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Structural Basis for Fluorescence Activation by Pepper RNA.

Huw C Rees¹, Wojciech Gogacz², Nan-Sheng Li²

¹Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States.

ACS Chemical Biology

|June 27, 2022

Summary

This summary is machine-generated.

Pepper RNA aptamers bind and activate fluorescence in benzylidene-cyanophenyl (HBC) derivatives. Structural analysis reveals a unique binding pocket, distinct from G-quadruplexes, enabling potential applications in small molecule detection.

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Area of Science:

Molecular Biology
Structural Biology
Biochemistry

Background:

Pepper is a fluorogenic RNA aptamer that binds benzylidene-cyanophenyl (HBC) derivatives, activating their fluorescence.
Understanding the structural basis of this binding is crucial for aptamer-based sensing applications.

Purpose of the Study:

To determine the high-resolution structures of Pepper RNA bound to HBC ligands.
To elucidate the folding mechanism and nucleotide organization responsible for creating the ligand binding site.

Main Methods:

Antibody-assisted crystallography was employed to determine the structures of Pepper-HBC complexes.
Structural data were obtained at 2.3 and 2.7 Å resolutions for two different HBC derivatives.

Main Results:

Pepper RNA adopts an elongated structure with an internal bulge forming the primary ligand binding site.
A unique base-quadruple·base-triple stack, not a G-quadruplex, sandwiches the HBC ligand, stabilized by a U·G wobble pair.
Site-bound Mg2+ ions contribute structurally and energetically to ligand binding.

Conclusions:

The study reveals the specific structural features of the Pepper aptamer responsible for high-affinity HBC binding.
These findings provide insights into aptamer-ligand interactions and suggest potential for Pepper's use in detecting other small molecules and metal ions in vivo.