RNA structural dynamics as captured by molecular simulations: a comprehensive overview
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 …
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 …
that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently …
Assessment of three‐dimensional RNA structure prediction in CASP15
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 …
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 …
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 …
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 …
nucleic acids. We explain physical chemistry limitations of the simulations, namely, the …
Crystal structure and mechanistic investigation of the twister ribozyme
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 …
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 …
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 …
concentrations (≥ 10 mM) of Mg2+ free, while actual cellular concentrations of Mg2+ free …
[图书][B] DNA in supramolecular chemistry and nanotechnology
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 …
chemistry in its broader sense. By taking DNA out of its biological role, this biomolecule has …