T. Yu. Nikolaienko¹, L. A. Bulavin¹, D. M. Hovorun^1,2, O. O. Missura¹

¹Taras Shevchenko Kyiv National University, Ukraine;
²Institute of Molecular Biology and Genetics,
National Academy of Sciences of Ukraine, Kyiv;
e-mail: tim_mail@ukr.net

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 K_γ > K_α′ > K_ε > K_β.

Keywords: 1_2-dideoxyribofuranose-5-phosphate, AP-sites, conformational analysis, DNA