A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control

EJ Strobel, L Cheng, KE Berman, PD Carlson… - Nature chemical …, 2019 - nature.com
Cotranscriptional folding is an obligate step of RNA biogenesis that can guide RNA structure
formation and function through transient intermediate folds. This process is particularly …

Real-time monitoring of single ZTP riboswitches reveals a complex and kinetically controlled decision landscape

B Hua, CP Jones, J Mitra, PJ Murray… - Nature …, 2020 - nature.com
RNAs begin to fold and function during transcription. Riboswitches undergo
cotranscriptional switching in the context of transcription elongation, RNA folding, and ligand …

Architectures and complex functions of tandem riboswitches

ME Sherlock, G Higgs, D Yu, DL Widner, NA White… - RNA biology, 2022 - Taylor & Francis
Riboswitch architectures that involve the binding of a single ligand to a single RNA aptamer
domain result in ordinary dose-response curves that require approximately a 100-fold …

Creating an in vivo bifunctional gene expression circuit through an aptamer-based regulatory mechanism for dynamic metabolic engineering in Bacillus subtilis

J Deng, C Chen, Y Gu, X Lv, Y Liu, J Li… - Metabolic …, 2019 - Elsevier
Aptamer-based regulatory biosensors can dynamically regulate the expression of target
genes in response to ligands and could be used in dynamic metabolic engineering for …

Translation regulation by a Guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity

CM Focht, DA Hiller, SG Grunseich, SA Strobel - Rna, 2023 - rnajournal.cshlp.org
Riboswitches function as important translational regulators in bacteria. Comprehensive
mutational analysis of transcriptional riboswitches has been used to probe the energetic …

Development and characterization of a glycine biosensor system for fine-tuned metabolic regulation in Escherichia coli

KQ Hong, J Zhang, B Jin, T Chen, ZW Wang - Microbial Cell Factories, 2022 - Springer
Background In vivo biosensors have a wide range of applications, ranging from the
detection of metabolites to the regulation of metabolic networks, providing versatile tools for …

Efficient quantitative monitoring of translational initiation by RelE cleavage

CM Focht, SA Strobel - Nucleic Acids Research, 2022 - academic.oup.com
The sequences of the 5′ untranslated regions (5′-UTRs) of mRNA alter gene expression
across domains of life. Transcriptional modulators can be easily assayed through …

Systematic evaluation of genetic and environmental factors affecting performance of translational riboswitches

R Kent, N Dixon - ACS synthetic biology, 2019 - ACS Publications
Since their discovery, riboswitches have been attractive tools for the user-controlled
regulation of gene expression in bacterial systems. Riboswitches facilitate small molecule …

The asymmetry and cooperativity of tandem glycine riboswitch aptamers

CD Torgerson, DA Hiller, SA Strobel - Rna, 2020 - rnajournal.cshlp.org
Glycine riboswitches utilize both single-and tandem-aptamer architectures. In the tandem
system, the relative contribution of each aptamer toward gene regulation is not well …

The Impact of Second-Shell Nucleotides on Ligand Specificity in Cyclic Dinucleotide Riboswitches

KM Barth, DA Hiller, SA Strobel - Biochemistry, 2024 - ACS Publications
Ligand specificity is an essential requirement for all riboswitches. Some variant riboswitches
utilize a common structural motif, yet through subtle sequence differences, they are able to …