Ukr.Biochem.J. 2011; Volume 83, Issue 1, Jan-Feb, pp. 54-62

Conformational variety and physical properties of the 1,2-dideoxyribofuranose-5-phosphate, the model DNA monomer structural unit

T. Yu. Nikolaienko1, L. A. Bulavin1, D. M. Hovorun1,2, O. O. Missura1

1Taras Shevchenko Kyiv National University, Ukraine;
2Institute of Molecular Biology and Genetics,
National Academy of Sciences of Ukraine, Kyiv;

The results of exhaustive quantum-mechani­cal conformational analysis of 1,2-dideoxyribofuranose-5-phosphate molecule, the model DNA backbone structural unit, are presented. As many as 282 conformations with the relative Gibbs energies from 0 to 8.9 kcal/mole have been obtained at the MP2/cc-pVTZ // DFT B3LYP/cc-pVTZ theory level. Among them seven structures are similar to those of the DNA backbone in its AI, BI and ZII forms, while the B-DNA-like conformation has the lowest Gibbs energy (ΔG = 3.3 kcal/mole). It is shown that the relaxed force constants values­ for conformational parameters of all DNA-like conformations satisfy inequality Kγ > Kα′ > Kε > Kβ.

Keywords: , , ,

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