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 …

Investigations on the interface of nucleic acid aptamers and binding targets

S Cai, J Yan, H Xiong, Y Liu, D Peng, Z Liu - Analyst, 2018 - pubs.rsc.org
Nucleic acid aptamers are single-stranded DNA or RNA of 20–100 nucleotides in length that
have attracted substantial scientific interest due to their ability to specifically bind to target …

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 …

Accurate assessment of mass, models and resolution by small-angle scattering

RP Rambo, JA Tainer - Nature, 2013 - nature.com
Modern small-angle scattering (SAS) experiments with X-rays or neutrons provide a
comprehensive, resolution-limited observation of the thermodynamic state. However …

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 …

Insights into RNA structure and function from genome-wide studies

SA Mortimer, MA Kidwell, JA Doudna - Nature Reviews Genetics, 2014 - nature.com
A comprehensive understanding of RNA structure will provide fundamental insights into the
cellular function of both coding and non-coding RNAs. Although many RNA structures have …

Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod‐Debye law

RP Rambo, JA Tainer - Biopolymers, 2011 - Wiley Online Library
Unstructured proteins, RNA or DNA components provide functionally important flexibility that
is key to many macromolecular assemblies throughout cell biology. As objective …

A G-quadruplex–containing RNA activates fluorescence in a GFP-like fluorophore

H Huang, NB Suslov, NS Li, SA Shelke… - Nature chemical …, 2014 - nature.com
Spinach is an in vitro–selected RNA aptamer that binds a GFP-like ligand and activates its
green fluorescence. Spinach is thus an RNA analog of GFP and has potentially widespread …

Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution

K Zhang, S Li, K Kappel, G Pintilie, Z Su… - Nature …, 2019 - nature.com
Specimens below 50 kDa have generally been considered too small to be analyzed by
single-particle cryo-electron microscopy (cryo-EM). The high flexibility of pure RNAs makes it …

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Z Miao, RW Adamiak, M Antczak, RT Batey, AJ Becka… - Rna, 2017 - rnajournal.cshlp.org
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here
a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch …