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 …

Self-cleaving ribozymes: substrate specificity and synthetic biology applications

H Peng, B Latifi, S Müller, A Lupták, IA Chen - RSC chemical biology, 2021 - pubs.rsc.org
Various self-cleaving ribozymes appearing in nature catalyze the sequence-specific
intramolecular cleavage of RNA and can be engineered to catalyze cleavage of appropriate …

Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning

J Singh, K Paliwal, T Zhang, J Singh, T Litfin… - …, 2021 - academic.oup.com
Motivation The recent discovery of numerous non-coding RNAs (long non-coding RNAs, in
particular) has transformed our perception about the roles of RNAs in living organisms. Our …

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 …

Mechanistic insight into homogeneous catalytic crosslinking behavior between cellulose and epoxide by explicit solvent models

Z Yan, Y Di, L Wang, P Fei, S Chen, X Yue… - International Journal of …, 2023 - Elsevier
Inspired by recent advances on functional modification of cellulosic materials, the
crosslinking behaviors of epoxide with cellulose under the catalysis of different …

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 …

[HTML][HTML] Cryo-EM structure of raiA ncRNA from Clostridium reveals a new RNA 3D fold

NG Badepally, TR de Moura, E Purta, EF Baulin… - Journal of Molecular …, 2024 - Elsevier
Advancements in genome-wide sequence analysis have led to the discovery of numerous
novel bacterial non-coding RNAs (ncRNAs). These ncRNAs have been categorized into …

Mechanisms of catalytic RNA molecules

D Alonso, A Mondragón - Biochemical Society Transactions, 2021 - portlandpress.com
Ribozymes are folded catalytic RNA molecules that perform important biological functions.
Since the discovery of the first RNA with catalytic activity in 1982, a large number of …

Impact of 3-deazapurine nucleobases on RNA properties

R Bereiter, M Himmelstoß, E Renard… - Nucleic Acids …, 2021 - academic.oup.com
Deazapurine nucleosides such as 3-deazaadenosine (c3A) are crucial for atomic
mutagenesis studies of functional RNAs. They were the key for our current mechanistic …

The mutual interactions of RNA, counterions and water–quantifying the electrostatics at the phosphate–water interface

BP Fingerhut - Chemical Communications, 2021 - pubs.rsc.org
The structure and dynamics of polyanionic biomolecules, like RNA, are decisively
determined by their electric interactions with the water molecules and the counterions in the …