title: Pre-organized structure of viral DNA at the binding-processing site of HIV-1 integrase.
abstract: The integration of the human immunodeficiency virus type 1 DNA into the host cell genome is catalysed by the viral integrase (IN). The reaction consists of a 3'-processing [dinucleotide released from each 3' end of the viral long terminal repeat (LTR)] followed by a strand transfer (insertion of the viral genome into the human chromosome). A 17 base pair oligonucleotide d(GGAAAATCTCTAGCAGT), d(ACTGCTAGAGATTTTCC) reproducing the U5-LTR extremity of viral DNA that contains the IN attachment site was analysed by NMR using the classical NOEs and scalar coupling constants in conjunction with a small set of residual dipolar coupling constants (RDCs) measured at the 13C/15N natural abundance. The combination of these two types of parameters in calculations significantly improved the DNA structure determination. The well-known features of A-tracts were clearly identified by RDCs in the first part of the molecule. The binding/cleavage site at the viral DNA end is distinguishable by a loss of regular base stacking and a distorted minor groove that can aid its specific recognition by IN.
authors.affiliation: Centre National de la Recherche Scientifique Unité Mixte de Recherche 8113, Laboratoire de Biotechnologies et Pharmacologie génétique Appliquée, Ecole Normale Supérieure de Cachan 94235 Cachan, France.
authors.forename: Jean-Guillaume
authors.initials: JG
authors.lastname: Renisio
authors.forename: Sylvain
authors.initials: S
authors.lastname: Cosquer
authors.forename: Ilham
authors.initials: I
authors.lastname: Cherrak
authors.forename: Saïd
authors.initials: S
authors.lastname: El Antri
authors.forename: Olivier
authors.initials: O
authors.lastname: Mauffret
authors.forename: Serge
authors.initials: S
authors.lastname: Fermandjian
mesh_terms: D001665:Binding Sites; D004279:DNA, Viral / Q000737:chemistry* / Q000378:metabolism; D019427:HIV Integrase / Q000378:metabolism*; D016325:HIV Long Terminal Repeat; D015497:HIV-1 / Q000201:enzymology / Q000235:genetics*; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D016662:Virus Integration
chemical_list: D004279:DNA, Viral; D019427:HIV Integrase