title: The apical loop of the HIV-1 TAR RNA hairpin is stabilized by a cross-loop base pair.
abstract: The TAR hairpin of the HIV-1 RNA genome is indispensable for trans-activation of the viral promoter and virus replication. The TAR structure has been studied extensively, but most attention has been directed at the three-nucleotide bulge that constitutes the binding site of the viral Tat protein. In contrast, the conformational properties of the apical loop have remained elusive. We performed biochemical studies and molecular dynamics simulations, which indicate that the TAR loop is structured and stabilized by a cross-loop base pair between residues C30 and G34. Mutational disruption of the cross-loop base pair results in reduced Tat response of the LTR promoter, which can be rescued by compensatory mutations that restore the base pair. Thus, Tat-mediated transcriptional activation depends on the structure of the TAR apical loop. The C30-G34 cross-loop base pair classes TAR in a growing family of hairpins with a structured loop that was recently identified in ribosomal RNA, tRNA, and several viral and cellular mRNAs.
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznañ, Poland.
authors.forename: Tadeusz
authors.initials: T
authors.lastname: Kulinski
authors.forename: Mikolaj
authors.initials: M
authors.lastname: Olejniczak
authors.forename: Hendrik
authors.initials: H
authors.lastname: Huthoff
authors.forename: Lukasz
authors.initials: L
authors.lastname: Bielecki
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Pachulska-Wieczorek
authors.forename: Atze T
authors.initials: AT
authors.lastname: Das
authors.forename: Ben
authors.initials: B
authors.lastname: Berkhout
authors.forename: Ryszard W
authors.initials: RW
authors.lastname: Adamiak
mesh_terms: D015075:2-Aminopurine / Q000737:chemistry; D001483:Base Sequence; D016325:HIV Long Terminal Repeat; D015497:HIV-1 / Q000378:metabolism*; D008156:Luciferases / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry; D010802:Phylogeny; D010957:Plasmids / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012313:RNA / Q000378:metabolism; D012335:RNA, Ribosomal / Q000737:chemistry; D012343:RNA, Transfer / Q000737:chemistry; D013696:Temperature; D013816:Thermodynamics; D014158:Transcription, Genetic; D015533:Transcriptional Activation; D014162:Transfection; D014466:Ultraviolet Rays
chemical_list: D009843:Oligoribonucleotides; D012335:RNA, Ribosomal; D015075:2-Aminopurine; D012313:RNA; D012343:RNA, Transfer; D008156:Luciferases