Titlebook: Riboswitches; Methods and Protocol Alexander Serganov Book 2009 The Editor(s) (if applicable) and The Author(s), under exclusive license to

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,Application of Fluorescent Measurements for Characterization of Riboswitch–Ligand Interactions,ription, translation, splicing, and mRNA degradation. Because riboswitches exhibit relatively complex structures, they are able to form highly complex ligand-binding sites, which enable the specific recognition of target metabolites in a complex cellular environment. Practically in all studied cases

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Time-Resolved NMR Spectroscopy: Ligand-Induced Refolding of Riboswitches,MR spectroscopy uniquely allows determination of static and dynamic processes at atomic level, including structured states often represented by a single state as well as by unstructured conformational ensembles. While a high-resolution description of structured states may also be obtained by other t

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Analysis of the RNA Backbone: Structural Analysis of Riboswitches by In-Line Probing and Selective rrangements and tertiary base interactions. Therefore, rapid and comprehensive methods for assessing RNA structure are highly desirable. Computational tools are oftentimes employed for prediction of secondary structure. However, a greater degree of accuracy is achieved when these methods are combine

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,Identification of Metabolite–Riboswitch Interactions Using Nucleotide Analog Interference Mapping a, the . riboswitch, is unique among riboswitches in that it modulates gene expression by undergoing self-cleavage in the presence of its metabolite glucosamine-6-phosphate (GlcN6P). In order to investigate the interactions between the . RNA and GlcN6P we performed nucleotide analog interference mapp

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Structural Probing of RNA Thermosensors,efined experimental conditions. The method monitors the sensitivity of each nucleotide to various chemicals, which reflects its hydrogen-bonding environment within the RNA molecule. The goal of this chapter is to provide the reader with an experimental guide to mapping the secondary structure of RNA