Results 11 to 20 of about 7,960 (219)

Riboswitch finder--a tool for identification of riboswitch RNAs [PDF]

Nucleic Acids Research, 2004
We describe a dedicated RNA motif search program and web server to identify RNA riboswitches. The Riboswitch finder analyses a given sequence using the web interface, checks specific sequence elements and secondary structure, calculates and displays the energy folding of the RNA structure and runs a number of tests including this information to ...
Peter Bengert, Thomas Dandekar
openaire   +5 more sources

Folding of the Adenine Riboswitch [PDF]

Chemistry & Biology, 2006
The pbuE adenine riboswitch undergoes metal ion-dependent folding that involves a loop-loop interaction. Binding of 2-aminopurine to the aptamer domain strongly correlates with the ability of the loops to interact, and single-molecule FRET studies reveal that folding proceeds via a discrete intermediate. Folding occurs in the absence of adenine ligand,
Lemay, Jean-François, Penedo, J. Carlos, Tremblay, Renaud, Lilley, David M.J., Lafontaine, Daniel A.   +4 more
openaire   +3 more sources

Riboswitch diversity and distribution [PDF]

RNA, 2017
Riboswitches are commonly used by bacteria to detect a variety of metabolites and ions to regulate gene expression. To date, nearly 40 different classes of riboswitches have been discovered, experimentally validated, and modeled at atomic resolution in complex with their cognate ligands.
Phillip J. McCown, Keith A. Corbino, Shira Stav, Madeline E. Sherlock, Ronald R. Breaker   +4 more
openaire   +4 more sources

Ligand response of guanidine-IV riboswitch at single-molecule level [PDF]

eLife
Riboswitches represent a class of non-coding RNA that possess the unique ability to specifically bind ligands and, in response, regulate gene expression.
Lingzhi Gao, Dian Chen, Yu Liu
doaj   +2 more sources

Design principles for riboswitch function. [PDF]

PLoS Computational Biology, 2009
Scientific and technological advances that enable the tuning of integrated regulatory components to match network and system requirements are critical to reliably control the function of biological systems. RNA provides a promising building block for the
Chase L Beisel, Christina D Smolke
doaj   +4 more sources

TaRTLEt: Transcriptionally-active Riboswitch Tracer Leveraging Edge deTection [PDF]

PeerJ
Structured RNAs have emerged as a major component of cellular regulatory systems, but their mechanism of action is often poorly understood. Riboswitches are structured RNAs that allosterically regulate gene expression through any of several different ...
Sachit Kshatriya, Sarah C. Bagby
doaj   +4 more sources

RATEX: A Scalable RNA-Based Platform for Logical and Multi-Layered Cellular Programming. [PDF]

Angew Chem Int Ed Engl
RATEX integrated ribosome‐mediated transcription control with synthetic RNA regulators, enabling simultaneous processing of RNA, metabolite, and small‐molecule inputs through complex logic operations within a single transcript. The platform achieves up to 1,492‐fold gene regulation, multi‐input hybrid logic gates, RNA‐programmed signaling cascades, and
Goh H, Kang H, Kim C, Kim J.
europepmc   +3 more sources

Polycationic Peptides That Bind T-Box Riboswitch Antiterminator RNA and Inhibit Riboswitch Function. [PDF]

Chem Biol Drug Des
Polycationic decapeptides inhibit T‐box riboswitch tRNA‐induced transcription readthrough. ABSTRACT Resistance to antibiotic treatments continues to be a significant health challenge and necessitates investigating novel antibacterial targets including noncoding regulatory RNA.
Fairchild E, Herath D, Lux S, Harvey SR, Amesaki D, McCartney D, Richter M, Hoffmann R, Hines JV.   +8 more
europepmc   +2 more sources

Riboswitches

Current Biology, 2023
Riboswitches are structured noncoding RNA domains that are typically found embedded in messenger RNAs, where they sense specific target molecules or elemental ions and regulate gene expression. These RNAs thus serve as genetic switches that can activate or repress gene expression in response to changing levels of their target ligand. To many observers,
Salvail, Hubert, Breaker, Ronald R.
openaire   +2 more sources

Reconsidering the czcD (NiCo) Riboswitch as an Iron Riboswitch

ACS Bio & Med Chem Au, 2022
Recent work has proposed a new mechanism of bacterial iron regulation: riboswitches that undergo a conformational change in response to FeII. The czcD (NiCo) riboswitch was initially proposed to be specific for NiII and CoII, but we recently showed via a czcD-based fluorescent sensor that FeII is also a plausible physiological ligand for this ...
Jiansong Xu, Joseph A. Cotruvo
openaire   +2 more sources