Targeting RNA structures with small molecules

JL Childs-Disney, X Yang, QMR Gibaut… - Nature Reviews Drug …, 2022 - nature.com
RNA adopts 3D structures that confer varied functional roles in human biology and
dysfunction in disease. Approaches to therapeutically target RNA structures with small …

RNA structural dynamics as captured by molecular simulations: a comprehensive overview

J Sponer, G Bussi, M Krepl, P Banáš, S Bottaro… - Chemical …, 2018 - ACS Publications
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Decoding the identification mechanism of an SAM-III Riboswitch on ligands through multiple independent Gaussian-accelerated molecular dynamics simulations

J Chen, Q Zeng, W Wang, H Sun… - Journal of Chemical …, 2022 - ACS Publications
S-Adenosyl-l-methionine (SAM)-responsive riboswitches play a central role in the regulation
of bacterial gene expression at the level of transcription attenuation or translation inhibition …

[HTML][HTML] The noncoding RNA revolution—trashing old rules to forge new ones

TR Cech, JA Steitz - Cell, 2014 - cell.com
Noncoding RNAs (ncRNAs) accomplish a remarkable variety of biological functions. They
regulate gene expression at the levels of transcription, RNA processing, and translation …

A decade of riboswitches

A Serganov, E Nudler - Cell, 2013 - cell.com
Riboswitches were discovered in 2002 in bacteria as RNA-based intracellular sensors of
vitamin derivatives. During the last decade, naturally occurring RNA sensor elements have …

RNA force field with accuracy comparable to state-of-the-art protein force fields

D Tan, S Piana, RM Dirks… - Proceedings of the …, 2018 - National Acad Sciences
Molecular dynamics (MD) simulation has become a powerful tool for characterizing at an
atomic level of detail the conformational changes undergone by proteins. The application of …

Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography

JR Stagno, Y Liu, YR Bhandari, CE Conrad, S Panja… - Nature, 2017 - nature.com
Riboswitches are structural RNA elements that are generally located in the 5′ untranslated
region of messenger RNA. During regulation of gene expression, ligand binding to the …

Fluorescence imaging of cellular metabolites with RNA

JS Paige, T Nguyen-Duc, W Song, SR Jaffrey - Science, 2012 - science.org
Genetically encoded sensors are powerful tools for imaging intracellular metabolites and
signaling molecules. However, developing sensors is challenging because they require …

Structural basis for activity of highly efficient RNA mimics of green fluorescent protein

KD Warner, MC Chen, W Song, RL Strack… - Nature structural & …, 2014 - nature.com
GFP and its derivatives revolutionized the study of proteins. Spinach is a recently reported in
vitro–evolved RNA mimic of GFP, which as genetically encoded fusions makes possible live …

Prospects for riboswitch discovery and analysis

RR Breaker - Molecular cell, 2011 - cell.com
An expanding number of metabolite-binding riboswitch classes are being discovered in the
noncoding portions of bacterial genomes. Findings over the last decade indicate that …