Abstract
The results of MNDO-PM3 theoretical study of H-bonds liability of watson-crick base pairs are discussed. Some microwave and IR spectral criteria are suggested for identification of hidden polymorphism of DNA base pairing.
Keywords: Hidden polymorphism, inertial defects, nitrous base pairs, normal modes analysis, propeller twisting, quantum-chemical calculations
Full Text
The Full Text of this article is available as a PDF (96.0 KB).
References
- 1.Yakushevich L.V. Nonlinear Physics of DNA. Chichester, New York, Brisbane, Singapure, Toronto: John Wiley & Sons; 1998. [Google Scholar]
- 2.Gaeta G., Reiss C., Peyrard M., Dauxois T. Simple models of nonlinear DNA dynamics. Rev. Nuovo Cimento. 1994;17:1–48. [Google Scholar]
- 3.Yakushevich L.V. Nonlinear dynamics of biopolymers: theoretical models, experimental data. Quart. Rev. Biophys. 1993;26:201–223. doi: 10.1017/s0033583500004078. [DOI] [PubMed] [Google Scholar]
- 4.Saenger W. Principles of Nucleic Acid Structure. Berlin: Springer-Verlag; 1984. [Google Scholar]
- 5.Wilson C.C. An analysis of conformational parameters in nucleic acid fragments. Nucleic Acid Res. 1987;15:8577–8591. doi: 10.1093/nar/15.21.8577. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Wilson C.C., Tollin P. Propeller twisting in single crystals of nucleosides. Nuleosides & Nucleotides. 1987;6:643–653. [Google Scholar]
- 7.Wilson C.C. The effect of exocyclic substituents on base-pair propeller twist. Nuleosides & Nucleotides. 1990;9:479–488. [Google Scholar]
- 8.Wilson C.C. Analysis of conformational parameters in nucleic acid fragments. III. Very short chain oligonucleotides. Nucleic Acid Res. 1988;16:4752–4759. doi: 10.1093/nar/16.11.4751. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Wilson C.C. Analysis of conformational parameters in nucleic acid fragments. II. Co-crystal complexes of nucleic acid bases. Nucleic Acid Res. 1988;16:385–393. doi: 10.1093/nar/16.2.385. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Dickerson R.E. Base sequence and helix structure variation in B and A DNA. J. Mol. Biol. 1983;166:419–441. doi: 10.1016/s0022-2836(83)80093-x. [DOI] [PubMed] [Google Scholar]
- 11.Alexandresen A., Drendel W.B., Sundaralingam M. A highly propeller-twisted adenineadenine base pair in 8-tret-butiladenine. Acta Crystallog. C. 1991;47:1041–1044. doi: 10.1107/s0108270190008824. [DOI] [PubMed] [Google Scholar]
- 12.Jursa J., Kypr J. Geometries and energies of Watson-Crick base pairs in oligonucleotide crystal structures. Gen. Physiol. Biophys. 1993;12:401–409. [PubMed] [Google Scholar]
- 13.Dickerson R.E., et al. Definitions and nomenclature of nucleic acid structure parameters. EMBO Journal. 1989;8:1–4. doi: 10.1002/j.1460-2075.1989.tb03339.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Komarov V.M., Polozov R.V. On the propeller structure of isolated Watson-Crick base pairs. Z. Naturforsch. B. 1990;45c:1080. doi: 10.1515/znc-1990-9-1025. [DOI] [PubMed] [Google Scholar]
- 15.Komarov V.M., Polozov R.V., Konoplev G.G. Non-planar structure of nitrous bases and non-coplanarity of Watson-Crick pairs. J. Theor. Biol. 1992;155:281–294. doi: 10.1016/s0022-5193(05)80600-9. [DOI] [PubMed] [Google Scholar]
- 16.Komarov V.M. Non-coplanar H-binding of the Hugstein base pairs. PCILO conformational evaluations. I. Adenine-adenine and adenine-thymine pairs. Biophysics. 1994;39:863–868. [Google Scholar]
- 17.Komarov V.M., Mevkh N.G. A model of plurality of Watson-Crick base pairing forms. Russian J. Phys. Chem. 1995;69:1281–1283. [Google Scholar]
- 18.Komarov V.M. Quantum-chemical semi-empirical study of polymorphism of Watson-Crick base pairing. Biofizika. 1998;43:967–974. [PubMed] [Google Scholar]
- 19.Dewar M.J.S., Thiel W. Ground states of molecules. 38. The MNDO method. Approximations and parameters. J. Am. Chem. Soc. 1977;99:4899–4907. [Google Scholar]
- 20.Liotard, D.A., Healy, E.F., Ruiz, J.M. and Dewar, M.J.S.: QCPE, Bloomington, Indiana, 1989, program 506, AMPAC (Version 2.1).
