RNA molecules perform a variety of biological functions for which the correct three-
dimensional structure is essential, including as ribozymes where they catalyze chemical …

Although site-bound Mg2+ ions have been proposed to influence RNA structure and
function, establishing the molecular properties of such sites has been challenging due …

The viability of living systems depends inextricably on enzymes that catalyze phosphoryl
transfer reactions. For many enzymes in this class, including several ribozymes, divalent …

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 …

Metal ions are required to stabilize RNA tertiary structure and to begin the folding process.
How different metal ions enable RNAs to fold depends on the electrostatic potential of the …

Nucleic acid processing enzymes use a two‐Mg2+‐ion motif to promote the formation and
cleavage of phosphodiester bonds. Yet, recent evidence demonstrates the presence of …

Pistol ribozymes comprise a class of small, self‐cleaving RNAs discovered via comparative
genomic analysis. Prior work in the field has probed the kinetics of the cleavage reaction, as …

The hairpin ribozyme is a minimalist paradigm for studying RNA folding and function. In this
enzyme, two domains dock by induced fit to form a catalytic core that mediates a specific …

Background: Ribozymes are biological catalysts that promote the hydrolysis and
transesterification of phosphate diesters of RNA. They typically require divalent magnesium …

Molecular dynamics simulations using a combined quantum mechanical/molecular
mechanical potential are used to determine the two-dimensional free energy profiles for the …