Quantum Chemical Studies of Recurrent Interactions in RNA 3D Motifs

  • Jiří Šponer
  • Judit E. Šponer
  • Neocles B. Leontis
Part of the Nucleic Acids and Molecular Biology book series (NUCLEIC, volume 27)


High-quality quantum mechanical (QM) calculations provide physically based descriptions of molecular systems that are free of empirical parameters. This contrasts with force-field computations based on simple and entirely nonphysical, analytical functions that must be completely parametrized for a given purpose. The costs of high-quality QM computations, however, can be enormous, limiting them to small model systems with ~50+ atoms. Thus, a major challenge of the QM approach is how to extrapolate data computed on model systems to intact biomolecules of biological interest. QM calculations have been used to study the basic molecular forces in nucleic acids. A notable accomplishment of these studies has been to clarify the nature of aromatic base stacking. Another important application of modern QM computations is to furnish reference data for parametrizing molecular modeling force fields. In this chapter, we provide a summary of the nature of QM calculations, their strengths, limitations, and relation to other methods. Then, we review the use of high-level ab initio (first principles) QM methods to calculate geometries and energies of fundamental nucleotide interactions in RNA 3D structures.


  1. Abu Almakarem AS, Petrov AI, Stombaugh J, Zirbel CL, Leontis NB (2011) Comprehensive survey and geometric classification of base triples in RNA structures. Nucleic Acids Res. doi:10.1093/nar/gkr810
  2. Banas P, Jurecka P, Walter NG, Sponer J, Otyepka M (2009) Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. Methods 49:202–216. doi:10.1016/j.ymeth.2009.04.007 PubMedCrossRefGoogle Scholar
  3. Banas P, Hollas D, Zgarbova M, Jurecka P, Orozco M, Cheatham TE, Sponer J, Otyepka M (2010) Performance of molecular mechanics force fields for RNA simulations: stability of UUCG and GNRA hairpins. J Chem Theory Comput 6:3836–3849. doi:10.1021/ct100481h CrossRefGoogle Scholar
  4. Blas JR, Luque FJ, Orozco M (2004) Unique tautomeric properties of isoguanine. J Am Chem Soc 126:154–164PubMedCrossRefGoogle Scholar
  5. Brandl M, Meyer M, Suhnel J (2000) Water-mediated base pairs in RNA: a quantum-chemical study. J Phys Chem A 104:11177–11187. doi:10.1021/jp002022d CrossRefGoogle Scholar
  6. Brandl M, Meyer M, Suhnel J (2001) Quantum-chemical analysis of C-H center dot center dot center dot O and C-H center dot center dot center dot N interactions in RNA base pairs – H-bond versus anti-H-bond pattern. J Biomol Struct Dyn 18:545–555PubMedCrossRefGoogle Scholar
  7. Bugg CE, Thomas JM, Rao ST, Sundaral M (1971) Stereochemistry of nucleic acids and their constituents. 10. Solid-state base-stacking patterns in nucleic acid constituents and polynucleotides. Biopolymers 10:175–219PubMedCrossRefGoogle Scholar
  8. Cieplak P, Cornell WD, Bayly C, Kollman PA (1995) Application of the multimolecule and multiconformational RESP methodology to biopolymers – charge derivation for DNA, RNA, AND proteins. J Comput Chem 16:1357–1377CrossRefGoogle Scholar
  9. Cieplak P, Dupradeau FY, Duan Y, Wang JM (2009) Polarization effects in molecular mechanical force fields. J Phys Condens Matter 21:333102. doi:33310210.1088/0953-8984/21/33/333102 PubMedCrossRefGoogle Scholar
