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

Nucleic Acids Res. 2015 Dec 2;43(21):10168-79. doi: 10.1093/nar/gkv1039. Epub 2015 Oct 17.


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 organizing structure (COS) that organize the genome into three major structural domains. Despite overlapping protein-coding regions the COS is supported by a particular high frequency of compensatory base changes, suggesting functional importance for this element. This new structural element potentially organizes the whole genome into three major domains protruding from a conserved core structure with potential roles in replication and evolution for the virus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genome, Viral*
  • HIV-1 / genetics*
  • Models, Genetic
  • Nucleic Acid Conformation
  • RNA, Viral / chemistry*
  • Software


  • RNA, Viral