title: Intrinsic nucleic acid dynamics modulates HIV-1 nucleocapsid protein binding to its targets.
abstract: HIV-1 nucleocapsid protein (NC) is involved in the rearrangement of nucleic acids occurring in key steps of reverse transcription. The protein, through its two zinc fingers, interacts preferentially with unpaired guanines in single-stranded sequences. In mini-cTAR stem-loop, which corresponds to the top half of the cDNA copy of the transactivation response element of the HIV-1 genome, NC was found to exhibit a clear preference for the TGG sequence at the bottom of mini-cTAR stem. To further understand how this site was selected among several potential binding sites containing unpaired guanines, we probed the intrinsic dynamics of mini-cTAR using (13)C relaxation measurements. Results of spin relaxation time measurements have been analyzed using the model-free formalism and completed by dispersion relaxation measurements. Our data indicate that the preferentially recognized guanine in the lower part of the stem is exempt of conformational exchange and highly mobile. In contrast, the unrecognized unpaired guanines of mini-cTAR are involved in conformational exchange, probably related to transient base-pairs. These findings support the notion that NC preferentially recognizes unpaired guanines exhibiting a high degree of mobility. The ability of NC to discriminate between close sequences through their dynamic properties contributes to understanding how NC recognizes specific sites within the HIV genome.
authors: Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, Centre National de la Recherche Scientifique, Cachan, France.
authors: Ali
authors: A
authors: Bazzi
authors: Loussiné
authors: L
authors: Zargarian
authors: Françoise
authors: F
authors: Chaminade
authors: Hugues
authors: H
authors: De Rocquigny
authors: Brigitte
authors: B
authors: René
authors: Yves
authors: Y
authors: Mély
authors: Philippe
authors: P
authors: Fossé
authors: Olivier
authors: O
authors: Mauffret
mesh_terms: D004279:DNA, Viral / Q000737:chemistry / Q000378:metabolism*; D024202:Electrophoretic Mobility Shift Assay; D015497:HIV-1 / Q000235:genetics / Q000378:metabolism*; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D019590:Nucleocapsid Proteins / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding
chemical_list: D004279:DNA, Viral; D019590:Nucleocapsid Proteins