RNA molecules are important players in all domains of life. The study of the relationship between their multiple flexible states and the associated biological roles has increased in recent years.
For several decades, chemical and enzymatic structural probing experiments have been used to determine RNA structure. During this time, there has been a steady improvement in reagents and experimental methods. While early experiments were carried out on single RNA molecules using radioactive labeling and polyacrylamide gel electrophoresis as read-out methods, recent advances in structural probes, sequencing and computer power now permit RNA structure to be determined in vitro or in cells on a genome-wide scale.
The technical aspects of different probing methods developed over the last 40 years are discussed by Elodie Mailler, Jean-Christophe Paillart, Roland Marquet, Redmond P. Smyth and Valerie Vivet-Boudou in WIREs RNA. The discussion goes from the initial probe choice to the challenges associated with the computational analysis of structural probing data. By discussing the underlying fields of application of each technique, as well as their biases and potential pitfalls, the review guides users and helps them to find the best method for their special biological study.
Kindly contributed by the authors.