Control Elements Secondary Structures of HIV-1 genome


This section of the CESSHIV-1 database contains the secondary structures of different fragments of HIV-1 complete poly(A) region, including upstream sequence element (USE), TAR, polyA hairpin and downstream sequence element (DSE) for approximately 2000 isolates of different subtypes and recombinant forms. The structural models for DSE region and 123 nt 3' terminus of HIV-1 pre-mRNA have been presented in our recent work (see Publications [5]).

The secondary structures of poly(A) region fragments have been predicted by mfold program of M. Zuker (2003). We chose parameters 10% suboptimality and window 0 for USE region (9481-9644 nt); USE domain, TAR, polyA (9493-9644 nt); USE, TAR, polyA (9516-9644 nt); 123 nt 3' terminus (9597-9719 nt); Core poly(A) site (9537-9672 nt); and 5% suboptimality and window 0 for longer fragments - Complete poly(A) region (9493-9672 nt) and 227 nt 3' terminus (9493-9719 nt). The optimal folding and suboptimal ones within ΔΔG ≤ 4 kcal/mol of the minimum free energy are presented in this section. The folding constraint is used to force both 5' and 3' terminal nucleotides to be single stranded. Base changes as compared to HIV-1 isolate HXB2 with accession number K03455 (RefSec) are marked by red, insertions - by blue, deletions - by green dash (in primary sequence) or green spot (in secondary structure).