Experimentally Derived Nearest-Neighbor Parameters for the Stability of RNA Three- and Four-Way Multibranch Loops
- 19 December 2001
- journal article
- research article
- Published by American Chemical Society (ACS) in Biochemistry
- Vol. 41 (3) , 869-880
- https://doi.org/10.1021/bi011441d
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.Keywords
This publication has 12 references indexed in Scilit:
- Comparative and functional anatomy of group II catalytic introns — a reviewPublished by Elsevier ,2003
- Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAsJournal of Molecular Biology, 1999
- Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structureJournal of Molecular Biology, 1999
- A dynamic programming algorithm for RNA structure prediction including pseudoknots 1 1Edited by I. TinocoJournal of Molecular Biology, 1999
- A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAsJournal of Molecular Biology, 1998
- Comprehensive Comparison of Structural Characteristics in Eukaryotic Cytoplasmic Large Subunit (23 S-like) Ribosomal RNAJournal of Molecular Biology, 1996
- The Computer Simulation of RNA Folding Pathways Using a Genetic AlgorithmJournal of Molecular Biology, 1995
- Conformation of the Central, Three-helix Junction of the 5 S Ribosomal RNA of Sulfolobus acidocaldariusJournal of Molecular Biology, 1994
- Thermodynamics of base interaction in (A)n and (A·U)nJournal of Molecular Biology, 1978
- The Heat of the Reaction between Polyriboadenylic Acid and Polyribouridylic AcidJournal of the American Chemical Society, 1963