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Ligand binding to a riboswitch is not dependant on protein intermediates.
The reason this result is important is that the structural change caused by ligand binding to a Riboswitch is sufficient to regulate gene expression [ 37, 45, 46].
As translating ribosomes can protect mRNA species from decay, when translation is inhibited by ligand binding to a riboswitch, an indirect consequence is mRNA degradation as hypothesized for the thiM and btuB riboswitches [ 94].
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RNA conformational changes induced by ligand binding to riboswitches have biologically important consequences (2− 4).
A riboswitch has been reported in plants and fungi that bind to TPP TPPP riboswitch) [ 53].
Motif M3 was found to be a part of aptamer structure (the region binding to small molecules) of FMN riboswitches [ 38, 39].
We have developed a fluorescence binding assay for SAM-II riboswitch aptamer and identified an S-adenosylmethionine (SAM) analogue that selectively binds to SAM-II riboswitch aptamer with comparable binding affinity to its native metabolite using structure-based design approach.
First, riboswitch binding to ligand depends on the local ions and their concentrations.
We are currently investigating whether BTH_s13 and BTH_s19 can function as riboswitches via binding to specific metabolites or secondary messengers to protect bacteria from accumulation of cytotoxic transcripts [ 23].
To analyze ligand binding to the Vc2 aptamer, we constructed a 96-plex 20%T3.3%3% C fsPAG for high-throughput riboswitch fsPAG-EMSAs.
Riboswitches change their state upon chemical binding to their aptamers.
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