title: NMR detection of intermolecular interaction sites in the dimeric 5'-leader of the HIV-1 genome.
abstract: HIV type-1 (HIV-1) contains a pseudodiploid RNA genome that is selected for packaging and maintained in virions as a noncovalently linked dimer. Genome dimerization is mediated by conserved elements within the 5'-leader of the RNA, including a palindromic dimer initiation signal (DIS) that has been proposed to form kissing hairpin and/or extended duplex intermolecular contacts. Here, we have applied a2H-edited NMR approach to directly probe for intermolecular interactions in the full-length, dimeric HIV-1 5'-leader (688 nucleotides; 230 kDa). The interface is extensive and includes DIS:DIS base pairing in an extended duplex state as well as intermolecular pairing between elements of the upstream Unique-5' (U5) sequence and those near the gag start site (AUG). Other pseudopalindromic regions of the leader, including the transcription activation (TAR), polyadenylation (PolyA), and primer binding (PBS) elements, do not participate in intermolecular base pairing. Using a2H-edited one-dimensional NMR approach, we also show that the extended interface structure forms on a time scale similar to that of overall RNA dimerization. Our studies indicate that a kissing dimer-mediated structure, if formed, exists only transiently and readily converts to the extended interface structure, even in the absence of the HIV-1 nucleocapsid protein or other RNA chaperones.
authors: Howard Hughes Medical Institute, University of Maryland Baltimore County, Baltimore, MD 21250.|Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250.
authors: Sarah C
authors: SC
authors: Keane
authors: Howard Hughes Medical Institute, University of Maryland Baltimore County, Baltimore, MD 21250.|Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250.
authors: Verna
authors: V
authors: Van
authors: Howard Hughes Medical Institute, University of Maryland Baltimore County, Baltimore, MD 21250.|Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250.
authors: Heather M
authors: HM
authors: Frank
authors: Howard Hughes Medical Institute, University of Maryland Baltimore County, Baltimore, MD 21250.|Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250.
authors: Carly A
authors: CA
authors: Sciandra
authors: Howard Hughes Medical Institute, University of Maryland Baltimore County, Baltimore, MD 21250.|Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250.
authors: Sayo
authors: S
authors: McCowin
authors: Howard Hughes Medical Institute, University of Maryland Baltimore County, Baltimore, MD 21250.|Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250.
authors: Justin
authors: J
authors: Santos
authors: Department of Biochemistry, University of Missouri, Columbia, MO 65211 summers@hhmi.umbc.edu hengx@missouri.edu.
authors: Xiao
authors: X
authors: Heng
authors: Howard Hughes Medical Institute, University of Maryland Baltimore County, Baltimore, MD 21250; summers@hhmi.umbc.edu hengx@missouri.edu.|Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250.
authors: Michael F
authors: MF
authors: Summers
mesh_terms: D020121:5' Untranslated Regions; D019281:Dimerization; D016679:Genome, Viral; D015497:HIV-1 / Q000235:genetics*; D009682:Magnetic Resonance Spectroscopy; D012367:RNA, Viral / Q000737:chemistry*
chemical_list: D020121:5' Untranslated Regions; D012367:RNA, Viral
keywords: 5′-leader; 5′-untranslated region; HIV-1; RNA; structure