- 21.Stewart J.J.P. Optimization of parameters for semi-empirical methods. I. Method. J. Comput. Chem. 1989;10:209–220. [Google Scholar]
- 22.Stewart J.J.P. Optimization of parameters for semi-empirical methods. II. Applications. J. Comput. Chem. 1989;10:221–264. [Google Scholar]
- 23.Herzberg, G.: Molecular spectra and molecular structure. Electronic spectra and electronic structure of polyatomic molecules, Toronto-New York-London, 1966.
- 24.Brown R.D., Godfrey P.D., Kleybomer B.K. The conformation of formamide. J. Molec. Spectrosc. 1987;124:34–35. [Google Scholar]
- 25.Brown R.D., Godfrey P.D., McNaughton D., Pierlot A.P. A study of the major gas-phase tautomer of adenine by microwave spectroscopy. Chem. Phys. Lett. 1989;156:61–63. [Google Scholar]
- 26.Brown R.D., Godfrey P.D., McNaughton D., Pierlot A.P. Tautomers of cytosine by microwave spectroscopy. J. Am. Chem. Soc. 1989;111:2308–2309. [Google Scholar]
- 27.Roussy G., Nonat A. Determination of the equilibrium molecular structure of inverting molecules by microwave spectroscopy: Application to anilone. J. Mol. Spectrosc. 1986;118:180–188. [Google Scholar]
- 28.Ogata T., Sugimoto K. Microwave spectrum, barrier to internal rotation and dipole moment of methoxuallene. J. Molec. Struct. 1988;190:61–67. [Google Scholar]
- 29.Hester R.E., Girling R.B. Spectroscopy of Biological Molecules. Cambridge: The Royal Society of Chemistry; 1991. [Google Scholar]
- 30.Sheina G.G., Radchenko E.D., Plokhotnichenko A.M., Blagoj Y. IR spectra of associated and hydrated pyrimidine bases of nucleic acids in Ar matrix. Biofizika. 1988;33:741–746. [PubMed] [Google Scholar]
- 31.Ivanov A., Plokhotnichenko A.M., Radchenko E.D., Sheina G.G., Blagoj Y. FTIR spectroscopy of uracil derivatives isolated in Kr, Ar and Ne matrices: Matrix effect and fermi resonance. J. Molec. Struct. 1995;372:91–100. [Google Scholar]
- 32.Nowak M.J. IR matrix-isolation studies of nucleic acid constituents – The spectrum of monomeric thymine. J. Molec. Struct. 1989;193:35–49. [Google Scholar]
- 33.Duguid J.G., Bloomfield V.A., Benevides J.M., Thomas G.J., Jr. DNA melting investigated by differential scanning calorimetry and Raman spectroscopy. Biophys. J. 1996;71:3350–3360. doi: 10.1016/S0006-3495(96)79528-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 34.Nowak M.J., Lapinski L., Kwiatkowski J.S., Leszczynski J. Infrared matrix isolation and ab initio quantum mechanical studies of purine and adenine. Spectrochim. Acta. 1991;47A:87–103. [Google Scholar]
- 35.Szczesniak M., Szczepaniak K., Kwiatkowski J.S., KuBulat K., Person W.B. Matrix isolation infrared studies of nucleic acid constituents. 5. Experimental matrix-isolation and theoretical ab initio SCF molecular orbital studies of infrared spectra of cytosine monomers. J. Am. Chem. Soc. 1988;110:8319–8330. [Google Scholar]
- 36.Florian J. Scaled quantum mechanical force fields and vibrational spectra of solid-state nucleic acid constituents. 6. Guanine and guanine residue. J. Phys. Chem. 1993;97:10649–10658. [Google Scholar]
- 37.MacPhail R.A., Williams L.D., Jones D.A., Shaw B.R. Variable temperature infrared-spectroscopy of cytosine-guanine base-pairs-tautomerism versus polarization. J. Biomol. Struct. Dynamics. 1992;9:881–898. doi: 10.1080/07391102.1992.10507964. [DOI] [PubMed] [Google Scholar]
- 38.Gould I.R., Vincent M.A., Hiller I.H., Lapinski L., Nowak M.J. A new theoretical prediction of the infrared spectra of cytosine tautomers. Spectrochim. Acta. 1992;48A:811–818. [Google Scholar]
- 39.Kwiatkowski J.S., Leszczynski J. Molecular structure and vibrational IR spectra of cytosine and its Thio and Seleno analogues by density functional theory and conventional ab initio calculations. J. Phys. Chem. 1996;100:941–953. [Google Scholar]
- 40.Tsuboi M. IR and Raman spectra. In: T.s'o O.P., editor. Basic Principles in Nucleic Acid Chemistry. NY, London: AP; 1974. [Google Scholar]
- 41.Hroda V., Florian J., Hobza P. Structure, energetics, and harmonic vibrational spectra of the adenine-thymine and adenine*-thymine* base pairs: Gradient nonempirical and semiempirical study. J. Phys. Chem. 1993;97:1542–1557. [Google Scholar]
