Biopolym. Cell. 2011; 27(4):291-299.
http://dx.doi.org/10.7124/bc.00010E
Molecular Biophysics
Conformational capacity of 5'-deoxyguanylic acid molecule investigated by quantum-mechanical methods
1Nikolaienko T. Yu., 1Bulavin L. A., 1, 2Hovorun D. M.
  1. Taras Shevchenko National University of Kyiv
    64, Volodymyrska Str., Kyiv, Ukraine, 01601
  2. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

Aim. Exhaustive conformational analysis of the isolated 5'-deoxyguanylic acid (dGA) molecule. Methods. Torsion angles β=PO5'C5'C4', γ=O5'C5'C4'C3', ε=C4'C3'O3'H03', χ=O4'C1'N9H4 α'=C5'O5'POP ζ1=O5'POP1HP1 ζ2=O5'POP2HP2 as well as sugar pseudorotation phase and amplitude have been used to identify the molecule conformation. Initial geometries were built using full sets of conformers of the 2'-deoxyguanosine, methyl dihydrogen phosphate and 1,2-dideoxyribofuranose-5-phosphate molecules obtained previously. Geometry optimization has been carried out at the DFT B3LYP/6-31G(d,p) theory level while the MP2/6-311++G(d,p) theory level has been used to calculate electronic energies of optimized structures. Results. As many as 745 different conformations of dGA molecule have been revealed with relative Gibbs free energies under standard conditions within 0÷16,4 kcal/ mole. Conformational variability of chemical bond lengths, valence angles and endo- and exocyclic torsion angles of guanine has been characterized. Conclusions. It has been found that the energetically most favorable structure has syn orientation of nitrogenous base and C exo sugar puckering. 13 conformers of isolated dGA have been shown to be similar to the structure of nucleotides in AI-, AII-, BI-, ZI- or ZIIforms of DNA. Among them the BI-DNA-like one has the lowest Gibbs free energy (ΔG=9,1 kcal/mole). The role of intramolecular hydrogen bonds in stabilizing dGA conformer structures has been demonstrated.
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Supplementary data

