Journal archive > 2010 > N 6 November-December

QUANTUM-MECHANICAL CONFORMATIONAL ANALYSIS OF?THE 5?-THYMIDILIC ACID MOLECULE

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

1Taras Shevchenko Kyiv National University, Ukraine;
2Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv;
е-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

The conformational analysis of the DNA structural unit – the nucleotide with thymine base and electroneutral phosphate group at 5?-position?– has been carried out with the applied quantum mechanics methods at the MP2/6-311++G(d,p) // B3LYP/6-31G(d,p) theory level. As many as 660 conformations with relative Gibbs energies under standard conditions from 0 to 11.1 kcal/mole have been found. Among them, six conformations are similar to the structure of the nucleotide of AI-DNA, one – to AII- and seven – to the DNA in BI-form. The lowest Gibbs energy among the DNA-like conformations (?G = 2.7 kcal/mole) belongs to BI-DNA-like structure. It is shown that the glycoside chemical bond is the most labile one. The role of intramolecular CH???O hydrogen bonds in formation of the 5?-thymidilic acid molecule structure is demonstrated.

Key words: nucleotide, 5?-thymidilic acid, conformational analysis, DNA, ab initio calculations, hydrogen bonds.

The original article in Ukrainian is available for download in PDF format.