title: Conversion of stable RNA hairpin to a metastable dimer in frozen solution.
abstract: Previous studies employing a 79-nucleotide (nt) RNA indicated that this RNA could form two bands in a native polyacrylamide gel while one band was observed in a denaturing gel. This report describes an investigation on the nature of the two corresponding structures and the segment responsible for forming the slower mobility band. Sedimentation equilibrium of the 79-nt RNA was consistent with the two gel bands corresponding to monomer and dimer forms. The portion of the RNA required for dimer formation was explored using a secondary structure prediction algorithm of two 79-nt RNAs linked in a head-to-tail fashion. The predicted structure suggested that the first 21-nt at the 5' end of each RNA formed a self-complementary duplex. A ribonuclease H assay carried out with RNA prepared as monomer (M), or a mixture of monomer and dimer (M/D), gave results consistent with the predicted M and D structures. Gel mobility experiments on 5' and 3' segments of the 79-nt RNA also indicated that dimer formation was due to the 21-nt 5' end. Studies on the 21-nt RNA molecule and sequence variants showed that this sequence can form a hairpin and a dimer complex. Unexpectedly, the hairpin to dimer conversion was shown to occur at high efficiency in frozen solution, although little or no conversion was observed above 0 degrees C. The results indicate that a freezing environment can promote formation of intermolecular RNA complexes from stable RNA hairpins, supporting the notion that this environment could have played a role in the evolution of RNA complexity.
authors.affiliation: School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
authors.forename: Xueguang
authors.initials: X
authors.lastname: Sun
authors.forename: J Michael
authors.initials: JM
authors.lastname: Li
authors.forename: Roger M
authors.initials: RM
authors.lastname: Wartell
mesh_terms: D001483:Base Sequence; D019281:Dimerization; D004355:Drug Stability; D005615:Freezing; D014644:Genetic Variation; D007700:Kinetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics* / Q000302:isolation & purification; D012996:Solutions; D014158:Transcription, Genetic
chemical_list: D012996:Solutions; D012313:RNA