  10. Colominas C, Luque FJ, Orozco M (1996) Tautomerism and protonation of guanine and cytosine. Implications in the formation of hydrogen-bonded complexes. J Am Chem Soc 118:6811–6821CrossRefGoogle Scholar
  11. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules. J Am Chem Soc 117:5179–5197CrossRefGoogle Scholar
  12. Dey M, Moritz F, Grotemeyer J, Schag EW (1994) Base-pair formation of free nucleobases and mononucleosides in the gas-phase. J Am Chem Soc 116:9211–9215CrossRefGoogle Scholar
  13. Ditzler MA, Otyepka M, Sponer J, Walter NG (2010) Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in. Acc Chem Res 43:40–47. doi:10.1021/ar900093g PubMedCrossRefGoogle Scholar
  14. Dong F, Miller RE (2002) Vibrational transition moment angles in isolated biomolecules: a structural tool. Science 298:1227–1230PubMedCrossRefGoogle Scholar
  15. Dudev T, Lim C (2003) Principles governing Mg, Ca, and Zn binding and selectivity in proteins. Chem Rev 103:773–787. doi:10.1021/cr020467n PubMedCrossRefGoogle Scholar
  16. Dudev T, Lim C (2008) Metal binding affinity and selectivity in metalloproteins: insights from computational studies. Annu Rev Biophys 37:97–116. doi:10.1146/annurev.biophys.37.032807.125811 PubMedCrossRefGoogle Scholar
  17. Egli M, Gessner RV (1995) Stereoelectronic effects Of deoxyribose O4′ on DNA conformation. Proc Natl Acad Sci USA 92:180–184PubMedCrossRefGoogle Scholar
  18. Ennifar E, Yusupov M, Walter P, Marquet R, Ehresmann B, Ehresmann C, Dumas P (1999) The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges. Structure 7:1439–1449CrossRefGoogle Scholar
  19. Feyereisen MW, Feller D, Dixon DA (1996) Hydrogen bond energy of the water dimer. J Phys Chem 100:2993–2997CrossRefGoogle Scholar
  20. Florian J, Sponer J, Warshel A (1999) Thermodynamic parameters for stacking and hydrogen bonding of nucleic acid bases in aqueous solution: ab initio/Langevin dipoles study. J Phys Chem B 103:884–892CrossRefGoogle Scholar
  21. Grimme S (2011) Density functional theory with London dispersion corrections. Wiley Interdiscip Rev Comput Mol Sci 1:211–228. doi:10.1002/wcms.30 CrossRefGoogle Scholar
  22. Hammond NB, Tolbert BS, Kierzek R, Turner DH, Kennedy SD (2010) RNA internal loops with tandem AG pairs: the structure of the 5′G(UG)U/3′U(GA)G loop can be dramatically different from others, including 5′A(AG)U/3′U(GA)A. Biochemistry 49:5817–5827. doi:10.1021/bi100332r PubMedCrossRefGoogle Scholar
  23. Hanus M, Ryjacek F, Kabelac M, Kubar T, Bogdan TV, Trygubenko SA, Hobza P (2003) Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution. Guanine: surprising stabilization of rare tautomers in aqueous solution. J Am Chem Soc 125:7678–7688. doi:10.1021/ja034245y PubMedCrossRefGoogle Scholar
  24. Hobza P, Sponer J (1999) Structure, energetics, and dynamics of the nucleic acid base pairs: nonempirical ab initio calculations. Chem Rev 99:3247–3276PubMedCrossRefGoogle Scholar
  25. Hobza P, Sponer J, Polasek M (1995) H-bonded and stacked 2nd-base pairs – cytosine dimer – an ab-initio 2nd-order Moller-Plesset study. J Am Chem Soc 117:792–798CrossRefGoogle Scholar
  26. Hobza P, Selzle HL, Schlag EW (1996) Potential energy surface for the benzene dimer. Results of ab initio CCSD(T) calculations show two nearly isoenergetic structures: T-shaped and parallel-displaced. J Phys Chem 100:18790–18794CrossRefGoogle Scholar
