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Uncovering Hidden Dynamics of Natural Photonic Structures Using Holographic Imaging

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Hidden Structural Modules in a Cooperative RNA Folding Transition.

Brant Gracia¹, Hashim M Al-Hashimi², Namita Bisaria³

¹Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.

|March 22, 2018

Summary

RNA folding involves modular, incremental steps, not just large cooperative shifts. This study reveals how local folding and modest cooperativity in P5abc RNA create concerted behavior, crucial for RNA function and gene regulation.

Keywords:

RNA folding RNA structure probing RNA tertiary structure folding cooperativity group I intron kinetics tetrahymena ribozyme

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Published on: October 17, 2011

Area of Science:

Molecular Biology
Biochemistry
Structural Biology

Background:

Large-scale RNA rearrangements are essential for RNA-protein machines and gene regulation.
Understanding the orchestration of these rearrangements is key to deciphering RNA function.

Purpose of the Study:

To dissect a complex RNA rearrangement in P5abc RNA using high-throughput chemical footprinting.
To investigate the mechanism of cooperative rearrangements in RNA folding.

Main Methods:

High-throughput chemical footprinting was employed to analyze P5abc RNA.
Mutational analysis was used to disrupt or restore putative structural elements.

Main Results:

The rearrangement in P5abc RNA results from local folding of structural modules with incremental cooperativity.
Two distant secondary structure changes are coupled via a three-way junction and Mg2+-dependent tertiary structure.
Long-range contacts between modules contribute to cooperativity.

Conclusions:

Modular folding and incremental cooperativity are likely general mechanisms for RNA structure formation and function.
This approach can identify modularity in other complex RNA molecules.
Understanding RNA folding pathways is critical for RNA-based technologies and therapeutics.