Multistrand Structure Prediction of Nucleic Acid Assemblies and Design of RNA Switches.

ABSTRACT: RNA is an attractive material for the creation of molecular logic gates that release programmed functionalities only in the presence of specific molecular interaction partners. Here we present HyperFold, a multistrand RNA/DNA structure prediction approach for predicting nucleic acid complexes that can contain pseudoknots. We show that HyperFold also performs competitively compared to other published folding algorithms. We performed a large variety of RNA/DNA hybrid reassociation experiments for different concentrations, DNA toehold lengths, and G+C content and find that the observed tendencies for reassociation correspond well to computational predictions. Importantly, we apply this method to the design and experimental verification of a two-stranded RNA molecular switch that upon binding

SUBMITTER: Bindewald E 

PROVIDER: S-EPMC6319913 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature