Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops. |
| |
Authors: | David H Mathews Douglas H Turner |
| |
Institution: | Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA. |
| |
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: | |
|
|