RNA Chemical Labeling with Site‐Specific, Relative Quantification by Mass Spectrometry for the Structural Study of a Neomycin‐Sensing Riboswitch Aptamer Domain
Sign Up to like & getrecommendations! Published in 2022 at "Chempluschem"
DOI: 10.1002/cplu.202200256
Abstract: Abstract High‐resolution mass spectrometry was used for the label‐free, direct localization and relative quantification of CMC+‐modifications of a neomycin‐sensing riboswitch aptamer domain in the absence and presence of the aminoglycoside ligands neomycin B, ribostamycin, and… read more here.
Keywords: mass spectrometry; relative quantification; riboswitch; neomycin sensing ... See more keywords
Dual genetic selection of the theophylline riboswitch with altered aptamer specificity for caffeine.
Sign Up to like & getrecommendations! Published in 2021 at "Biochemical and biophysical research communications"
DOI: 10.1016/j.bbrc.2021.09.058
Abstract: The aptamer domain of the theophylline riboswitch was randomized to generate a library containing millions of different variants. Dual genetic selection utilizing the cat-upp fusion gene was performed for the library, which successfully led to… read more here.
Keywords: caffeine; genetic selection; theophylline riboswitch; dual genetic ... See more keywords
Genetic regulation mechanism of the yjdF riboswitch.
Sign Up to like & getrecommendations! Published in 2018 at "Journal of theoretical biology"
DOI: 10.1016/j.jtbi.2017.12.007
Abstract: The yjdF riboswitch resides in potential 5' UTRs of homologues of protein-coding gene yjdF in Firmicutes. Unlike other 30 riboswitch classes previously validated, this riboswitch class, can sense and bind to a broad collection of… read more here.
Keywords: transcription; yjdf riboswitch; transcriptional folding; ligand ... See more keywords
Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class.
Sign Up to like & getrecommendations! Published in 2017 at "Molecular cell"
DOI: 10.1016/j.molcel.2016.11.019
Abstract: The guanidyl moiety is a component of fundamental metabolites, including the amino acid arginine, the energy carrier creatine, and the nucleobase guanine. Curiously, reports regarding the importance of free guanidine in biology are sparse, and… read more here.
Keywords: guanidine; bacteria regulated; guanidine bacteria; metabolism free ... See more keywords
Coupling Green Fluorescent Protein Expression with Chemical Modification to Probe Functionally Relevant Riboswitch Conformations in Live Bacteria.
Sign Up to like & getrecommendations! Published in 2018 at "Biochemistry"
DOI: 10.1021/acs.biochem.8b00316
Abstract: Noncoding RNAs engage in numerous biological activities including gene regulation. To fully understand RNA function it is necessary to probe biologically relevant conformations in living cells. To address this challenge, we coupled RNA-mediated regulation of… read more here.
Keywords: green fluorescent; fluorescent protein; chemical modification; preq1 ... See more keywords
Broad-Spectrum Detection of Tetracyclines by Riboswitch-Based Cell-Free Expression Biosensing.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of agricultural and food chemistry"
DOI: 10.1021/acs.jafc.3c02137
Abstract: We describe a sensitive and selective method for the determination of tetracycline content in foods using a riboswitch sensor. The sensor is based on a cell-free expression system that can be lyophilized to produce paper-based… read more here.
Keywords: cell free; expression; detection; riboswitch ... See more keywords
Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery.
Sign Up to like & getrecommendations! Published in 2022 at "ACS chemical biology"
DOI: 10.1021/acschembio.1c00880
Abstract: RNA molecules can show high levels of cooperativity in their global folding and interactions with divalent ions. However, cooperativity at individual ligand-RNA interaction sites remains poorly understood. Here, we investigated the binding of thiamine and… read more here.
Keywords: fragment linking; cooperativity; mdp; rna ... See more keywords
Affinity-Based Profiling of the Flavin Mononucleotide Riboswitch
Sign Up to like & getrecommendations! Published in 2022 at "Journal of the American Chemical Society"
DOI: 10.1021/jacs.2c02685
Abstract: Riboswitches are structural RNA elements that control gene expression. These naturally occurring RNA sensors are of continued interest as antibiotic targets, molecular sensors, and functional elements of synthetic circuits. Here, we describe affinity-based profiling of… read more here.
Keywords: fmn riboswitch; riboswitch; affinity based; based profiling ... See more keywords
Synthesis of All Possible Canonical (3'-5'-Linked) Cyclic Dinucleotides and Evaluation of Riboswitch Interactions and Immune-Stimulatory Effects.
Sign Up to like & getrecommendations! Published in 2017 at "Journal of the American Chemical Society"
DOI: 10.1021/jacs.7b06141
Abstract: The cyclic dinucleotides (CDNs) c-di-GMP, c-di-AMP, and c-AMP-GMP are widely utilized as second messengers in bacteria, where they signal lifestyle changes such as motility and biofilm formation, cell wall and membrane homeostasis, virulence, and exo-electrogenesis.… read more here.
Keywords: cyclic dinucleotides; immune stimulatory; synthesis possible; possible canonical ... See more keywords
Single-molecule analysis reveals multi-state folding of a guanine riboswitch.
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DOI: 10.1038/nchembio.2252
Abstract: Guanine-responsive riboswitches undergo ligand-dependent structural rearrangements to control gene expression by transcription termination. While the molecular basis for ligand recognition is well established, the associated structural rearrangements and the kinetics involved in the formation of… read more here.
Keywords: state; guanine; single molecule; molecule analysis ... See more keywords
Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation
Sign Up to like & getrecommendations! Published in 2017 at "Nature Communications"
DOI: 10.1038/ncomms13892
Abstract: On the basis of nascent transcript sequencing, it has been postulated but never demonstrated that transcriptional pausing at translation start sites is important for gene regulation. Here we show that the Escherichia coli thiamin pyrophosphate… read more here.
Keywords: pausing; site; translation; transcriptional pausing ... See more keywords