Liquid water and ices: understanding the structure and physical properties.

A review of the structure and some properties of condensed phases of water is given. Since the discovery of the polymorphism of crystalline ice (beginning of the twentieth century), 15 ice modifications have been found and their structures have been determined. If we do not take into consideration proton ordering or disordering, nine distinct crystalline ice modifications in which water molecules retain their individuality are known.

Sequence-dependent B<-->A transition in DNA evaluated with dimeric and trimeric scales.

Experimental data on the sequence-dependent B<-->A conformational transition in 24 oligo- and polymeric duplexes yield optimal dimeric and trimeric scales for this transition. The 10 sequence dimers and the 32 trimers of the DNA duplex were characterized by the free energy differences between the B and A forms in water solution. In general, the trimeric scale describes the sequence-dependent DNA conformational propensities more accurately than the dimeric scale, which is likely related to the trimeric model accounting for the two interfaces between adjacent base pairs on both sides (rather than only one interface in the dimeric model).

Monte Carlo simulation of DNA fragment hydration in the presence of alkaline cations using novel atom-atom potential functions.

The set of atom-atom potential functions specially adjusted to simulation of nucleic acid fragment hydration (Poltev, Grokhlina & Malenkov, J. Biomol. Struct.

Modeling DNA hydration: comparison of calculated and experimental hydration properties of nuclic acid bases.

Hydration properties of individual nucleic acid bases were calculated and compared with the available experimental data. Three sets of classical potential functions (PF) used in simulations of nucleic acid hydration were juxtaposed: (i) the PF developed by Poltev and Malenkov (PM), (ii) the PF of Weiner and Kollman (WK), which together with Jorgensen's TIP3P water model are widely used in the AMBER program, and (iii) OPLS (optimized potentials for liquid simulations) developed by Jorgensen (J). The global minima of interaction energy of single water molecules with all the natural nucleic acid bases correspond to the formation of two water-base hydrogen bonds (water bridging of two hydrophilic atoms of the base).

[The mechanism of tautomeric transitions of nucleic acid bases with limited access to water molecules].

Pathways of tautomeric transformations of nucleic acid bases have been considered in the conditions when only few separate water molecules can interact with the bases. Field ionization mass-spectrometric study has demonstrated that substitution of one of the labile hydrogen atoms for deuterium takes place when thymine (or 1-methylthymine) interacts with heavy water in vacuo. This observation was explained by a supposition that a transient water-thymine complex is formed and then tautomeric transition of the base occurs via double proton transfer along hydrogen bonds.