title: Diversity of DIS, SD and psi hairpins in HIV-1 isolates of group M: in silico study.
abstract: The primary sequence and secondary structure of the region encompassing DIS, SD and psi 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 m fold 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 psi hairpins (DIS-, SD- and psi-like hairpins) in 96% of the isolates studied. The phylogenetic analysis showed that the most frequent variants of DIS hairpin (DIS(Lai), DIS(Mal) and DIS(C)) tolerate certain base changes. Particularly, base changes at stem position 23 occur 5 and 33 times more frequently in DIS(Lai) than in DIS(Mal) and DIS(C), respectively, while A insertion at the 5'end of apical loop is tolerated in DIS(Mal) and DIS(C) but not in DIS(Lai). 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 psi 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 psi hairpins were found to adopt several conformations.
authors.affiliation: Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv. m.i.zarudna@imbg.org.ua
authors.forename: M I
authors.initials: MI
authors.lastname: Zarudnaya
authors.forename: A L
authors.initials: AL
authors.lastname: Potyahaylo
authors.forename: I N
authors.initials: IN
authors.lastname: Kolomiets
authors.forename: D M
authors.initials: DM
authors.lastname: Hovorun
mesh_terms: D001483:Base Sequence; D030541:Databases, Genetic; D016679:Genome, Viral; D015497:HIV-1 / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics*
chemical_list: D012367:RNA, Viral