  27. Hobza P, Kabelac M, Sponer J, Mejzlik P, Vondrasek J (1997) Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree-Fock method for interaction of DNA bases: comparison with nonempirical beyond Hartree-Fock results. J Comput Chem 18:1136–1150CrossRefGoogle Scholar
  28. Hunter CA (1993) Sequence-dependent DNA-structure – the role of base stacking interactions. J Mol Biol 230:1025–1054PubMedCrossRefGoogle Scholar
  29. Jurecka P, Sponer J, Hobza P (2004) Potential energy surface of the cytosine dimer: MP2 complete basis set limit interaction energies, CCSD(T) correction term, and comparison with the AMBER force field. J Phys Chem B 108:5466–5471. doi:10.1021/jp049956c CrossRefGoogle Scholar
  30. Jurecka P, Sponer J, Cerny J, Hobza P (2006) Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs. Phys Chem Chem Phys 8:1985–1993. doi:10.1039/b600027d PubMedCrossRefGoogle Scholar
  31. Katz AK, Glusker JP, Beebe SA, Bock CW (1996) Calcium ion coordination: a comparison with that of beryllium, magnesium, and zinc. J Am Chem Soc 118:5752–5763CrossRefGoogle Scholar
  32. Klamt A, Mennucci B, Tomasi J, Barone V, Curutchet C, Orozco M, Luque FJ (2009) On the performance of continuum solvation methods. A comment on “Universal approaches to solvation modeling”. Acc Chem Res 42:489–492. doi:10.1021/ar800187p PubMedCrossRefGoogle Scholar
  33. Koller AN, Bozilovic J, Engels JW, Gohlke H (2010) Aromatic N versus aromatic F: bioisosterism discovered in RNA base pairing interactions leads to a novel class of universal base analogs. Nucleic Acids Res 38:3133–3146PubMedCrossRefGoogle Scholar
  34. Kollman PA, Massova I, Reyes C, Kuhn B, Huo SH, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33:889–897. doi:10.1021/ar000033j PubMedCrossRefGoogle Scholar
  35. Kopitz H, Zivkovic A, Engels JW, Gohlke H (2008) Determinants of the unexpected stability of RNA fluorobenzene self pairs. ChemBioChem 9:2619–2622. doi:10.1002/cbic.200800461 PubMedCrossRefGoogle Scholar
  36. Kratochvil M, Engkvist O, Sponer J, Jungwirth P, Hobza P (1998) Uracil dimer: potential energy and free energy surfaces. Ab initio beyond Hartree-Fock and empirical potential studies. J Phys Chem A 102:6921–6926CrossRefGoogle Scholar
  37. Kratochvil M, Sponer J, Hobza P (2000) Global minimum of the adenine center dot center dot center dot thymine base pair corresponds neither to Watson-Crick nor to Hoogsteen structures. Molecular dynamic/quenching/AMBER and ab initio beyond Hartree-Fock studies. J Am Chem Soc 122:3495–3499CrossRefGoogle Scholar
  38. Leontis NB, Westhof E (2001) Geometric nomenclature and classification of RNA base pairs. RNA 7:499–512PubMedCrossRefGoogle Scholar
  39. Leontis NB, Stombaugh J, Westhof E (2002) The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res 30:3497–3531PubMedCrossRefGoogle Scholar
  40. Luisi B, Orozco M, Sponer J, Luque FJ, Shakked Z (1998) On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules. J Mol Biol 279:1123–1136PubMedCrossRefGoogle Scholar
  41. Mathews DH, Turner DH (2006) Prediction of RNA secondary structure by free energy minimization. Curr Opin Struct Biol 16:270–278. doi:10.1016/j.sbi.2006.05.010 PubMedCrossRefGoogle Scholar
  42. Mathews DH, Sabina J, Zuker M, Turner DH (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288:911–940PubMedCrossRefGoogle Scholar
  43. Miller JL, Kollman PA (1996) Solvation free energies of the nucleic acid bases. J Phys Chem 100:8587–8594CrossRefGoogle Scholar
