Abstract
RNA molecules are key players in a variety of biological events, and this is particularly true for viral RNAs. To better understand the replication of those pathogens and try to block them, special attention has been paid to the structure of their RNAs. Methods to probe RNA structures have been developed since the 1960s; even if they have evolved over the years, they are still in use today and provide useful information on the folding of RNA molecules, including viral RNAs. The aim of this review is to offer a historical perspective on the structural probing methods used to decipher RNA structures before the development of the selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) methodology and to show how they have influenced the current probing techniques. Actually, these technological breakthroughs, which involved advanced detection methods, were made possible thanks to the development of next-generation sequencing (NGS) but also to the previous works accumulated in the field of structural RNA biology. Finally, we will also discuss how high-throughput SHAPE (hSHAPE) paved the way for the development of sophisticated RNA structural techniques.
Highlights
The aim of this review is to offer a historical perspective on the structural probing methods used to decipher RNA structures before the development of the high-throughput selective 20 -hydroxyl acylation analyzed via the primer extension methodology, discussing examples taken from the world of viruses and how they have influenced the probing techniques since 2005
Research on enzymatic and chemical probes in the second half of the last century has led, in barely 20 years, to the creation of a toolbox of probes that complement each other and that have allowed for the identification of many RNAs structures, as well as ligand-binding sites
In 2005, these shortcomings were addressed with the development of a new class of chemical probes targeting the sugar 20 -OH, regardless of the nature of the base and, later, the use of fluorescent primers and analysis of the cDNAs by capillary electrophoresis
Summary
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. By the second half of the 20th century, methods to probe the structure of RNA in solution were developed; even if these techniques have evolved over the years, they are still in use today and provide useful information on the folding of RNA molecules, including vRNAs. The aim of this review is to offer a historical perspective on the structural probing methods used to decipher RNA structures before the development of the high-throughput selective 20 -hydroxyl acylation analyzed via the primer extension (hSHAPE) methodology, discussing examples taken from the world of viruses and how they have influenced the probing techniques since 2005. Nowadays, we have numerous sophisticated tools to assess RNA structure in vitro, in cellula, and even in viro, either alone or in complex with various macromolecules These technological breakthroughs using enzymatic and chemical probes, which are detected through advanced methods [8], were made possible thanks to next-generation sequencing (NGS) approaches and to the previous works accumulated in the field of structural RNA biology [9]. The crosslinking-based structural methods, which have been developed recently and are complementary to the RNA probing methods, are not reviewed here (for recent reviews of these techniques, see [10,11,12])
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
