title: Characterization of a "kissing" hairpin complex derived from the human immunodeficiency virus genome.
abstract: Base-pair formation between two hairpin loops--a "kissing" complex--is an RNA-folding motif that links two elements of RNA secondary structure. It is also a unique protein recognition site involved in regulation of ColE1 plasmid DNA replication. The trans-activation response element (TAR), a hairpin and bulge at the 5' end of the untranslated leader region of the human immunodeficiency virus 1 mRNA, enhances the transcription of the virus and is necessary for viral replication. Gel electrophoresis and absorbance melting curves indicate that a synthesized RNA hairpin (Tar*-16) with a loop sequence complementary to the TAR loop sequence (CUGGGA) associates specifically with a 16-nucleotide TAR hairpin (Tar-16) to form a stable complex. RNase T1 probing indicates that the three guanines in the Tar-16 loop become inaccessible in the complex. NMR imino proton spectra reveal that 5 base pairs are formed between the two hairpin loops (Tar-16 and Tar*-16); only the adenine at the 3' terminus of the TAR loop does not form a base pair with the 5'-terminal uracil of the complementary loop. A 14-nucleotide hairpin [CCUA(UCCCAG)UAGG] with a loop sequence complementary to the TAR loop is conserved within the gag gene of human immunodeficiency virus 1. A synthesized RNA hairpin corresponding to this conserved sequence also binds to the Tar-16 hairpin with high affinity. It is possible that the same RNA loop-loop interaction occurs during the viral life cycle.
authors.affiliation: Department of Chemistry, University of California, Berkeley 94720.
authors.forename: K Y
authors.initials: KY
authors.lastname: Chang
authors.forename: I
authors.initials: I
authors.lastname: Tinoco
mesh_terms: D001483:Base Sequence; D015497:HIV-1 / Q000648:ultrastructure*; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000648:ultrastructure*; D012045:Regulatory Sequences, Nucleic Acid
chemical_list: D012367:RNA, Viral