  44. Mladek A, Sharma P, Mitra A, Bhattacharyya D, Sponer J, Sponer JE (2009) Trans Hoogsteen/sugar edge base pairing in RNA. Structures, energies, and stabilities from quantum chemical calculations. J Phys Chem B 113:1743–1755. doi:10.1021/jp808357m PubMedCrossRefGoogle Scholar
  45. Mladek A, Sponer JE, Jurecka P, Banas P, Otyepka M, Svozil D, Sponer J (2010) Conformational energies of DNA sugar-phosphate backbone: reference QM calculations and a comparison with density functional theory and molecular mechanics. J Chem Theory Comput 6:3817–3835. doi:10.1021/ct1004593 CrossRefGoogle Scholar
  46. Mladek A, Sponer JE, Kulhanek P, Lu XJ, Olson WK, Sponer J (2012) Understanding the sequence preference of recurrent RNA building blocks using quantum chemistry: the intrastrand RNA dinucleotide platform. J Chem Theory Comput 8:335–347. doi:10.1021/ct200712b Google Scholar
  47. Mokdad A, Krasovska MV, Sponer J, Leontis NB (2006) Structural and evolutionary classification of G/U wobble basepairs in the ribosome. Nucleic Acids Res 34:1326–1341. doi:10.1093/nar/gkl025 PubMedCrossRefGoogle Scholar
  48. Morgado CA, Jurecka P, Svozil D, Hobza P, Sponer 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. J Chem Theory Comput 5:1524–1544. doi:10.1021/ct9000125 CrossRefGoogle Scholar
  49. Nir E, Kleinermanns K, de Vries MS (2000) Pairing of isolated nucleic-acid bases in the absence of the DNA backbone. Nature 408:949–951PubMedCrossRefGoogle Scholar
  50. Nissen P, Ippolito JA, Ban N, Moore PB, Steitz TA (2001) RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc Natl Acad Sci USA 98:4899–4903PubMedCrossRefGoogle Scholar
  51. Oliva R, Cavallo L, Tramontano A (2006) Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions. Nucleic Acids Res 34:865–879. doi:10.1093/nar/gkj491 PubMedCrossRefGoogle Scholar
  52. Oliva R, Tramontano A, Cavallo L (2007) Mg2+ binding and archaeosine modification stabilize the G15-C48 Levitt base pair in tRNAs. RNA 13:1427–1436. doi:10.1261/rna.574407 PubMedCrossRefGoogle Scholar
  53. Perez A, Sponer J, Jurecka P, Hobza P, Luque FJ, Orozco M (2005) Are the hydrogen bonds of RNA (A U) stronger than those of DNA (A T)? A quantum mechanics study. Chem Eur J 11:5062–5066. doi:10.1002/chem.200500255 PubMedCrossRefGoogle Scholar
  54. Perez A, Marchan I, Svozil D, Sponer J, Cheatham TE, Laughton CA, Orozco M (2007) Refinenement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys J 92:3817–3829. doi:10.1529/biophysj.106.097782 PubMedCrossRefGoogle Scholar
  55. Petrov AI, Zirbel CL, Leontis NB (2011a) WebFR3D–a server for finding, aligning and analyzing recurrent RNA 3D motifs. Nucleic Acids Res 39:W50–W55. doi:10.1093/nar/gkr249 PubMedCrossRefGoogle Scholar
  56. Petrov AS, Bowman JC, Harvey SC, Williams LD (2011b) Bidentate RNA-magnesium clamps: On the origin of the special role of magnesium in RNA folding. RNA 17:291–297. doi:10.1261/rna.2390311 PubMedCrossRefGoogle Scholar
  57. Prive G, Heinemann U, Chandrasegaran S, Kan L, Kopka M, Dickerson R (1987) Helix geometry, hydration, and G.A mismatch in a B-DNA decamer. Science 238:498–504. doi:10.1126/science.3310237 PubMedCrossRefGoogle Scholar
  58. Rappoport D, Crawford NRM, Furche F, Burke K (2009) Approximate density functionals: Which should I choose? In: Solomon EI, Scott RA, King RB (eds) Computational inorganic and bioinorganic chemistry. Wiley-VCH, New York, pp 159–172Google Scholar
