title: Preservation of a kinetically originated folding of the cis antirepressor sequence for transport of HIV-1 viral RNA.
abstract: We compute a metastable secondary structure for the cis antirepressor sequence (CAR) in the viral RNA of human immunodeficiency virus 1 (HIV-1) whose lifetime is long enough to allow for further stabilization by interaction with the ribosomal machinery. The structure emerges as the viral genome RNA is being synthesized by RNA polymerase II and corresponds to the biologically active structure sustained between units 7364 and in env RNA. It is the most probable among the fast-formed structures which emerge during transcription. No tertiary interactions appear to influence the statistical weight of this metastable state. The structure is predicted by means of a Monte Carlo simulation which computes refolding events occurring as the CAR portion of viral RNA is being assembled. The final emerging structure is preserved for transportation of viral RNA and spliced env RNA from the nucleus to the cytoplasm of the host cell.
authors.affiliation: Department of Chemistry, University of Miami, Coral Gables, FL 33124.
authors.forename: A
authors.initials: A
authors.lastname: Belinky
authors.forename: A
authors.initials: A
authors.lastname: Fernández
mesh_terms: D001483:Base Sequence; D002467:Cell Nucleus / Q000378:metabolism; D003593:Cytoplasm / Q000378:metabolism; D015752:Genes, env; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D012319:RNA Polymerase II / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid; D014158:Transcription, Genetic
chemical_list: D012367:RNA, Viral; D012319:RNA Polymerase II