Structural and dynamic characterization of the upper part of the HIV-1 cTAR DNA hairpin.
First strand transfer is essential for HIV-1 reverse transcription. During this step, the TAR RNA hairpin anneals to the cTAR DNA hairpin; this annealing reaction is promoted by the nucleocapsid protein and involves an initial loop-loop interaction between the apical loops of TAR and cTAR. Using NMR and probing methods, we investigated the structural and dynamic properties of the top half of the cTAR DNA (mini-cTAR). We show that the upper stem located between the apical and the internal loops is stable, but that the lower stem of mini-cTAR is unstable. The residues of the internal loop undergo slow motions at the NMR time-scale that are consistent with conformational exchange phenomena. In contrast, residues of the apical loop undergo fast motions. The lower stem is destabilized by the slow interconversion processes in the internal loop, and thus the internal loop is responsible for asymmetric destabilization of mini-cTAR. These findings are consistent with the functions of cTAR in first strand transfer: its apical loop is suitably exposed to interact with the apical loop of TAR RNA and its lower stem is significantly destabilized to facilitate the subsequent action of the nucleocapsid protein which promotes the annealing reaction.
Zargarian
Loussiné
L
Laboratoire de Biotechnologies et Pharmacologie génétique Appliquée (LBPA), UMR 8113 CNRS, Ecole Normale Supérieure de Cachan, 61 Avenue du Président Wilson, 94235 Cachan cedex, France.
Kanevsky
Igor
I
Bazzi
Ali
A
Boynard
Jonathan
J
Chaminade
Françoise
F
Fossé
Philippe
P
Mauffret
Olivier
O
D001483:Base Sequence; D002247:Carbon Isotopes; D018076:DNA, Complementary / Q000737:chemistry; D004279:DNA, Viral / Q000737:chemistry*; D016325:HIV Long Terminal Repeat; D015497:HIV-1 / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D010759:Phosphorus Isotopes
D002247:Carbon Isotopes; D018076:DNA, Complementary; D004279:DNA, Viral; D010759:Phosphorus Isotopes