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Updated: Apr 16, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Multiscale methods for computational RNA enzymology.

Maria T Panteva¹, Thakshila Dissanayake¹, Haoyuan Chen¹

¹Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA.

Methods in Enzymology

|March 2, 2015

Summary

This summary is machine-generated.

Multiscale modeling approaches are crucial for understanding complex RNA catalysis, including conformational changes and chemical reactions. This study applies various methods to investigate RNA backbone cleavage transesterification mechanisms.

Keywords:

3D-RISM CpHMD HREMD Molecular dynamics Multiscale modeling QM/MM RNA catalysis

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A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

Published on: December 2, 2009

Area of Science:

Biochemistry
Computational Biology
Structural Biology

Background:

RNA catalysis is vital but complex, involving conformational changes, ion effects, and chemical steps.
Understanding these factors is key to deciphering RNA enzyme mechanisms.

Purpose of the Study:

To summarize and apply multiscale modeling methods to the problem space of RNA catalysis.
To investigate the mechanistic strategies of RNA backbone cleavage transesterification in ribozymes and proteins.

Main Methods:

Classical molecular dynamics (MD) simulations.
Reference interaction site model (RISM) calculations.
Constant pH molecular dynamics (CpHMD) simulations.
Hamiltonian replica exchange MD.
Quantum mechanical/molecular mechanical (QM/MM) simulations.

Main Results:

Application of multiscale methods to analyze RNA catalysis.
Examination of RNA backbone cleavage transesterification.
Comparison of mechanistic strategies in hepatitis delta virus ribozyme and RNase A.

Conclusions:

Multiscale modeling provides insights into the complex problem space of RNA catalysis.
Different enzymes employ distinct strategies for RNA backbone cleavage transesterification.