title: Stabilities of HIV-1 DIS type RNA loop-loop interactions in vitro and in vivo.
abstract: RNA loop-loop interactions are a prevalent motif in the formation of tertiary structure and are well suited to trigger molecular recognition between RNA molecules. We determined the stabilities of several loop-loop interactions with a constant 6 bp core sequence and varying unpaired flanking nucleotides and found that the flanking bases have a strong influence on the stability and ion dependence of the kissing complex. In general, the stabilities determined in 1 M Na+ are equivalent to those in the presence of near physiological Mg2+ concentrations. Therefore we further tested whether the stabilities determined in vitro and within yeast cells correlate, using a recently developed yeast RNA-hybrid system. For the majority of the loop types analyzed here, the melting temperatures determined in vitro are in good agreement with the relative beta-galactosidase activity in yeast cells, showing that data derived from in vitro measurements reflect in vivo properties. The most stable interactions are the naturally occurring HIV-1 DIS MAL and LAI derived loops with the motif (5' A(A)/(G)N6A 3'), emphasizing the crucial role of stable kissing complexes in HIV genome dimerization.
authors.affiliation: Max F. Perutz Laboratories, Department of Biochemistry, University of Vienna, Dr Bohrgasse 9/5, A-1030 Vienna, Austria.
authors.forename: Christina
authors.initials: C
authors.lastname: Lorenz
authors.forename: Nicolas
authors.initials: N
authors.lastname: Piganeau
authors.forename: Renée
authors.initials: R
authors.lastname: Schroeder
mesh_terms: D020029:Base Pairing; D015497:HIV-1 / Q000235:genetics*; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009711:Nucleotides / Q000737:chemistry; D009994:Osmolar Concentration; D020871:RNA Stability; D012367:RNA, Viral / Q000737:chemistry*; D013056:Spectrophotometry, Ultraviolet; D013696:Temperature; D001616:beta-Galactosidase / Q000032:analysis
chemical_list: D009711:Nucleotides; D012367:RNA, Viral; D001616:beta-Galactosidase