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 …

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 …

DSSR: an integrated software tool for dissecting the spatial structure of RNA

XJ Lu, HJ Bussemaker, WK Olson - Nucleic acids research, 2015 - academic.oup.com
Insight into the three-dimensional architecture of RNA is essential for understanding its
cellular functions. However, even the classic transfer RNA structure contains features that …

Inferring protein 3D structure from deep mutation scans

NJ Rollins, KP Brock, FJ Poelwijk, MA Stiffler… - Nature …, 2019 - nature.com
We describe an experimental method of three-dimensional (3D) structure determination that
exploits the increasing ease of high-throughput mutational scans. Inspired by the success of …

Hydrolytic endonucleolytic ribozyme (HYER) is programmable for sequence-specific DNA cleavage

ZX Liu, S Zhang, HZ Zhu, ZH Chen, Y Yang, LQ Li… - Science, 2024 - science.org
Ribozymes are catalytic RNAs with diverse functions including self-splicing and
polymerization. This work aims to discover natural ribozymes that behave as hydrolytic and …

New classes of self-cleaving ribozymes revealed by comparative genomics analysis

Z Weinberg, PB Kim, TH Chen, S Li, KA Harris… - Nature chemical …, 2015 - nature.com
Enzymes made of RNA catalyze reactions that are essential for protein synthesis and RNA
processing. However, such natural ribozymes are exceedingly rare, as evidenced by the fact …

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 …

Crystal structure of a DNA catalyst

A Ponce-Salvatierra, K Wawrzyniak-Turek… - Nature, 2016 - nature.com
Catalysis in biology is restricted to RNA (ribozymes) and protein enzymes, but synthetic
biomolecular catalysts can also be made of DNA (deoxyribozymes) or synthetic genetic …

Crystal structure of the Varkud satellite ribozyme

NB Suslov, S DasGupta, H Huang, JR Fuller… - Nature chemical …, 2015 - nature.com
The Varkud satellite (VS) ribozyme mediates rolling-circle replication of a plasmid found in
the Neurospora mitochondrion. We report crystal structures of this ribozyme from …

Scaling catalytic contributions of small self‐cleaving ribozymes

M Egger, R Bereiter, S Mair, R Micura - Angewandte Chemie, 2022 - Wiley Online Library
Nucleolytic ribozymes utilize general acid‐base catalysis to perform phosphodiester
cleavage. In most ribozyme classes, a conserved active site guanosine is positioned to act …