title: Three-dimensional folding of an RNA hairpin required for packaging HIV-1.
abstract: An NMR-based structure is presented for a 20 mer hairpin model of the SL3 stem-loop from the HIV-1 packaging signal. The stem has an A-family structure. However, the GGAG tetraloop appears to be flexible with the second (G10) and fourth (G12) bases extruded from the normal stacking arrangement. The A-base (A11) occupies a cavity large enough for it to jump rapidly between stacking upon G9 (in the loop) and G13 (from the base-pair adjacent to the loop). The H-bonding loci of G10, A11, and G12 are unoccupied in the free RNA structure. The loop should be easily adaptable to binding by the HIV-1 nucleocapsid protein or loop receptors.
authors.affiliation: Department of Chemistry, Syracuse University, Syracuse, NY, 13244-4100, USA.
authors.forename: L
authors.initials: L
authors.lastname: Pappalardo
authors.forename: D J
authors.initials: DJ
authors.lastname: Kerwood
authors.forename: I
authors.initials: I
authors.lastname: Pelczer
authors.forename: P N
authors.initials: PN
authors.lastname: Borer
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D002244:Carbon / Q000737:chemistry / Q000378:metabolism; D016384:Consensus Sequence / Q000235:genetics; D019281:Dimerization; D016679:Genome, Viral; D015497:HIV-1 / Q000235:genetics* / Q000502:physiology; D006859:Hydrogen / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D009584:Nitrogen / Q000737:chemistry / Q000378:metabolism; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D010710:Phosphates / Q000737:chemistry / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000502:physiology; D012045:Regulatory Sequences, Nucleic Acid; D013696:Temperature; D013816:Thermodynamics; D019065:Virus Assembly / Q000235:genetics*
chemical_list: D010710:Phosphates; D012367:RNA, Viral; D002244:Carbon; D006859:Hydrogen; D009584:Nitrogen