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Related Concept Videos

RNA Structure01:23

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The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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Related Experiment Video

Updated: Sep 10, 2025

Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes
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A Multiscale Study to Characterize SHAPE Probe/RNA Molecules Prereactive Complex and Its Role in Initiating the SHAPE

Cécilia Hognon1, Ameni Ben Abdeljaoued1, Pierre Hardouin1

  • 1Université Paris Cité, CiTCoM, CNRS, F-75006 Paris, France.

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Understanding RNA structure is key to cell function. This study reveals how the SHAPE chemical probe interacts with RNA, clarifying its reactivity through molecular simulations and quantum mechanics.

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Area of Science:

  • Structural Biology
  • Computational Chemistry
  • Molecular Biophysics

Background:

  • RNA 3D structure dictates function, but high-resolution determination is challenging.
  • Chemical probing, like SHAPE, is popular but its reaction mechanism is poorly understood.
  • SHAPE reactivity is linked to RNA local structure and dynamics.

Purpose of the Study:

  • To elucidate the relationship between RNA local structure, dynamics, and SHAPE chemical reactivity.
  • To provide molecular insights into the SHAPE probe's prereactive complex formation and binding mode.

Main Methods:

  • Multiscale approach combining biased molecular dynamics (MD) simulations and QM/MM calculations.
  • Umbrella sampling (US) MD simulations to analyze the binding angle and prereactive complex formation.
  • QM/MM simulations to characterize the acylation reaction's initial steps and hydroxyl deprotonation.

Main Results:

  • The local RNA environment critically influences SHAPE probe recruitment and accommodation.
  • Favorable binding, influenced by the binding angle, is essential for prereactive complex formation.
  • Hydroxyl deprotonation and acylation depend on the local environment and probe proximity; oxyanion formation is not required beforehand.

Conclusions:

  • This study provides novel molecular-level understanding of SHAPE probe reactivity.
  • Findings clarify unexplained SHAPE reactivities and highlight the importance of local RNA structure and dynamics.
  • The results advance the application of chemical probing for RNA structure determination.