Use of phosphorothioates to identify sites of metal-ion binding in RNA

M Forconi, D Herschlag - Methods in enzymology, 2009 - Elsevier
Single atom substitutions provide an exceptional opportunity to investigate RNA structure
and function. Replacing a phosphoryl oxygen with a sulfur represents one of the most …

Identification of catalytic metal ion ligands in ribozymes

JK Frederiksen, JA Piccirilli - Methods, 2009 - Elsevier
Site-bound metal ions participate in the catalytic mechanisms of many ribozymes.
Understanding these mechanisms therefore requires knowledge of the specific ligands on …

[HTML][HTML] Functional identification of catalytic metal ion binding sites within RNA

JL Hougland, AV Kravchuk, D Herschlag… - PLoS biology, 2005 - journals.plos.org
The viability of living systems depends inextricably on enzymes that catalyze phosphoryl
transfer reactions. For many enzymes in this class, including several ribozymes, divalent …

Probing the role of metal ions in RNA catalysis: Kinetic and thermodynamic characterization of a metal ion interaction with the 2 '-moiety of the guanosine nucleophile …

S Shan, D Herschlag - Biochemistry, 1999 - ACS Publications
Deciphering the role of individual metal ions in RNA catalysis is a tremendous challenge, as
numerous metal ions coat the charged backbone of a folded RNA. Metal ion specificity …

Three metal ions at the active site of the Tetrahymena group I ribozyme

S Shan, A Yoshida, S Sun… - Proceedings of the …, 1999 - National Acad Sciences
Metal ions are critical for catalysis by many RNA and protein enzymes. To understand how
these enzymes use metal ions for catalysis, it is crucial to determine how many metal ions …

Dissection of a metal-ion-mediated conformational change in Tetrahymena ribozyme catalysis

S Shan, D Herschlag - RNA, 2002 - cambridge.org
Conformational changes are often required for the biological function of RNA molecules. In
the Tetrahymena group I ribozyme reaction, a conformational change has been suggested …

Metal ion binding to catalytic RNA molecules

VJ DeRose - Current opinion in structural biology, 2003 - Elsevier
Cations play critical roles in ribozyme structure and catalysis. Unraveling the contributions of
cations as catalytic cofactors is a complex process, due to their role in inducing RNA folding …

Defining the Catalytic Metal Ion Interactions in the Tetrahymena Ribozyme Reaction

S Shan, AV Kravchuk, JA Piccirilli, D Herschlag - Biochemistry, 2001 - ACS Publications
Divalent metal ions play a crucial role in catalysis by many RNA and protein enzymes that
carry out phosphoryl transfer reactions, and defining their interactions with substrates is …

An unconventional origin of metal-ion rescue and inhibition in the Tetrahymena group I ribozyme reaction

S Shan, D Herschlag - Rna, 2000 - cambridge.org
The presence of catalytic metal ions in RNA active sites has often been inferred from metal-
ion rescue of modified substrates and sometimes from inhibitory effects of alternative metal …

Functional identification of ligands for a catalytic metal ion in group I introns

M Forconi, J Lee, JK Lee, JA Piccirilli, D Herschlag - Biochemistry, 2008 - ACS Publications
Many enzymes use metal ions within their active sites to achieve enormous rate
acceleration. Understanding how metal ions mediate catalysis requires elucidation of metal …