Improving RNA nearest neighbor parameters for helices by going beyond the two-state model.

ABSTRACT: RNA folding free energy change nearest neighbor parameters are widely used to predict folding stabilities of secondary structures. They were determined by linear regression to datasets of optical melting experiments on small model systems. Traditionally, the optical melting experiments are analyzed assuming a two-state model, i.e. a structure is either complete or denatured. Experimental evidence, however, shows that structures exist in an ensemble of conformations. Partition functions calculated with existing nearest neighbor parameters predict that secondary structures can be partially denatured, which also directly conflicts with the two-state model. Here, a new approach for determining RNA nearest neighbor parameters is presented. Available optical melting data for 34 Watson-Crick heli

SUBMITTER: Spasic A 

PROVIDER: S-EPMC6007268 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature