In-line probing analysis of riboswitches.
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.
Regulski
Elizabeth E
EE
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA.
Breaker
Ronald R
RR
D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D017931:DNA Primers / Q000235:genetics; D004591:Electrophoresis, Polyacrylamide Gel; D008024:Ligands; D015336:Molecular Probe Techniques; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020871:RNA Stability; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D014158:Transcription, Genetic
D017931:DNA Primers; D008024:Ligands; D012329:RNA, Bacterial; D022661:RNA, Untranslated