Existence of efficient divalent metal ion-catalyzed and inefficient divalent metal ion-independent channels in reactions catalyzed by a hammerhead ribozyme

JM Zhou, DM Zhou, Y Takagi, Y Kasai… - Nucleic acids …, 2002 - academic.oup.com
The hammerhead ribozyme is generally accepted as a well characterized metalloenzyme.
However, the precise nature of the interactions of the RNA with metal ions remains to be fully …

Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble

Y Bai, VB Chu, J Lipfert, VS Pande… - Journal of the …, 2008 - ACS Publications
Electrostatic forces, acting between helices and modulated by the presence of the ion
atmosphere, are key determinants in the energetic balance that governs RNA folding …

RNA folding and catalysis

DMJ Lilley - Genetica, 1999 - Springer
Catalysis in RNA is intimately connected to the folding. The small nucleolytic ribozymes
function by a nucleophilic attack of the 2′-oxygen on the 3′-phosphate, in an SN 2 …

Extraordinary rates of transition metal ion-mediated ribozyme catalysis

M Roychowdhury-Saha, DH Burke - Rna, 2006 - rnajournal.cshlp.org
In pre-steady-state, fast-quench kinetic analysis, the tertiary-stabilized hammerhead
ribozyme “RzB” cleaves its substrate RNA with maximal measured k obs values of∼ 3000 …

The roles of metal ions in regulation by riboswitches

AR Ferré-D'Amaré, WC Winkler - 2011 - books.rsc.org
Metal ions are required by all organisms in order to execute an array of essential molecular
functions. They play a critical role in many catalytic mechanisms and structural properties …

Determining the Mg2+ Stoichiometry for Folding an RNA Metal Ion Core

R Das, KJ Travers, Y Bai… - Journal of the American …, 2005 - ACS Publications
The folding and catalytic function of RNA molecules depend on their interactions with
divalent metal ions, such as magnesium. As with every molecular process, the most basic …

Modulation of ribozyme and deoxyribozyme activities using tetraalkylammonium ions

S Nakano, T Watabe, N Sugimoto - ChemPhysChem, 2017 - Wiley Online Library
Nucleic acid enzymes require specific metal ions to be catalytically active. The functions of
the metal ions having structural and catalytic roles are affected by competing cations. Large …

A ribozyme that uses lanthanides as cofactor

KJ Sweeney, X Han, UF Müller - Nucleic Acids Research, 2023 - academic.oup.com
To explore how an early, RNA-based life form could have functioned, in vitro selection
experiments have been used to develop catalytic RNAs (ribozymes) with relevant functions …

Organic nanoelectronics inside us: charge transport and localization in RNA could orchestrate ribosome operation

A Sosorev, O Kharlanov - Physical Chemistry Chemical Physics, 2021 - pubs.rsc.org
Translation–protein synthesis at the ribonucleic acid (RNA) based molecular machine, the
ribosome,–proceeds in a similar manner in all life forms. However, despite several decades …

Selective inactivation of functional RNAs by ribozyme-catalyzed covalent modification

RR Poudyal, M Benslimane… - ACS Synthetic …, 2017 - ACS Publications
The diverse functions of RNA provide numerous opportunities for programming biological
circuits. We describe a new strategy that uses ribozyme K28min to covalently tag a specific …