title: Regulation of primate lentiviral RNA dimerization by structural entrapment.
abstract: BACKGROUND
  Genomic RNA dimerization is an important process in the formation of an infectious lentiviral particle. One of the signals involved is the stem-loop 1 (SL1) element located in the leader region of lentiviral genomic RNAs which also plays a role in encapsidation and reverse transcription. Recent studies revealed that HIV types 1 and 2 leader RNAs adopt different conformations that influence the presentation of RNA signals such as SL1. To determine whether common mechanisms of SL1 regulation exist among divergent lentiviral leader RNAs, here we compare the dimerization properties of SIVmac239, HIV-1, and HIV-2 leader RNA fragments using homologous constructs and experimental conditions. Prior studies from several groups have employed a variety of constructs and experimental conditions.
  
  
  RESULTS
  Although some idiosyncratic differences in the dimerization details were observed, we find unifying principles in the regulation strategies of the three viral RNAs through long- and short-range base pairing interactions. Presentation and efficacy of dimerization through SL1 depends strongly upon the formation or dissolution of the lower stem of SL1 called stem B. SL1 usage may also be down-regulated by long-range interactions involving sequences between SL1 and the first codons of the gag gene.
  
  
  CONCLUSIONS
  Despite their sequence differences, all three lentiviral RNAs tested in this study showed a local regulation of dimerization through the stabilization of SL1.
authors.affiliation: Division of Biological Sciences, The University of Montana, Missoula, MT, 59812, USA. tayyba.baig@umontana.edu
authors.forename: Tayyba T
authors.initials: TT
authors.lastname: Baig
authors.forename: Christy L
authors.initials: CL
authors.lastname: Strong
authors.forename: J Stephen
authors.initials: JS
authors.lastname: Lodmell
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Lanchy
mesh_terms: D000818:Animals; D020029:Base Pairing; D001483:Base Sequence; D019281:Dimerization; D015497:HIV-1 / Q000235:genetics / Q000378:metabolism; D015498:HIV-2 / Q000235:genetics / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D017958:Lentiviruses, Primate / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016376:Oligonucleotides, Antisense; D020038:RNA, Spliced Leader / Q000737:chemistry* / Q000235:genetics*; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D015302:Simian Immunodeficiency Virus / Q000235:genetics / Q000378:metabolism
chemical_list: D016376:Oligonucleotides, Antisense; D020038:RNA, Spliced Leader; D012367:RNA, Viral