Biopolymers and Cell. 2011; 27(4): 291-299

CONFORMATIONAL CAPACITY OF 5'-DEOXYGUANYLIC ACID MOLECULE INVESTIGATED BY QUANTUM-MECHANICAL METHODS

Nikolaienko T. Yu., Bulavin L. A., ¹Hovorun D. M.

Taras Shevchenko National University of Kyiv
64, Volodymyrska Str., Kyiv, Ukraine, 01601
¹Institute of Molecular Biology and Genetics, NAS of Ukraine
150, Akademika Zabolotnogo Str., Kyiv, Ukraine, 03680

    Aim. Exhaustive conformational analysis of the isolated 5'-deoxyguanylic acid (dGA) molecule. Methods. Torsion angles β=PO_5'C_5'C_4', γ=O_5'C_5'C_4'C_3', ε=C_4'C_3'O_3'H_03', χ=O_4'C_1'N₉H₄ α'=C_5'O_5'PO_P ζ₁=O_5'PO_P1H_P1 ζ₂=O_5'PO_P2H_P2 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 (9,1 kcal/mole). The role of intramolecular hydrogen bonds in stabilizing dGA conformer structures has been demonstrated.

Keywords: 5'-deoxyguanylic acid, conformational analysis, DNA, ab initio calculations

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