Search

Your search keyword '"Soulière, Marie F."' showing total 17 results
Start Over Author "Soulière, Marie F."
17 results on '"Soulière, Marie F."'

5. Tuning a riboswitch response through structural extension of a pseudoknot

Author

Soulière, Marie F., Altman, Roger B., Schwarz, Veronika, Haller, Andrea, Blanchard, Scott C., and Micura, Ronald

Subjects
RNA Folding, PNAS Plus, Riboswitch, Mutation, Temperature, Nucleic Acid Conformation, RNA
Abstract

Structural and dynamic features of RNA folding landscapes represent critical aspects of RNA function in the cell and are particularly central to riboswitch-mediated control of gene expression. Here, using single-molecule fluorescence energy transfer imaging, we explore the folding dynamics of the preQ1 class II riboswitch, an upstream mRNA element that regulates downstream encoded modification enzymes of queuosine biosynthesis. For reasons that are not presently understood, the classical pseudoknot fold of this system harbors an extra stem-loop structure within its 3'-terminal region immediately upstream of the Shine-Dalgarno sequence that contributes to formation of the ligand-bound state. By imaging ligand-dependent preQ1 riboswitch folding from multiple structural perspectives, we reveal that the extra stem-loop strongly influences pseudoknot dynamics in a manner that decreases its propensity to spontaneously fold and increases its responsiveness to ligand binding. We conclude that the extra stem-loop sensitizes this RNA to broaden the dynamic range of the ON/OFF regulatory switch.

Published
2013

16. Use of SHAPE to select 2AP substitution sites for RNA-ligand interactions and dynamics studies.

Author

Soulière MF and Micura R

Subjects
Acylation, Hydroxyl Radical chemistry, Ligands, Molecular Biology methods, RNA metabolism, Nucleic Acid Conformation, RNA chemistry, RNA Folding
Abstract

Most regulatory RNA molecules must adopt a precise secondary fold and tertiary structure to allow their function in cells. A number of experimental approaches, such as the 2-Aminopurine-Based RNA Folding Analysis (2ApFold), have therefore been developed to offer insights into the folding and folding dynamics of RNA. A crucial requirement for this method is the selection of proper 2AP labeling positions. In that regard, we recently discovered that Selective 2'-Hydroxyl Acylation analyzed by Primer Extension (SHAPE) offers a reliable path to identify appropriate nucleotides for 2AP substitution on a target RNA. This chapter describes the straightforward procedure to select 2AP substitution sites in RNA molecules using SHAPE probing. The protocols detail the preparation of the target RNA by transcription, and the SHAPE steps including (1) probing of the RNA, (2) reverse transcription with a radiolabeled primer, (3) sequencing gel, and (4) analysis of the obtained band pattern.

Published
2014
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results