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Riboswitches

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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
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Related Experiment Video

Updated: May 11, 2026

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study.

Olof Allnér¹, Lennart Nilsson, Alessandra Villa

¹Department of Biosciences and Nutrition, Karolinska Institutet, Center for Biosciences, SE-14183 Huddinge, Sweden. alessandra.villa@ki.se

RNA (New York, N.Y.)

|May 30, 2013

Summary

This summary is machine-generated.

Molecular dynamics simulations reveal how the adenine-sensing add A-riboswitch breaks its kissing loop. This study details the two-step process and identifies key interactions for riboswitch function.

Keywords:

RNA aptamer adenine riboswitch atomic interactions free energy calculation kissing loops molecular dynamics simulation

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Last Updated: May 11, 2026

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Area of Science:

Molecular Biology
Biophysics
Computational Biology

Background:

Riboswitches are RNA molecules that regulate gene expression through ligand binding and conformational changes.
Understanding riboswitch mechanisms requires detailed knowledge of their molecular interactions and structural rearrangements.

Purpose of the Study:

To investigate the breaking of the kissing loop in the adenine-sensing add A-riboswitch using all-atom molecular dynamics simulations.
To analyze the role of specific interactions in the tertiary structure formation and stabilization of the riboswitch aptamer domain.

Main Methods:

All-atom molecular dynamics simulations were employed to study the add A-riboswitch aptamer domain.
Umbrella sampling simulations were used to model the opening of hairpins, with the distance between loops as the reaction coordinate.
Simulations were performed both with and without the cognate ligand (adenine).

Main Results:

A two-step process was observed during kissing loop opening, involving initial loss of stacking and hydrogen bonds.
Specific base pairs (G37-C61 and G38-C60) were the last to break but did not significantly impact the energy profile.
Residue A24 was identified as crucial for anchoring loop helices, and differential hairpin flexibility was observed during loop opening.

Conclusions:

The study elucidates the dynamics of kissing loop disassembly in the add A-riboswitch, highlighting its importance in riboswitch function.
The findings contribute to a deeper understanding of RNA structural dynamics and the intricate mechanisms governing riboswitch-mediated gene regulation.