Discovering riboswitches: the past and the future

K Kavita, RR Breaker - Trends in biochemical sciences, 2023 - cell.com
Riboswitches are structured noncoding RNA domains used by many bacteria to monitor the
concentrations of target ligands and regulate gene expression accordingly. In the past 20 …

Riboswitches: structures and mechanisms

AD Garst, AL Edwards… - Cold Spring Harbor …, 2011 - cshperspectives.cshlp.org
SUMMARY A critical feature of the hypothesized RNA world would have been the ability to
control chemical processes in response to environmental cues. Riboswitches present …

Repurposing an adenine riboswitch into a fluorogenic imaging and sensing tag

SK Dey, GS Filonov, AO Olarerin-George… - Nature chemical …, 2022 - nature.com
Fluorogenic RNA aptamers are used to genetically encode fluorescent RNA and to construct
RNA-based metabolite sensors. Unlike naturally occurring aptamers that efficiently fold and …

Magnesium ion–water coordination and exchange in biomolecular simulations

O Allnér, L Nilsson, A Villa - Journal of chemical theory and …, 2012 - ACS Publications
Magnesium ions have an important role in the structure and folding mechanism of
ribonucleic acid systems. To properly simulate these biophysical processes, the applied …

The structural and functional diversity of metabolite-binding riboswitches

A Roth, RR Breaker - Annual review of biochemistry, 2009 - annualreviews.org
The cellular concentrations of certain metabolites are assiduously monitored to achieve
appropriate levels of gene expression. Although proteins have long been known to act as …

The distributions, mechanisms, and structures of metabolite-binding riboswitches

JE Barrick, RR Breaker - Genome biology, 2007 - Springer
Background Riboswitches are noncoding RNA structures that appropriately regulate genes
in response to changing cellular conditions. The expression of many proteins involved in …

[HTML][HTML] The dynamic landscapes of RNA architecture

JA Cruz, E Westhof - Cell, 2009 - cell.com
A wealth of information on RNA folding and ribonucleoprotein assembly has emerged from
analyses of structures and from the use of innovative biophysical tools. Although integrating …

Direct observation of hierarchical folding in single riboswitch aptamers

WJ Greenleaf, KL Frieda, DAN Foster, MT Woodside… - Science, 2008 - science.org
Riboswitches regulate genes through structural changes in ligand-binding RNA aptamers.
With the use of an optical-trapping assay based on in situ transcription by a molecule of RNA …

RNA dynamics: it is about time

HM Al-Hashimi, NG Walter - Current opinion in structural biology, 2008 - Elsevier
Many recently discovered RNA functions rely on highly complex multistep conformational
transitions that occur in response to an array of cellular signals. These dynamics accompany …

Fluorescent nucleic acid base analogues

LM Wilhelmsson - Quarterly reviews of biophysics, 2010 - cambridge.org
The use of fluorescent nucleic acid base analogues is becoming increasingly important in
the fields of biology, biochemistry and biophysical chemistry as well as in the field of DNA …