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Characterizing 3D RNA structural features from DMS reactivity.

D H Sanduni Deenalattha1, Chris P Jurich1, Bret Lange1

  • 1Department of Chemistry, University of Nebraska, 639 North 12 St, Lincoln, NE 68588, USA.

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Summary
This summary is machine-generated.

Dimethyl sulfate (DMS) chemical mapping reveals RNA structure nuances. Deviations from standard Watson-Crick base pairing rules in DMS reactivity offer insights into complex RNA 3D conformations and dynamics.

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • Dimethyl sulfate (DMS) is a chemical probe used to study RNA structure.
  • DMS reactivity typically indicates nucleotide accessibility: low reactivity suggests Watson-Crick (WC) base pairs, while high reactivity implies unpaired nucleotides.
  • Previous studies noted exceptions to this rule, but the frequency and structural basis of these outliers were not fully understood.

Purpose of the Study:

  • To systematically analyze DMS reactivity patterns in a large dataset of RNA structures.
  • To identify recurring 3D structural features associated with non-canonical DMS reactivity.
  • To explore the potential of DMS reactivity for detailed RNA structure and dynamics modeling.

Main Methods:

  • Systematic analysis of DMS reactivity data from 7,500 RNA constructs with known 3D structures.
  • Correlation of DMS reactivity values with base pairing status (WC vs. non-WC), solvent accessibility, hydrogen bonding, base stacking, and junction dynamics.
  • Investigation of DMS reactivity in non-canonical pairs against atomic distances and base pair geometry.

Main Results:

  • DMS reactivity spans four orders of magnitude, with a ~10% overlap between WC and non-WC nucleotides.
  • Non-WC bases with protected DMS reactivity showed increased hydrogen bonding and reduced solvent accessibility.
  • WC pairs with higher DMS reactivity were often located at junctions, associated with weaker base stacking and increased dynamics.
  • DMS reactivity in non-canonical pairs correlated with geometric parameters, allowing discrimination of 3D conformations.

Conclusions:

  • DMS chemical mapping provides atomic-scale resolution of RNA 3D structures beyond simple base-pairing status.
  • Deviations in DMS reactivity are linked to specific structural features like hydrogen bonding, solvent accessibility, and junction dynamics.
  • DMS reactivity patterns can be leveraged to build more accurate models of RNA structure and dynamics.