References

[1] G-Quadruplex DNA: methods and protocols / Ed. P. Baumann New York: Humana Press, 2010 276 p.
[2] Morris G. K., Williams W. L. Inhibition of growth of Lactobacillus bulgaricus by purine deoxyribonucleotides J. Bacteriol 1965 90, N 3 P. 715–719.
[3] Kimura N., Shimada N., Ishijima Y., Fukuda M., Takagi Y., Ishikawa N. Nucleoside diphosphate kinases in mammalian signal transduction systems: Recent development and perspective J. Bioenerg. Biomembr 2003 35, N 1 P. 41–47.
[4] Young D. W., Tollin P., Wilson H. R. The structure of disodium deoxyguanosine-5'-phosphate tetrahydrate Acta Cryst 1974 30, N 8 P. 2012–2018.
[5] Nafissi S., Aghabozorgh H., Sadjadi S. A. S. Interaction of T1+ with mononucleotides: metal ion binding and sugar conformation J. Inorg. Biochem 1997 66, N 4 P. 253–258.
[6] Robinson J. M., Greig M. J., Griffey R. H., Mohan V., Laude D. A. Hydrogen/deuterium exchange of nucleotides in the gas phase Anal. Chem 1998 70, N 17 P. 3566–3571.
[7] Santamaria R., Quiroz-Gutierrez A., Juarez C. Structures and energetic properties of B-DNA nucleotides J. Mol. Struct.: Theochem 1995 357, N 1–2 P. 161–170.
[8] Shishkin O. V., Gorb L., Zhikol O. A., Leszczynski J. Conformational analysis of canonical 2-deoxyribonucleotides. 2. Purine nucleotides J. Biomol. Struct. Dyn 2004 22, N 2 P. 227– 243.
[9] Nikolaienko T. Yu., Hovorun D. M. Quantum-mechanical conformational analysis of 2'-deoxycytidilic acid molecule — the DNA structural unit Dopovidi . Nat. Acad. Sci. Ukraine 2010 N 9 P. 173–184.
[10] Nikolaienko T. Yu., Bulavin L. A., Hovorun D. M. Quantummechanical conformational analysis of the 5'-thymidilic acid molecule Ukr. Biokhim. Zh 2010 82, N 6 P. 76–86.
[11] Liu D., Wyttenbach T., Bowers M. T. Hydration of mononucleotides J. Am. Chem. Soc 2006 128, N 47 P. 15155–15163.
[12] Boryskina O. P., Tkachenko M. Yu., Shestopalova A. V. Variability of DNA structure and protein-nucleic acid reconginition Biopolym. Cell 2010 26, N 5 P. 360–372.
[13] Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
[14] Nikolaienko T. Yu., Bulavin L. A., Hovorun D. M. The 5'-deoxyadenylic acid molecule conformational capacity investigated using density functional theory (DFT). Ukr Biokhim Zh. 2011 83(4):16-28
[15] Zhurakivsky RO, Hovorun DM. Complete conformational analysis of 2'-deoxycytidine molecule by density functional theory. Dopovidi Nats Akad Nauk Ukrainy. 2007; (4):187-95.
[16] Nikolaienko T. Yu., Bulavin L. A., Hovorun D. M. How many conformers of the methyl dihydrogen phosphate molecule exist? Detailed quantum-mechanical investigation Biophysical bulletin 2010 Iss. 25 (2) P. 17–25.
[17] Nikolaienko T. Yu., Bulavin L. A., Hovorun D. M., Missura O. O. Conformational variety and physical properties of the 1,2dideoxyribofuranose-5-phosphate, the model DNA monomer structural unit Ukr. Biokhim. Zh 2011 83, N 1 P. 54–62.
[18] Frisch M. J., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A., Cheeseman J. R., Montgomery Jr., J. A., Vreven T., Kudin K. N., Burant J. C., Millam J. M., Iyengar S. S., Tomasi J., Barone V., Mennucci B., Cossi M., Scalmani G., Rega N., Petersson G. A., Nakatsuji H., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Klene M., Li X., Knox J. E., Hratchian, H. P., Cross J. B., Bakken V., Adamo C., Jaramillo J., Gomperts R., Stratmann R. E., Yazyev O., Austin A. J., Cammi R., Pomelli C., Ochterski J. W., Ayala P. Y., Morokuma K., Voth G. A., Salvador P., Dannenberg J. J., Zakrzewski V. G., Dapprich S., Daniels A. D., Strain M. C., Farkas O., Malick D. K., Rabuck A. D., Raghavachari K., Foresman J. B., Ortiz J. V., Cui Q., Baboul A. G., Clifford S., Cioslowski J., Stefanov B. B., Liu G., Liashenko A., Piskorz P., Komaromi I., Martin R. L., Fox D. J., Keith T., Al-Laham M. A., Peng C. Y., Nanayakkara A., Challacombe M., Gill P. M. W., Johnson B., Chen W., Wong M. W., Gonzalez C., Pople J. A. Gaussian 03, Revision E.01 Wallingford CT: Gaussian Inc., 2004.
[19] Bader R. F. W. Atoms in Molecules: a quantum theory Oxford: Univ. Press, 1990 458 p.
[20] Iogansen A. V. Direct proportionality of the hydrogen bonding energy and the intensification of the stretching (XH) vibration in infrared spectra Spectrochim. Acta A 1999 55, N 7–8 P. 1585–1612.
[21] Espinosa E., Molins E., Lecomte C. Hydrogen bond strengths revealed by topological analyses of experimentally observed electron densities Chem. Phys. Lett 1998 285, N 3–4 P. 170– 173.
[22] Kitamura K, Wakahara A, Mizuno H, Baba Y, Tomita K. Conformationally 'concerted' changes in nucleotide structures. A new description using circular correlation and regression analyses. J Am Chem Soc. 1981; 103(13):3899–904.
[23] Svozil D., Kalina J., Omelka M., Schneider B. DNA conformations and their sequence preferences Nucl. Acids Res 2008 36, N 11 P. 3690–3706.
[24] Schneide B., Neidle S., Berman H. M. Conformations of the sugar-phosphate backbone in helical DNA crystal structures Biopolymers 1997 42, N 1 P. 113–124.