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 …
Insight into G-quadruplex-hemin DNAzyme/RNAzyme: adjacent adenine as the intramolecular species for remarkable enhancement of enzymatic activity
W Li, Y Li, Z Liu, B Lin, H Yi, F Xu, Z Nie… - Nucleic acids …, 2016 - academic.oup.com
Abstract G-quadruplex (G4) with stacked G-tetrads structure is able to bind hemin (iron (III)-
protoporphyrin IX) to form a unique type of DNAzyme/RNAzyme with peroxidase-mimicking …
protoporphyrin IX) to form a unique type of DNAzyme/RNAzyme with peroxidase-mimicking …
Self-cleaving ribozymes: substrate specificity and synthetic biology applications
Various self-cleaving ribozymes appearing in nature catalyze the sequence-specific
intramolecular cleavage of RNA and can be engineered to catalyze cleavage of appropriate …
intramolecular cleavage of RNA and can be engineered to catalyze cleavage of appropriate …
Experimental approaches for measuring pKa's in RNA and DNA
P Thaplyal, PC Bevilacqua - Methods in enzymology, 2014 - Elsevier
RNA and DNA carry out diverse functions in biology including catalysis, splicing, gene
regulation, and storage of genetic information. Interest has grown in understanding how …
regulation, and storage of genetic information. Interest has grown in understanding how …
Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction
A Mir, J Chen, K Robinson, E Lendy, J Goodman… - Biochemistry, 2015 - ACS Publications
The hammerhead ribozyme is a self-cleaving RNA broadly dispersed across all kingdoms of
life. Although it was the first of the small, nucleolytic ribozymes discovered, the mechanism …
life. Although it was the first of the small, nucleolytic ribozymes discovered, the mechanism …
Simulation-Guided Conformational Space Exploration to Assess Reactive Conformations of a Ribozyme
S Forget, M Juillé, E Duboué-Dijon… - Journal of Chemical …, 2024 - ACS Publications
Self-splicing ribozymes are small ribonucleic acid (RNA) enzymes that catalyze their own
cleavage through a transphosphoesterification reaction. While this process is involved in …
cleavage through a transphosphoesterification reaction. While this process is involved in …
Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme
The hepatitis delta virus (HDV) ribozyme catalyzes a self-cleavage reaction using a
combination of nucleobase and metal ion catalysis. Both divalent and monovalent ions can …
combination of nucleobase and metal ion catalysis. Both divalent and monovalent ions can …
A Stably Protonated Adenine Nucleotide with a Highly Shifted pKa Value Stabilizes the Tertiary Structure of a GTP‐Binding RNA Aptamer
AC Wolter, AK Weickhmann, AH Nasiri… - Angewandte Chemie …, 2017 - Wiley Online Library
RNA tertiary structure motifs are stabilized by a wide variety of hydrogen‐bonding
interactions. Protonated A and C nucleotides are normally not considered to be suitable …
interactions. Protonated A and C nucleotides are normally not considered to be suitable …
A mini‐twister variant and impact of residues/cations on the phosphodiester cleavage of this ribozyme class
M Košutić, S Neuner, A Ren, S Flür… - Angewandte Chemie …, 2015 - Wiley Online Library
Nucleolytic ribozymes catalyze site‐specific cleavage of their phosphodiester backbones. A
minimal version of the twister ribozyme is reported that lacks the phylogenetically conserved …
minimal version of the twister ribozyme is reported that lacks the phylogenetically conserved …
The effect of adenine protonation on RNA phosphodiester backbone bond cleavage elucidated by deaza-nucleobase modifications and mass spectrometry
E Fuchs, C Falschlunger, R Micura… - Nucleic Acids …, 2019 - academic.oup.com
The catalytic strategies of small self-cleaving ribozymes often involve interactions between
nucleobases and the ribonucleic acid (RNA) backbone. Here we show that multiply …
nucleobases and the ribonucleic acid (RNA) backbone. Here we show that multiply …