Genome sequence analysis suggests coevolution of the DIS, SD, and Psi hairpins in HIV-1 genomes.

HIV-1 RNA dimerization is a critical step in viral life cycle. It is a prerequisite for genome packaging and plays an important role in reverse transcription and recombination. Dimerization is promoted by the DIS (dimerization initiation site) hairpin located in the 5' leader of HIV-1 genome. Despite the high genetic diversity in HIV-1 group M, only five apical loops (AAGCGCGCA, AAGUGCGCA, AAGUGCACA, AGGUGCACA and AGUGCAC) are commonly found in DIS hairpins. We refer to the parent DISes with these apical loops as DISLai, DISTrans, DISF, DISMal, and DISC, respectively. Based on identity or similarity of DIS hairpins to parent DISes, we distributed HIV-1 M genomes into five dimerization groups. Comparison of the primary and secondary structures of DIS, SD and Psi hairpins in about 3000 HIV-1 M genomes showed that the mutation frequencies at particular nucleotide positions of these hairpins differ among the dimerization groups, and DISF may be an origin of other parent DISes. We found that DIS, SD and Psi hairpins have hundreds of variants, only some of them occurring rather frequently. The lower part of DIS hairpin with G x AGG internal loop is highly conserved in both HIV-1 and SIV genomes. We supposed that the G-quadruplex, located 56 nts downstream of the Gag start codon, may participate in switching of HIV-1 leader RNA from BMH (branched multiple hairpins) to LDI (long distance interaction) conformation.

Application of quantum chemical approximations to environmental problems: prediction of water solubility for nitro compounds.

Water solubility values for 27 nitro compounds with experimentally measured values were computed using the conductor-like screening model for real solvent (COSMO-RS) based on the density functional theory and COSMO technique. We have found that the accuracy of the COSMO-RS approach for prediction of water solubility of liquid nitro compounds is impressively high (the errors are lower than 0.1 LU). However, for some solid nitro compounds, especially nitramines, there is sufficient disagreement between calculated and experimental values. In order to increase the accuracy of predictions the quantitative structure-property relationship (QSPR) part of the COSMO-RS approach has been modified. The solubility values calculated by the modified COSMO-RS method have shown much better agreement with the experimental values (the mean absolute errors are lower than 0.5 LU). Furthermore, this technique has been used for prediction of water solubility for an expanded set of 23 nitro compounds including nitroaromatic, nitramines, nitroanisoles, nitrogen rich compounds, and some their nitroso and amino derivatives with unknown experimental values. The solubility values predicted using the proposed computational technique could be useful for the determination of the environmental fate of military and industrial wastes and the development of remediation strategies for contaminated soils and waters. This predictive capability is especially important for unstable compounds and for compounds that have yet to be synthesized.