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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
Characterizing RNA 3D structural features from DMS reactivity
D H Sanduni Deenalattha1, Chris P Jurich1, Bret Lange1
1Department of Chemistry, University of Nebraska - Lincoln, 639 North 12th St, Lincoln, NE 68588, United States.
Nucleic Acids Research
|July 17, 2026
Summary
Dimethyl sulfate (DMS) chemical mapping reveals RNA 3D structure. DMS reactivity provides geometric insights, improving RNA 3D modeling accuracy for Watson-Crick and non-canonical base pairs.
Area of Science:
- Molecular Biology
- Structural Biology
- Biochemistry
Background:
- Dimethyl sulfate (DMS) chemical mapping is used to probe RNA structure.
- Low DMS reactivity typically indicates Watson-Crick (WC) base pairs, while high reactivity suggests unpaired nucleotides.
- Deviations from this interpretation in known RNA structures highlight the need for further investigation into outlier nucleotides and their structural features.
Purpose of the Study:
- To systematically analyze DMS reactivity across a large RNA dataset with known 3D structures.
- To understand the frequency and recurring 3D structural features of nucleotides deviating from standard DMS reactivity interpretations.
- To establish DMS reactivity as a predictive tool for RNA 3D modeling.
Main Methods:
- Systematic analysis of DMS reactivity in 7500 RNA constructs with known 3D structures.
- Correlation of DMS reactivity with solvent accessibility, hydrogen bonding, base stacking, and junction dynamics.
- Application of reactivity-derived distance constraints in Rosetta Full-Atom Refinement (FARFAR) for RNA structure modeling.
Main Results:
- DMS reactivity spans four orders of magnitude with approximately 10% overlap between WC and non-WC nucleotides.
- Non-WC bases with WC-like protection show increased hydrogen bonding and reduced solvent accessibility.
- Reactive WC pairs are often located near junctions, associated with weaker base stacking and increased dynamics.
- Reactivity in noncanonical pairs correlates with specific atomic distances, enabling discrimination of base-pair conformations.
- Reactivity-distance correlations are reproducible under in vivo-like conditions.
- A single reactivity-derived distance constraint in Rosetta FARFAR accurately recovers native base-pair conformations and improves structural model accuracy.
Conclusions:
- DMS reactivity provides predictive geometric information for RNA 3D structures.
- The study refines the interpretation of DMS reactivity, accounting for structural nuances beyond simple WC pairing.
- DMS chemical mapping, combined with computational modeling, offers a powerful approach for high-resolution RNA structure determination.
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