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


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.

Supplementary data


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