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 …

[HTML][HTML] Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes

R Micura, C Höbartner - Chemical Society Reviews, 2020 - pubs.rsc.org
This review aims at juxtaposing common versus distinct structural and functional strategies
that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently …

Assessment of three‐dimensional RNA structure prediction in CASP15

R Das, RC Kretsch, AJ Simpkin… - Proteins: Structure …, 2023 - Wiley Online Library
The prediction of RNA three‐dimensional structures remains an unsolved problem. Here, we
report assessments of RNA structure predictions in CASP15, the first CASP exercise that …

Chemistry and biology of self-cleaving ribozymes

RM Jimenez, JA Polanco, A Lupták - Trends in biochemical sciences, 2015 - cell.com
Self-cleaving ribozymes were discovered 30 years ago, but their biological distribution and
catalytic mechanisms are only beginning to be defined. Each ribozyme family is defined by a …

[HTML][HTML] Nucleic acid catalysis: metals, nucleobases, and other cofactors

WL Ward, K Plakos, VJ DeRose - Chemical reviews, 2014 - ACS Publications
The discovery of RNA-catalyzed phosphodiester bond cleavage by Cech and Altman in
1982− 1983 shattered the paradigm of protein-dependent biological catalysis and opened …

Molecular dynamics simulations of nucleic acids. From tetranucleotides to the ribosome

J Šponer, P Banáš, P Jurecka… - The journal of …, 2014 - ACS Publications
We present a brief overview of explicit solvent molecular dynamics (MD) simulations of
nucleic acids. We explain physical chemistry limitations of the simulations, namely, the …

Crystal structure and mechanistic investigation of the twister ribozyme

Y Liu, TJ Wilson, SA McPhee, DMJ Lilley - Nature chemical biology, 2014 - nature.com
We present a crystal structure at 2.3-Å resolution of the recently described nucleolytic
ribozyme twister. The RNA adopts a previously uncharacterized compact fold based on a …

HDV-like self-cleaving ribozymes

CHT Webb, A Lupták - RNA biology, 2011 - Taylor & Francis
HDV ribozymes catalyze their own scission from the transcript during rolling circle replication
of the hepatitis delta virus. In vitro selection of self-cleaving ribozymes from a human …

[HTML][HTML] Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis

R Yamagami, JL Bingaman, EA Frankel… - Nature …, 2018 - nature.com
Most RNA folding studies have been performed under non-physiological conditions of high
concentrations (≥ 10 mM) of Mg2+ free, while actual cellular concentrations of Mg2+ free …

[图书][B] DNA in supramolecular chemistry and nanotechnology

E Stulz, GH Clever - 2015 - books.google.com
This book covers the emerging topic of DNA nanotechnology and DNA supramolecular
chemistry in its broader sense. By taking DNA out of its biological role, this biomolecule has …