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Methods Mol Biol. 2008;419:53-67. doi: 10.1007/978-1-59745-033-1_4.

In-line probing analysis of riboswitches.

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Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA.


Riboswitches are intricate, metabolite-binding RNA structures found in the non-coding regions of mRNA. Allosteric changes in the riboswitch that are induced by metabolite binding are harnessed to control the genes of a variety of essential metabolic pathways in eubacteria and in some eukaryotes. In this chapter, we describe an RNA structure analysis technique called "in-line probing." This assay makes use of the natural instability of RNA to elucidate secondary structure characteristics and ligand-binding capabilities of riboswitches in an entirely protein-free manner. Although this method has most frequently been used to examine riboswitches, the structures of any RNAs can be examined using this technique.

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