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Updated: May 26, 2026
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DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition
Published on: February 9, 2024
Mapping the Structure and Conformational Landscape of the 10-23 DNAzyme
Evan R Cramer1, Holly L Shultz1, Michael D Purdy2
1Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia 26506, United States.
ACS Chemical Biology
|May 25, 2026
Summary
This study reveals the structure of the 10-23 deoxyribozyme (DNAzyme), a DNA catalyst with therapeutic potential. A protein scaffold enabled cryo-EM visualization, showing how metal ions activate the DNAzyme for RNA knockdown.
Area of Science:
- Biochemistry
- Structural Biology
- Molecular Biology
Background:
- Deoxyribozymes (DNAzymes) are DNA molecules with catalytic activity.
- The 10-23 DNAzyme is a key RNA-cleaving DNAzyme with potential for in vivo RNA knockdown.
- Limited structural data hinders rational design and optimization of DNAzymes for therapeutic applications.
Purpose of the Study:
- To determine the structure of the 10-23 DNAzyme-substrate complex.
- To investigate the dynamics and activation mechanism of the 10-23 DNAzyme.
- To establish a protein scaffolding method for DNAzyme structural studies.
Main Methods:
- Developed a T7 RNA polymerase-based protein scaffold for DNAzyme stabilization.
- Utilized cryo-electron microscopy (cryo-EM) to visualize the DNAzyme-substrate complex.
- Employed dimethyl sulfate (DMS) labeling to probe DNAzyme dynamics and metal ion interactions.
Main Results:
- Obtained a 4.5 Å cryo-EM reconstruction of the 10-23 DNAzyme-substrate complex.
- Identified a pseudoknot structure in the palindromic core, stabilized by guanine stacking.
- DMS probing revealed magnesium-dependent collapse of a loop onto the pseudoknot, compacting the catalytic core.
Conclusions:
- The structural and dynamic data support a metal-dependent hinged activation mechanism for the 10-23 DNAzyme.
- Protein scaffolding is a viable strategy for visualizing and studying DNAzyme structures.
- These findings provide a foundation for improving DNAzyme design for therapeutic and diagnostic applications.
