“…The regulation mechanism of thiamin biosynthesis by ThDP riboswitch is also discussed. As drug targets of existing antimicrobial compound pyrithiamin, the ThDP riboswitch might serves as alternative targets for more antibiotics.…”
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“…We predicted six to be riboswitches, which are mRNA elements that regulate gene expression on binding a specific metabolite. …”
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“…One type of c-di-GMP receptor is the class I riboswitch, representatives of which have been shown to bind c-di-GMP in vitro. …”
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“…We observe a dynamic change of the SAM-I riboswitch conformations depending on its binding partners. …”
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“…Moreover, we address a riboswitch design problem by applying StreAM-[Formula: see text] on six long term molecular dynamics simulation of a synthetic tetracycline dependent riboswitch (500 ns) in combination with five different antibiotics. …”
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“…Among the most common groups of ncRNAs in bacteria are riboswitches. These cis-regulatory, metabolite-binding RNAs are present in many species where they regulate various metabolic and signaling pathways. …”
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“…The different multi-layer control systems combine a promoter–operator system on a transcriptional level with a riboswitch for translational control. Additionally, replicational control is ensured by using a strain that reduces the plasmid copy number. …”
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“…Structures of riboswitch receptor domains bound to their effector have revealed how mRNAs recognize diverse small molecules, but mechanistic details into its linkage with regulation of gene expression remain elusive(1,2). …”
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“…We identified fragments and cooperatively binding fragment pairs that bind to the thiamine pyrophosphate (TPP) riboswitch with millimolar to micromolar affinities. …”
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“…We validated TECprobe-ML by replicating and extending previous analyses of ZTP and fluoride riboswitch folding, and mapped the folding pathway of a ppGpp-sensing riboswitch. …”
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“…Genome analysis found that sYJ5 and sYJ118 mapped between the 16S and 23S rRNA encoding genes. sYJ20 (also known as SroA) is encoded upstream of the tbpAyabKyabJ operon and is classed as a riboswitch, whilst its role in antibiotic stress-response appears independent of its riboswitch function. sYJ75 is encoded between genes that are involved in enterobactin transport and metabolism. …”
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“…Here, we study the PreQ(1) riboswitch system, assessing sixteen diverse PreQ(1)-derived probes for their ability to selectively modify the class-I PreQ(1) riboswitch aptamer covalently. …”
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“…For certain RNAs (e.g. riboswitches), a single sequence must adopt at least two alternative secondary structures to effectively regulate the message. …”
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“…A computer program written to examine relative helical orientation identified the three-way junction of the Arabidopsis TPP riboswitch as an elaborated k-turn. The Escherichia coli TPP riboswitch contains a related k-junction, and analysis of >11 000 sequences shows that the structure is common to these riboswitches. …”
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“…This hybrid ‘Ribosolve’ pipeline detects and falsifies homologies and conformational rearrangements in eleven previously unknown 119- to 338-nucleotide protein-free RNA structures: full-length Tetrahymena ribozyme, hc16 ligase with and without substrate, full-length V. cholerae and F. nucleatum glycine riboswitch aptamers with and without glycine, Mycobacterium SAM-IV riboswitch with and without S-adenosylmethionine, and computer-designed ATP-TTR-3 aptamer with and without AMP. …”
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“…Riboswitch aptamers adopt diverse and complex tertiary structural folds that contain both single-stranded and double-stranded regions. …”
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“…Landscape analysis reveals that kanamycin B stabilizes a non-native, idiosyncratic conformation of the riboswitch that inhibits c-di-GMP binding. This demonstrates that allosteric control of folding, rather than direct competition with cognate effectors, is a viable approach for pharmacologically targeting riboswitches and other structured RNA molecules.…”
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“…To fill this gap, we used in vitro selection to isolate a novel riboswitch that selectively binds the trans isoform of a stiff-stilbene (amino-tSS)–a rapidly and reversibly photoisomerizing small molecule. …”
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“…The magnetically aligned polymer-nanodiscs were used as an alignment medium to measure RDCs from a (13)C/(15)N-labeled fluoride riboswitch aptamer using 2D ARTSY-HSQC NMR experiments. …”
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“…MiR-122 has at least three roles in the HCV life cycle: it acts as an RNA chaperone, or ‘riboswitch’, allowing formation of the viral internal ribosomal entry site; it provides genome stability; and promotes viral translation. …”
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