Control Elements Secondary Structures of HIV-1 genome

Section PBS region, Introduction

Various models for the 5' terminal region of HIV-1 are reported in recent publications, for review see Lu (2011). In particular the extended long distance interaction (LDI) and branched multiple hairpin (BMH) structure for HIV-1 5' UTR have been proposed by Abbink and Berkhout (2003). In our database the secondary structures of PBS region are given in the context of the BMH model. In future we plan to present the secondary structure prediction of PBS region also in the context of other models reported in literature.

This section of the CESSHIV-1 database contains the Secondary structures of the PBS region for 2039 HIV-1 genomic RNAs of different subtypes, recombinant forms and groups (last updated October, 2010).

The secondary structures of this region have been predicted by mfold program of M. Zuker (2003) with 5% 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 the PBS region in BMH model of Abbink and Berkhout (2003) in HIV-1 isolate HXB2 with accession number K03455 (RefSec) plus one nucleotide located immediately upstream and seven nucleotides located immediately downstream (up to the first nucleotide of DIS hairpin). 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).


The Analytical information contains the most frequent base changes in PBS region (within BMH model for 5' UTR of HIV-1 genome) and frequent examples of PBS hairpin and U5 hairpin structures of HIV-1 isolates of B, C, D, and F1 subtypes (see Publications [6]).