Control Elements Secondary Structures of HIV-1 genome

Various models for the 5' terminal region of HIV-1 are reported in recent publications, in particular the extended long distance interaction (LDI) and branched multiple hairpin (BMH) structure have been proposed by Abbink and Berkhout (2003). In our database the secondary structures of DIS, SD, Psi region are given in the context of the BMH model. The local folding of this region is also compatible with a new model of dimer linkage sequence proposed by Sakuragi et al. (Nucleic Acids Research, 2012, Advance Access). In future we plan to present the secondary structures of DIS, SD, Psi region in the context of other models, e.g., Wilkinson (2008).

This section of the CESSHIV-1 database contains the Secondary structures of the region encompassing DIS, SD and Psi hairpins for 2466 HIV-1 genomic RNAs of different subtypes and recombinant forms (last updated October, 2010).

The secondary structures of this region have been predicted by mfold program of M. Zuker (2003) with 15% suboptimality and window 0. The optimal folding and suboptimal ones within ΔΔ G ≤ 4 kcal/mol of the minimum free energy are presented in this section. The folding region corresponds to that encompassing DIS, SD, and Psi hairpins in BMH model of Abbink and Berkhout (2003) in HIV-1 isolate HXB2 with accession number K03455 (RefSec) plus three nucleotides located immediately upstream and three nucleotides located immediately downstream. The folding constraint is used to force both 5' and 3' terminal nucleotides to be single stranded. Base changes as compared to RefSec are marked by red, insertions - by blue, deletions - by green dash (in primary sequence) or green spot (in secondary structure).


Analytical Information to this section includes the most frequent variants of DSI, SD, and Psi hairpins above the error level 0.5% and evolution schemes of transitions between these variants through one base change. By considering literature data on DIS variability and our phylogenetic findings we have chosen DISLai, DISMal, DISC, DISF, and DISTrans as five parental DISes and classified all DIS hairpin variants found by these parental DISes (see Publications [3]). We early presented the evolution schemes of transitions between these variants for 757 isolates (see Publications [2]) and updated them here for 1212 isolates.