Charged nucleobases and their potential for RNA catalysis

JL Wilcox, AK Ahluwalia… - Accounts of chemical …, 2011 - ACS Publications
Catalysis in living cells is carried out by both proteins and RNA. Protein enzymes have been
known for over 200 years, but RNA enzymes, or “ribozymes”, were discovered only 30 years …

A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis

JA Liberman, M Guo, JL Jenkins… - Journal of the …, 2012 - ACS Publications
One mechanism by which ribozymes can accelerate biological reactions is by adopting folds
that favorably perturb nucleobase ionization. Herein we used Raman crystallography to …

Complexity in pH-Dependent Ribozyme Kinetics: Dark pKa Shifts and Wavy Rate–pH Profiles

EA Frankel, PC Bevilacqua - Biochemistry, 2018 - ACS Publications
Charged bases occur in RNA enzymes, or ribozymes, where they play key roles in catalysis.
Cationic bases donate protons and perform electrostatic catalysis, while anionic bases …

RNA electrostatics: how ribozymes engineer active sites to enable catalysis

S Ekesan, E McCarthy, DA Case… - The Journal of Physical …, 2022 - ACS Publications
Electrostatic interactions are fundamental to RNA structure and function, and intimately
influenced by solvation and the ion atmosphere. RNA enzymes, or ribozymes, are catalytic …

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 …

Nucleic acid enzymes: playing with a fuller deck

GF Joyce - Proceedings of the National Academy of …, 1998 - National Acad Sciences
Poor RNA. Being comprised of only four subunits, and chemically similar subunits at that, it
is a wonder that RNA can have efficient enzymatic activity. Nonetheless, beginning with the …

Nucleobase catalysis in ribozyme mechanism

PC Bevilacqua, R Yajima - Current opinion in chemical biology, 2006 - Elsevier
RNA performs a wide range of functions in biology including catalysis of chemical reactions.
A major goal in the field of ribozyme chemical biology is to understand these functions in …

The ionic environment determines ribozyme cleavage rate by modulation of nucleobase pK a

MD Smith, R Mehdizadeh, JE Olive, RA Collins - Rna, 2008 - rnajournal.cshlp.org
Several small ribozymes employ general acid–base catalysis as a mechanism to enhance
site-specific RNA cleavage, even though the functional groups on the ribonucleoside …

Bioinorganic chemistry: a maturing frontier

SJ Lippard - Science, 1993 - science.org
RNA enzymes as they have in metalloproteins. Will the principles governing catalysis in
hydrolytic protein enzymes such as carboxypeptidase, a zinc metalloprotein that catalyzes …

Two decades of RNA catalysis

VJ DeRose - Chemistry & biology, 2002 - cell.com
Twenty years have passed since the initial discovery of catalytic RNA. Although initial
discoveries of ribozymes (RNA enzymes) involved phosphoryl transfer reactions on RNA …