- 42.Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Fergusson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., Kollman P.A. A second generation force field for simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995;117:5179–5197. [Google Scholar]
- 43.Govorun D.N., Danchuk V.D., Misuchuk Y., Kondratyuk I.V., Radomsky N.F., Zeltovsky N.V. AM1 calculation of the nucleic acid bases structure and vibrational spectra. J. Mol. Structure. 1992;267:99–104. [Google Scholar]
- 44.Santamaria R., Vazquez A. Structural and electronic property changes of the nucleic acid bases upon base pair formation. J. Comput. Chem. 1994;15:981–996. [Google Scholar]
- 45.Verkin B.I., Yanson I.K., Sukhodub L.F., Teplytski A.B. Interactions of biomolecules. New experimental approaches and techniques. Kiev: Naukova Dumka; 1985. [Google Scholar]
- 46.Lowen J.N., Jenneskens L.W. Comparison between some semi-empirical and ab-initio Hartree-Fock models for the description of amides (Formamide revised) J. Phys. Organic Chem. 1990;3:711–722. [Google Scholar]
- 47.Leszczynski J. Are the amino groups in the nucleic acid bases coplanar with the molecular rings? Ab initio HF/6-31G* and MP2/6-31G* studies. Int. J. Quant. Chem.: Quant. Biol. Symp. 1992;19:43–45. [Google Scholar]
- 48.Sponer J., Hobza P. Nonplanar geometries of DNA bases: ab initio second-order MP study. J. Phys. Chem. 1994;98:3161–3164. [Google Scholar]
- 49.Sponer J., Hobza P. DNA Base amino groups and their role in molecular interactions: Ab initio and preliminary density functional theory calculations. Int. J. Quant. Chem. 1996;57:959–970. [Google Scholar]
- 50.Sponer J., Leszczynski J., Hobza P. Hydrogen bonding and stacking of DNA bases: A review of quantum-chemical ab initio studies. J. Biomol. Struct. Dynamics. 1996;14:117–135. doi: 10.1080/07391102.1996.10508935. [DOI] [PubMed] [Google Scholar]
- 51.Sponer J., Leszczynski J., Hobza P. Structure and energy of hydrogen-bonded DNA-base pairs – A nonempirical study with inclusion of electron correlation. J. Phys. Chem. 1996;100:1965–1974. [Google Scholar]
- 52.Sponer J., Hobza P. Nonempirical ab initio calculations on DNA-base pairs. Chem. Phys. 1996;204:365–372. doi: 10.1021/cr9800255. [DOI] [PubMed] [Google Scholar]
- 53.Sponer J., Florian J., Hobza P., Leszczynski J. Nonplanar DNA base pairs. J. Biomol. Struct. Dynamics. 1996;13:827–833. doi: 10.1080/07391102.1996.10508895. [DOI] [PubMed] [Google Scholar]
- 54.Gould I.R., Kollman P.A. Theoretical investigation of the hydrogen bond strength in guanine-cytosine and adenine-thymine base pairs. J. Am. Chem. Soc. 1994;116:2493–2499. [Google Scholar]
- 55.Dive G., Dehareng D., Ghuysen J.M. Energy analysis on small to medium sized Hbonded complexes. Theor. Chim. Acta. 1993;85:409–421. [Google Scholar]
- 56.Leszczynski J. Electron correlation effects in the ab initio study on tautomerism of guanine. Chem. Phys. Lett. 1990;174:347–349. [Google Scholar]
- 57.Stewart E.L., Foley C.K., Allinger N.L., Bowen J.P. Ab initio calculations with electronic correlation (MP2) on nucleic acid bases and their methyl derivatives. J. Am. Chem. Soc. 1994;116:7282–7286. [Google Scholar]
- 58.Florian J., Leszczynski J., Johnson B.G. Intermolecular vibrational modes of the G-C, A-T and formamide-formamide H-bonded dimers. J. Mol. Structure. 1995;349:421–426. [Google Scholar]
- 59.Florian J., Leszczynski J. What changes occur in vibrational spectra of guanine and cytosine when they form the Watson-Crick base pair? A quantum chemical SCRF/6-31G* study. Int. J. Quant. Chem.: Quant. Biol. Symp. 1995;22:207–225. [Google Scholar]
- 60.Spirko V., Sponer J., Hobza P. Anharmonic and harmonic intermolecular vibrational modes of the DNA base pairs. J. Phys. Chem. 1997;106:1472–1479. [Google Scholar]
- 61.Govorun D.N., Misuchuk Y., Kondratyuk I.V., Zeltovsky N.V. Dynamic stereo isomerism of Watson-Crick nucleotide base pairs. Dopovidi NAN Ukrainy. 1995;11:121–123. [Google Scholar]
- 62.Govorun D.N., Mishchuk Y., Kondratyuk I.V. Topological properties of potential energy hypersurfer of canonical nucleotide bases. Biopolimeri i Kletka. 1996;12:13–17. [Google Scholar]
