of the Czech Republic LC06030 and Academy of Sciences of the Czech Republic, grants no. AV0Z50040507 and AV0Z50040702. MKS and JL are thankful for supports from NSF-CREST Grant No. HRD-0833178 and NSF EPSCoR Grant No. 362492-190200-01\(\setminus \)NSFEPS-0903787 and computational support from Mississippi Center for Supercomputing Research (MCSR).

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Authors and Affiliations

  1. Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic

    Jiřı́ Šponer

  2. Department of Chemistry and Biochemistry, Interdisciplinary Center for Nanotoxicity, Jackson State University, 39217, Jackson, Mississippi, USA

    Manoj K. Shukla

  3. Environmental Laboratory, US Army Engineer Research and Development Center, 39180, Vicksburg, Mississippi, USA

    Jerzy Leszczynski

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  1. Jiřı́ Šponer
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  2. Manoj K. Shukla
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  1. Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, 39217, USA

    Jerzy Leszczynski

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Šponer, J., Shukla, M.K., Leszczynski, J. (2012). Computational Modeling of DNA and RNA Fragments. In: Leszczynski, J. (eds) Handbook of Computational Chemistry. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-0711-5_35

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