Hidden messages in the nef gene of human immunodeficiency virus type 1 suggest a novel RNA secondary structure.

ABSTRACT: The coexistence of multiple codes in the genome of human immunodeficiency virus type 1 (HIV-1) was analyzed. We explored factors constraining the variability of the virus genome primarily in relation to conserved RNA secondary structures overlapping coding sequences, and used a simple combination of algorithms for RNA secondary structure prediction based on the nearest-neighbor thermodynamic rules and a statistical approach. In our previous study, we applied this combination to a non- redundant data set of env nucleotide sequences, confirmed the conservative secondary structure of the rev-responsive element (RRE) and found a new RNA structure in the first conserved (C1) region of the env gene. In this study, we analyzed the variability of putative RNA secondary structures inside the nef ge

SUBMITTER: Peleg O 

PROVIDER: S-EPMC165969 | biostudies-literature | 2003 Jul

REPOSITORIES: biostudies-literature