M. I. Zarudnaya, A. L. Potyahaylo, I. N. Kolomiets, D. M. Hovorun
The primary sequence and secondary structure of the region encompassing DIS, SD and ? hairpins in HIV-1 genomic RNAs have been analyzed for 731 group M isolates from NCBI database. The secondary structures have been predicted by the mfold program (M. Zuker). Though the primary sequence of the region studied was found to be highly heterogeneous, this region is folded into DIS, SD and ? hairpins (DIS-, SD- and ?-like hairpins) in 96% of the isolates studied. The phylogenetic analysis showed that the most frequent variants of DIS hairpin (DISLai, DISMal and DISC) tolerate certain base changes. Particularly, base changes at stem position 23 occur 5 and 33 times more frequently in DISLai than in DISMal and DISC, respectively, while A insertion at the 5? end of apical loop is tolerated in DISMal and DISC but not in DISLai. We have revealed that the bottom base pair substitution G-C?A-U in SD hairpin is highly specific for subtype D isolates. All variants of DIS, SD and ? hairpins found in our database are discussed, systematized and presented in schemes of hypothetical transitions between variants via a single base change. Most variants of DIS and ? hairpins were found to adopt several conformations.
Key words: HIV-1, phylogenetic analysis, RNA folding, DIS hairpin, SD hairpin, ? hairpin, genome dimerization, HIV-1 packaging.
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