title: Thermodynamics of three-way multibranch loops in RNA.
abstract: RNA multibranch loops (junctions) are loops from which three or more helices exit. They are nearly ubiquitous in RNA secondary structures determined by comparative sequence analysis. In this study, systems in which two strands combine to form three-way junctions were used to measure the stabilities of RNA multibranch loops by UV optical melting and isothermal titration calorimetry (ITC). These data were used to calculate the free energy increment for initiation of a three-way junction on the basis of a nearest neighbor model for secondary structure stability. Imino proton NMR spectra were also measured for two systems and are consistent with the hypothesized helical structures. Incorporation of the experimental data into the mfold and RNA structure computer programs has contributed to an improvement in prediction of RNA secondary structure from sequence.
authors.affiliation: Department of Chemistry, University of Rochester, RC Box 270216, Rochester, New York 14627-0216, USA.
authors.forename: J M
authors.initials: JM
authors.lastname: Diamond
authors.forename: D H
authors.initials: DH
authors.lastname: Turner
authors.forename: D H
authors.initials: DH
authors.lastname: Mathews
mesh_terms: D017123:Bacteriophage T7 / Q000201:enzymology; D002151:Calorimetry; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D008274:Magnesium / Q000737:chemistry; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009841:Oligonucleotides / Q000737:chemistry; D012313:RNA / Q000138:chemical synthesis / Q000737:chemistry* / Q000235:genetics; D012341:RNA, Ribosomal, 5S / Q000737:chemistry; D013698:Templates, Genetic; D013816:Thermodynamics; D014764:Viral Proteins
chemical_list: D009841:Oligonucleotides; D012341:RNA, Ribosomal, 5S; D014764:Viral Proteins; D012313:RNA; C062210:bacteriophage T7 RNA polymerase; D012321:DNA-Directed RNA Polymerases; D008274:Magnesium