RNA Secondary Structure Analysis Using RNAstructure

Sara E Ali; Abhinav Mittal; David H Mathews

doi:10.1002/cpz1.846

RNA Secondary Structure Analysis Using RNAstructure

Curr Protoc. 2023 Jul;3(7):e846. doi: 10.1002/cpz1.846.

Authors

Sara E Ali¹, Abhinav Mittal¹, David H Mathews¹

Affiliation

¹ Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York.

PMID: 37487054
DOI: 10.1002/cpz1.846

Abstract

RNAstructure is a user-friendly program for the prediction and analysis of RNA secondary structure. It is available as a web server, a program with a graphical user interface, or a set of command line tools. The programs are available for Microsoft Windows, macOS, or Linux. This article provides protocols for prediction of RNA secondary structure (using the web server, the graphical user interface, or the command line) and high-affinity oligonucleotide binding sites to a structured RNA target (using the graphical user interface). © 2023 Wiley Periodicals LLC. Basic Protocol 1: Predicting RNA secondary structure using the RNAstructure web server Alternate Protocol 1: Predicting secondary structure and base pair probabilities using the RNAstructure graphical user interface Alternate Protocol 2: Predicting secondary structure and base pair probabilities using the RNAstructure command line interface Basic Protocol 2: Predicting binding affinities of oligonucleotides complementary to an RNA target using OligoWalk.

Keywords: RNA secondary structure prediction; free energy minimization; oligonucleotide binding affinity; thermodynamics.

MeSH terms

Binding Sites
Oligonucleotides*
Probability
Protein Structure, Secondary
RNA*

Substances

Oligonucleotides
RNA