RNA Secondary Structure Analysis Using RNAstructure

• Published in: Current protocols Vol. 3; no. 7; p. e846
• Main Authors: Ali, Sara E, Mittal, Abhinav, Mathews, David H
• Format: Journal Article
• Language: English
• Published: United States 01.07.2023
• Subjects: Binding Sites; Oligonucleotides; Probability; Protein Structure, Secondary; RNA; thermodynamics; oligonucleotide binding affinity; RNA secondary structure prediction; free energy minimization
• ISSN: 2691-1299
• DOI: 10.1002/cpz1.846

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.