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 …

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 …

Structure-based mechanistic insights into catalysis by small self-cleaving ribozymes

A Ren, R Micura, DJ Patel - Current opinion in chemical biology, 2017 - Elsevier
Highlights•Small self-cleaving ribozymes are essential for rolling-circle-based replication of
satellite and pathogenic RNAs.•Structure–function research on active site alignments and …

High‐throughput mutational analysis of a twister ribozyme

S Kobori, Y Yokobayashi - Angewandte Chemie International …, 2016 - Wiley Online Library
Recent discoveries of new classes of self‐cleaving ribozymes in diverse organisms have
triggered renewed interest in the chemistry and biology of ribozymes. Functional analysis …

1-Deazaguanosine-modified RNA: The missing piece for functional RNA atomic mutagenesis

R Bereiter, E Renard, K Breuker, C Kreutz… - Journal of the …, 2022 - ACS Publications
Atomic mutagenesis is the key to advance our understanding of RNA recognition and RNA
catalysis. To this end, deazanucleosides are utilized to evaluate the participation of specific …

Elucidation of catalytic strategies of small nucleolytic ribozymes from comparative analysis of active sites

DD Seith, JL Bingaman, AJ Veenis, AC Button… - ACS …, 2018 - ACS Publications
A number of small, self-cleaving ribozyme classes have been identified including the
hammerhead, hairpin, hepatitis delta virus (HDV), Varkud satellite (VS), glmS, twister …

Metals induce transient folding and activation of the twister ribozyme

S Panja, B Hua, D Zegarra, T Ha… - Nature chemical …, 2017 - nature.com
Twister is a small ribozyme present in almost all kingdoms of life that rapidly self-cleaves in
variety of divalent metal ions. We used activity assays, bulk FRET and single-molecule FRET …

Structural and biochemical properties of novel self-cleaving ribozymes

KY Lee, BJ Lee - Molecules, 2017 - mdpi.com
Fourteen well-defined ribozyme classes have been identified to date, among which nine are
site-specific self-cleaving ribozymes. Very recently, small self-cleaving ribozymes have …

Unwinding the twister ribozyme: from structure to mechanism

J Gebetsberger, R Micura - Wiley Interdisciplinary Reviews …, 2017 - Wiley Online Library
The twister ribozyme motif has been identified by bioinformatic means very recently.
Currently, four crystal structures with ordered active sites together with a series of chemical …