title: Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops.
abstract: Algorithms for predicting RNA secondary structure require approximations for the free energies of multibranch loops, also called junctions. The stabilities of 62 RNA duplexes with three- and four-way multibranch loops were determined by optical melting. To account for the observed sequence dependence, a revised loop free-energy approximation is proposed that accounts for the strain in three-way junctions with fewer than two unpaired nucleotides, penalizes asymmetry in the distribution of unpaired nucleotides, and gives a bonus for four-way loops relative to three-way loops. Parameters for this equation were determined by linear regression.
authors.affiliation: Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA.
authors.forename: David H
authors.initials: DH
authors.lastname: Mathews
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Turner
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D004355:Drug Stability; D007202:Indicators and Reagents; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009692:Nucleic Acid Heteroduplexes / Q000138:chemical synthesis; D012313:RNA / Q000138:chemical synthesis / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D007202:Indicators and Reagents; D009692:Nucleic Acid Heteroduplexes; D012313:RNA