  59. Razga F, Koca J, Sponer J, Leontis NB (2005) Hinge-like motions in RNA kink-turns: the role of the second A-minor motif and nominally unpaired bases. Biophys J 88:3466–3485. doi:10.1529/biophysj.104.054916 PubMedCrossRefGoogle Scholar
  60. Reblova K, Strelcova Z, Kulhanek P, Besscova I, Mathews DH, Van Nostrand K, Yildirim I, Turner DH, Sponer J (2010) An RNA molecular switch: intrinsic flexibility of 23S rRNA helices 40 and 68 5′-UAA/5′-GAN internal loops studied by molecular dynamics methods. J Chem Theory Comput 6:910–929. doi:10.1021/ct900440t CrossRefGoogle Scholar
  61. Reblova K, Sponer JE, Spackova N, Besseova I, Sponer J (2011) A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis. J Phys Chem B 115:13897–13910PubMedCrossRefGoogle Scholar
  62. Roy A, Panigrahi S, Bhattacharyya M, Bhattacharyya D (2008) Structure, stability, and dynamics of canonical and noncanonical base pairs: quantum chemical studies. J Phys Chem B 112:3786–3796. doi:10.1021/jp076921e PubMedCrossRefGoogle Scholar
  63. Shankar N, Kennedy SD, Chen G, Krugh TR, Turner DH (2006) The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50S ribosomal subunits. Biochemistry 45:11776–11789. doi:10.1021/bi0605787 PubMedCrossRefGoogle Scholar
  64. Sharma P, Mitra A, Sharma S, Singh H, Bhattacharyya D (2008) Quantum chemical studies of structures and binding in noncanonical RNA base pairs: the trans Watson-Crick: Watson-Crick family. J Biomol Struct Dyn 25:709–732PubMedCrossRefGoogle Scholar
  65. Sharma P, Sharma S, Chawla M, Mitra A (2009) Modeling the noncovalent interactions at the metabolite binding site in purine riboswitches. J Mol Model 15:633–649. doi:10.1007/s00894-008-0384-y PubMedCrossRefGoogle Scholar
  66. Sharma P, Chawla M, Sharma S, Mitra A (2010a) On the role of Hoogsteen:Hoogsteen interactions in RNA: Ab initio investigations of structures and energies. RNA 16:942–957. doi:papers://8F282AF1-C00B-4965-8450-641CADBEB600/Paper/p1255 PubMedCrossRefGoogle Scholar
  67. Sharma P, Sponer JE, Sponer J, Sharma S, Bhattacharyya D, Mitra A (2010b) On the role of the cis Hoogsteen:sugar-edge family of base pairs in platforms and triplets-quantum chemical insights into RNA structural biology. J Phys Chem B 114:3307–3320. doi:10.1021/jp910226e PubMedCrossRefGoogle Scholar
  68. Siegfried NA, Metzger SL, Bevilacqua PC (2007) Folding cooperativity in RNA and DNA is dependent on position in the helix. Biochemistry 46:172–181. doi:10.1021/bi0613751 PubMedCrossRefGoogle Scholar
  69. Špacková N, Cheatham TE, Ryjácek F, Lankaš F, van Meervelt L, Hobza P, Šponer J (2003) Molecular dynamics simulations and thermodynamics analysis of DNA–drug complexes. Minor groove binding between 4′,6-diamidino-2-phenylindole and DNA duplexes in solution. J Am Chem Soc 125:1759–1769. doi:10.1021/ja025660d PubMedCrossRefGoogle Scholar
  70. Spirko V, Sponer J, Hobza P (1997) Anharmonic and harmonic intermolecular vibrational modes of the DNA base pairs. J Chem Phys 106:1472–1479CrossRefGoogle Scholar
  71. Sponer J, Hobza P (1994a) Bifurcated hydrogen-bonds in DNA crystal-structures – an ab-initio quantum-chemical study. J Am Chem Soc 116:709–714CrossRefGoogle Scholar
  72. Sponer J, Hobza P (1994b) Nonplanar geometries of DNA bases – ab-initio 2nd-order Moller-Plesset study. J Phys Chem 98:3161–3164CrossRefGoogle Scholar
  73. Sponer J, Lankas F (eds) (2006) Computational studies of RNA and DNA. Challenges and advances in computational chemistry and physics. Springer, DordrechtGoogle Scholar
