title: Structural determinants of TAR RNA-DNA annealing in the absence and presence of HIV-1 nucleocapsid protein.
abstract: Annealing of the TAR RNA hairpin to the cTAR DNA hairpin is required for the minus-strand transfer step of HIV-1 reverse transcription. HIV-1 nucleocapsid protein (NC) plays a crucial role by facilitating annealing of the complementary hairpins. To gain insight into the mechanism of NC-mediated TAR RNA-DNA annealing, we used structural probes (nucleases and potassium permanganate), gel retardation assays, fluorescence anisotropy and cTAR mutants under conditions allowing strand transfer. In the absence of NC, cTAR DNA-TAR RNA annealing depends on nucleation through the apical loops. We show that the annealing intermediate of the kissing pathway is a loop-loop kissing complex involving six base-pairs and that the apical stems are not destabilized by this loop-loop interaction. Our data support a dynamic structure of the cTAR hairpin in the absence of NC, involving equilibrium between both the closed conformation and the partially open 'Y' conformation. This study is the first to show that the apical and internal loops of cTAR are weak and strong binding sites for NC, respectively. NC slightly destabilizes the lower stem that is adjacent to the internal loop and shifts the equilibrium toward the 'Y' conformation exhibiting at least 12 unpaired nucleotides in its lower part.
authors: LBPA, ENS de Cachan, CNRS, 61 avenue du Président Wilson, 94235 Cachan, France.
authors: Igor
authors: I
authors: Kanevsky
authors: Françoise
authors: F
authors: Chaminade
authors: Yingying
authors: Y
authors: Chen
authors: Julien
authors: J
authors: Godet
authors: Brigitte
authors: B
authors: René
authors: Jean-Luc
authors: JL
authors: Darlix
authors: Yves
authors: Y
authors: Mély
authors: Olivier
authors: O
authors: Mauffret
authors: Philippe
authors: P
authors: Fossé
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D004279:DNA, Viral / Q000737:chemistry*; D024202:Electrophoretic Mobility Shift Assay; D005454:Fluorescence Polarization; D016325:HIV Long Terminal Repeat; D015497:HIV-1 / Q000235:genetics*; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry*; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000378:metabolism*
chemical_list: D004279:DNA, Viral; C071884:NCP7 protein, Human immunodeficiency virus 1; D012367:RNA, Viral; D054301:gag Gene Products, Human Immunodeficiency Virus