Results 1 to 10 of about 12,134 (129)

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   +7 more sources

Folding Kinetics of Riboswitch Transcriptional Terminators and Sequesterers

Entropy, 2013
To function as gene regulatory elements in response to environmental signals, riboswitches must adopt specific secondary structures on appropriate time scales.
Ben Sauerwine, Michael Widom
doaj   +4 more sources

Cyclic Amide-Linked Oxazolidinone Triazoles as Inhibitors of the T-Box Riboswitch [PDF]

Molecules
Antimicrobial resistance remains a critical global health challenge, and was intensified by the COVID-19 pandemic. To address this growing threat, novel antibacterial agents targeting unconventional mechanisms are urgently needed.
Eric Parsons, Ali H. Aldhumani, Emily A. Fairchild, Oluwaseun B. Adegbite, Jessica M. Roberts, Jennifer V. Hines, Stephen C. Bergmeier   +6 more
doaj   +2 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   +3 more sources

Identification of potential riboswitch elements in Homo sapiens mRNA 5'UTR sequences using positive-unlabeled machine learning. [PDF]

PLoS ONE
Riboswitches are a class of noncoding RNA structures that interact with target ligands to cause a conformational change that can then execute some regulatory purpose within the cell.
William S Raymond, Jacob DeRoo, Brian Munsky   +2 more
doaj   +2 more sources

Designing molecular RNA switches with Restricted Boltzmann machines [PDF]

Nature Communications
Riboswitches are structured allosteric RNA molecules that change conformation upon metabolite binding, triggering a regulatory response. Here we focus on the de novo design of riboswitch-like aptamers, the core part of the riboswitch undergoing ...
Jorge Fernandez-de-Cossio-Diaz, Pierre Hardouin, Francois-Xavier Lyonnet du Moutier, Andrea Di Gioacchino, Bertrand Marchand, Yann Ponty, Bruno Sargueil, Rémi Monasson, Simona Cocco   +8 more
doaj   +2 more sources

Novel TPP-riboswitch activators bypass metabolic enzyme dependency [PDF]

Frontiers in Chemistry, 2014
Riboswitches are conserved regions within mRNA molecules that bind specific metabolites and regulate gene expression. TPP-riboswitches, which respond to thiamine pyrophosphate (TPP), are involved in the regulation of thiamine metabolism in numerous ...
Günter eMayer, Christina eLünse, Colin eSuckling, Fraser eScott   +3 more
doaj   +3 more sources

Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection

Frontiers in Molecular Biosciences, 2021
Short, structured fragments of non-coding mRNA may act as molecular switches upon binding specific ligands, regulating the translation of proteins encoded downstream this mRNA sequence.
Piotr Chyży, Piotr Chyży, Marta Kulik, Marta Kulik, Suyong Re, Suyong Re, Yuji Sugita, Yuji Sugita, Yuji Sugita, Joanna Trylska   +9 more
doaj   +1 more source

Signal amplification and optimization of riboswitch-based hybrid inputs by modular and titratable toehold switches

Journal of Biological Engineering, 2021
Background Synthetic biological circuits are widely utilized to control microbial cell functions. Natural and synthetic riboswitches are attractive sensor modules for use in synthetic biology applications.
Yunhee Hwang, Seong Gyeong Kim, Sungho Jang, Jongmin Kim, Gyoo Yeol Jung   +4 more
doaj   +1 more source

TPP riboswitch-dependent regulation of an ancient thiamin transporter in Candida. [PDF]

PLoS Genetics, 2018
Riboswitches are non-coding RNA molecules that regulate gene expression by binding to specific ligands. They are primarily found in bacteria. However, one riboswitch type, the thiamin pyrophosphate (TPP) riboswitch, has also been described in some plants,
Paul D Donovan, Linda M Holland, Lisa Lombardi, Aisling Y Coughlan, Desmond G Higgins, Kenneth H Wolfe, Geraldine Butler   +6 more
doaj   +1 more source