Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain.

ABSTRACT: A distance constrained secondary structural model of the ≈10 kb RNA genome of the HIV-1 has been predicted but higher-order structures, involving long distance interactions, are currently unknown. We present the first global RNA secondary structure model for the HIV-1 genome, which integrates both comparative structure analysis and information from experimental data in a full-length prediction without distance constraints. Besides recovering known structural elements, we predict several novel structural elements that are conserved in HIV-1 evolution. Our results also indicate that the structure of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core orga

SUBMITTER: Sukosd Z 

PROVIDER: S-EPMC4666355 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature