Solvation of nucleic acid backbone: A DFT study

Ladislav Benda^1,2, Bohdan Schneider³, Vladimír Sychrovský¹

¹ Institute of Organic Chemistry and Biochemistry AS CR, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic

² Faculty of Mathematics and Physics, Charles University Prague, Ke Karlovu 3, 121 16 Praha 2, Czech Republic

³ Institute of Biotechnology AS CR, Vídeňská 1083, 142 20 Praha 4, Czech Republic

ladislav.benda@marge.uochb.cas.cz

A negatively charged phosphate group of nucleic acid backbone interconnecting two (2-deoxy)ribose units represents one of the most important solvation sites in nucleic acids. An impressive amount of work has been done on characterizing the structure of the solvation shell of canonical DNA as well as of other backbone patterns found in RNA. Surprisingly narrow regions of water occurrence in the direct contact (H-bond) with phosphate group have been observed in crystals. The presence of physiological monovalent and divalent cations in the phosphate first solvation shell was also confirmed [1].

The X-ray identification of 3^rd period alkali metal ions (Na⁺, Mg²⁺) is not a straightforward task since these ions and the water molecule possess the same number of electrons. In many cases, the methods of molecular spectroscopy can be used for metal ion recognition [2-4]. We investigated the possibility of characterizing the specific interactions of metal ions with nucleic acids by NMR spectroscopy. Ab-initio computational methods were applied to selected nucleic acid structural patterns including explicit solvent molecules. We outline several options for monitoring the presence of metal ions in contact with nucleic acids.

1. B. Schneider, M. Kabeláč, J. Am. Chem. Soc., 120, (1998), 161.

2. Y. Tanaka, K. Taira, Chem. Commun., (2005), 2069.

3. B. Halle, V. P. Denisov, Proc. Natl. Acad. Sci. USA, 97, (2000), 629.

4. E. Freisinger, R. K. O. Sigel, Coord. Chem. Rev., 251, (2007), 1834.