  74. Sponer J, Leszczynski J, Hobza P (1996a) Nature of nucleic acid-base stacking: nonempirical ab initio and empirical potential characterization of 10 stacked base dimers. Comparison of stacked and H-bonded base pairs. J Phys Chem 100:5590–5596CrossRefGoogle Scholar
  75. Sponer J, Leszczynski J, Hobza P (1996b) Structures and energies of hydrogen-bonded DNA base pairs. A nonempirical study with inclusion of electron correlation. J Phys Chem 100:1965–1974CrossRefGoogle Scholar
  76. 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. J Biomol Struct Dyn 13:695–706PubMedCrossRefGoogle Scholar
  77. Sponer J, Gabb HA, Leszczynski J, Hobza P (1997) Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study. Biophys J 73:76–87PubMedCrossRefGoogle Scholar
  78. Sponer J, Sabat M, Gorb L, Leszczynski J, Lippert B, Hobza P (2000) The effect of metal binding to the N7 site of purine nucleotides on their structure, energy, and involvement in base pairing. J Phys Chem B 104:7535–7544. doi:10.1021/jp001711m CrossRefGoogle Scholar
  79. Sponer J, Leszczynski J, Hobza P (2001) Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases. Biopolymers 61:3–31. doi:10.1002/bip.10048 PubMedCrossRefGoogle Scholar
  80. Sponer J, Mokdad A, Sponer JE, Spackova N, Leszczynski J, Leontis NB (2003) Unique tertiary and neighbor interactions determine conservation patterns of cis Watson-Crick A/G base-pairs. J Mol Biol 330:967–978. doi:10.1016/s0022-2836(03)00667-3 PubMedCrossRefGoogle Scholar
  81. Sponer J, Jurecka P, Hobza P (2004) Accurate interaction energies of hydrogen-bonded nucleic acid base pairs. J Am Chem Soc 126:10142–10151. doi:10.1021/ja048436s PubMedCrossRefGoogle Scholar
  82. Sponer JE, Leszczynski J, Sychrovsky V, Sponer J (2005a) Sugar edge/sugar edge base pairs in RNA: stabilities and structures from quantum chemical calculations. J Phys Chem B 109:18680–18689. doi:10.1021/jp053379q PubMedCrossRefGoogle Scholar
  83. Sponer JE, Spackova N, Kulhanek P, Leszczynski J, Sponer J (2005b) Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family. J Phys Chem A 109:2292–2301. doi:10.1021/jp050132k PubMedCrossRefGoogle Scholar
  84. Sponer JE, Spackova N, Leszczynski J, Sponer J (2005c) Principles of RNA base pairing: structures and energies of the trans Watson-Crick/sugar edge base pairs. J Phys Chem B 109:11399–11410. doi:10.1021/jp051126r PubMedCrossRefGoogle Scholar
  85. Sponer J, Jurecka P, Marchan I, Luque FJ, Orozco M, Hobza P (2006) Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps. Chem Eur J 12:2854–2865. doi:10.1002/chem.200501239 PubMedCrossRefGoogle Scholar
  86. Sponer JE, Reblova K, Mokdad A, Sychrovsky V, Leszczynski J, Sponer J (2007) Leading RNA tertiary interactions: structures, energies, and water insertion of a-minor and p-interactions. A quantum chemical view. J Phys Chem B 111:9153–9164. doi:10.1021/jp0704261 PubMedCrossRefGoogle Scholar
  87. Sponer J, Riley KE, Hobza P (2008) Nature and magnitude of aromatic stacking of nucleic acid bases. Phys Chem Chem Phys 10:2595–2610. doi:10.1039/b719370j PubMedCrossRefGoogle Scholar
  88. Sponer J, Zgarbova M, Jurecka P, Riley KE, Sponer JE, Hobza P (2009) Reference quantum chemical calculations on RNA base pairs directly involving the 2′-OH group of ribose. J Chem Theory Comput 5:1166–1179. doi:10.1021/ct800547k CrossRefGoogle Scholar
