title: The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges.
abstract: BACKGROUND
  An important step in retroviral replication is dimerization of the genomic RNA prior to encapsidation. Dimerization is initiated by the formation of a transient 'kissing-loop complex' that is thought to be subsequently matured into an extended duplex by the nucleocapsid protein (NCp). Although chemical probing and nuclear magnetic resonance spectroscopy have provided insight into the structure of the kissing-loop structure, no structural information concerning the extended-duplex state is available so far.
  
  
  RESULTS
  The structure of a minimal HIV-1 RNA dimerization initiation site has been solved at 2.3 A resolution in two different space groups. It reveals a 22 base pair extended duplex with two noncanonical Watson-Crick-like G-A mismatches, each adjacent to a bulged-out adenine. The structure shows significant asymmetry in deep groove width and G-A base-pair conformations. A network of eight magnesium cations was clearly identified, one being unusually chelated by the 3' phosphate of each bulge across an extremely narrowed deep major groove.
  
  
  CONCLUSIONS
  These crystal structures represent the putative matured form of the initial kissing-loop complex. They show the ability of this self-complementary RNA hairpin loop to acquire a more stable extended duplex structure. Both bulged adenines form a striking 'base grip' that could be a recognition signal, either in cis for another viral RNA sequence, or in trans for a protein, possibly the NCp. Magnesium binding might be important to promote and stabilize the observed extrahelical conformation of these bulges.
authors.affiliation: UPR9002 - Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg cedex, F-67084, France.
authors.forename: E
authors.initials: E
authors.lastname: Ennifar
authors.forename: M
authors.initials: M
authors.lastname: Yusupov
authors.forename: P
authors.initials: P
authors.lastname: Walter
authors.forename: R
authors.initials: R
authors.lastname: Marquet
authors.forename: B
authors.initials: B
authors.lastname: Ehresmann
authors.forename: C
authors.initials: C
authors.lastname: Ehresmann
authors.forename: P
authors.initials: P
authors.lastname: Dumas
mesh_terms: D000225:Adenine / Q000737:chemistry*; D020137:Base Pair Mismatch; D001483:Base Sequence; D018360:Crystallography, X-Ray; D019281:Dimerization; D015497:HIV-1 / Q000235:genetics*; D008274:Magnesium / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D008345:Manganese / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism
chemical_list: D012367:RNA, Viral; D008345:Manganese; D008274:Magnesium; D000225:Adenine