Investigation of the pKa of the Nucleophilic O2′ of the Hairpin Ribozyme

AJ Veenis, P Li, AV Soudackov… - The Journal of …, 2021 - ACS Publications
Small ribozymes cleave their RNA phosphodiester backbone by catalyzing a
transphosphorylation reaction wherein a specific O2′ functions as the nucleophile. While …

Metal ions in the structure and function of RNA

A Pyle - JBIC Journal of Biological Inorganic Chemistry, 2002 - Springer
It is becoming increasingly clear that RNA is more than a passive carrier of genetic
information. Folded RNA molecules play key roles in almost every aspect of cellular …

Evidence for a catalytic strategy to promote nucleophile activation in metal-dependent RNA-cleaving ribozymes and 8-17 DNAzyme

A Ganguly, BP Weissman, JA Piccirilli, DM York - ACS catalysis, 2019 - ACS Publications
An unique catalytic strategy was recently reported for the glm S ribozyme [Bingaman et al.,
Nat. Chem. Biol. 2017, 13, 439− 445] that involves promotion of productive hydrogen …

Multiple roles of metal ions in large ribozymes

D Donghi, J Schnabl - 2011 - books.rsc.org
Since the discovery of catalytic RNA molecules (ribozymes), intense research has been
devoted to understand their structure and activity. Among RNA molecules, the large …

The catalytic diversity of RNAs

MJ Fedor, JR Williamson - Nature reviews Molecular cell biology, 2005 - nature.com
The natural RNA enzymes catalyse phosphate-group transfer and peptide-bond formation.
Initially, metal ions were proposed to supply the chemical versatility that nucleotides lack. In …

Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding

JK Frederiksen, NS Li, R Das, D Herschlag, JA Piccirilli - Rna, 2012 - rnajournal.cshlp.org
Within the three-dimensional architectures of RNA molecules, divalent metal ions populate
specific locations, shedding their water molecules to form chelates. These interactions help …

NMR Localization of Divalent Cations at the Active Site of the Neurospora VS Ribozyme Provides Insights into RNA–Metal-Ion Interactions

E Bonneau, P Legault - Biochemistry, 2014 - ACS Publications
Metal cations represent key elements of RNA structure and function. In the Neurospora VS
ribozyme, metal cations play diverse roles; they are important for substrate recognition …

The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone

JB Murray, AA Seyhan, NG Walter, JM Burke… - Chemistry & biology, 1998 - cell.com
Background: The catalytic activity of RNA enzymes is thought to require divalent metal ions,
which are believed to facilitate RNA folding and to play a direct chemical role in the reaction …

Establishing the catalytic and regulatory mechanism of RNA‐based machineries

J Borišek, J Aupič, A Magistrato - Wiley Interdisciplinary …, 2023 - Wiley Online Library
Ribonucleoprotein (RNP)‐machineries are comprised of intricate networks of long
noncoding RNAs and proteins that allow them to actively participate in transcription, RNA …

Structure determination of catalytic RNAs and investigations of their metal ion-binding properties

MC Erat, RKO Sigel - Chimia, 2005 - chimia.ch
Naturally occurring RNA molecules exhibit many unexpected and fascinating properties in
living cells such as protein synthesis and transport, regulation of metabolic functions, and …