  89. Sponer J, Sponer JE, Petrov AI, Leontis NB (2010) Quantum chemical studies of nucleic acids can we construct a bridge to the RNA structural biology and bioinformatics communities? J Phys Chem B 114:15723–15741. doi:10.1021/jp104361m PubMedCrossRefGoogle Scholar
  90. Stombaugh J, Zirbel CL, Westhof E, Leontis NB (2009) Frequency and isostericity of RNA base pairs. Nucleic Acids Res 37:2294–2312. doi:10.1093/nar/gkp011 PubMedCrossRefGoogle Scholar
  91. 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? J Phys Chem B 114:1191–1203. doi:10.1021/jp910788e PubMedCrossRefGoogle Scholar
  92. Swart M, Guerra CF, Bickelhaupt FM (2004) Hydrogen bonds of RNA are stronger than those of DNA, but NMR monitors only presence of methyl substituent in uracil/thymine. J Am Chem Soc 126:16718–16719. doi:10.1021/ja045276b PubMedCrossRefGoogle Scholar
  93. Tomasi J, Mennucci B, Cammi R (2005) Quantum mechanical continuum solvation models. Chem Rev 105:2999–3093. doi:10.1021/cr9904009 PubMedCrossRefGoogle Scholar
  94. Vlieghe D, Sponer J, Van Meervelt L (1999) Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode. Biochemistry 38:16443–16451PubMedCrossRefGoogle Scholar
  95. Vokacova Z, Sponer J, Sponer JE, Sychrovsky V (2007) Theoretical study of the scalar coupling constants across the noncovalent contacts in RNA base pairs: the cis- and trans-Watson-Crick/sugar edge base pair family. J Phys Chem B 111:10813–10824. doi:10.1021/jp072822p PubMedCrossRefGoogle Scholar
  96. Yanson IK, Teplitsky AB, Sukhodub LF (1979) Experimental studies of molecular-interactions between nitrogen bases of nucleic-acids. Biopolymers 18:1149–1170PubMedCrossRefGoogle Scholar
  97. Yildirim I, Turner DH (2005) RNA challenges for computational chemists. Biochemistry 44:13225–13234. doi:10.1021/bi051236o PubMedCrossRefGoogle Scholar
  98. Yildirim I, Stern HA, Sponer J, Spackova N, Turner DH (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. J Chem Theory Comput 5:2088–2100. doi:10.1021/ct800540c PubMedCrossRefGoogle Scholar
  99. Zgarbova M, Otyepka M, Sponer J, Hobza P, Jurecka P (2010) Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations. Phys Chem Chem Phys 12:10476–10493PubMedCrossRefGoogle Scholar
  100. Zgarbova M, Jurecka P, Banas P, Otyepka M, Sponer JE, Leontis NB, Zirbel CL, Sponer J (2011a) Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations. J Phys Chem A 115:11277–11292. doi:10.1021/jp204820b Google Scholar
  101. Zgarbová M, Otyepka M, Sponer J, Mládek A, Banáš P, Cheatham TE, Jurečka P (2011b) Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles. J Chem Theory Comput 7:2886–2902PubMedCrossRefGoogle Scholar
  102. Zhao Y, Truhlar DG (2008) Density functionals with broad applicability in chemistry. Acc Chem Res 41:157–167. doi:10.1021/ar700111a PubMedCrossRefGoogle Scholar
  103. Zirbel CL, Sponer JE, Sponer J, Stombaugh J, Leontis NB (2009) Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res 37:4898–4918. doi:10.1093/nar/gkp468 PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Jiří Šponer
    • 1
    • 2
  • Judit E. Šponer
    • 1
    • 2
  • Neocles B. Leontis
    • 3
  1. 1.Institute of Biophysics, Academy of Sciences of the Czech RepublicBrnoCzech Republic
  2. 2.CEITEC – Central European Institute of TechnologyBrnoCzech Republic
  3. 3.Chemistry DepartmentBowling Green State UniversityBowling GreenUSA

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