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On-Origami Molecular Crowding Control of G-Quadruplex DNAzymes.

Bei Yang1, Rujie Wang1, Weiying Li2

  • 1School of Chemical Science and Engineering, Shanghai Research Institute for Intelligent Autonomous Systems, Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Tongji University, Shanghai, 200092, China.

Small Methods
|February 12, 2025
PubMed
Summary

DNA origami precisely controls biomacromolecule crowding, optimizing DNAzyme (G-quadruplex-hemin complex) catalytic efficiency. This approach enables the development of a novel sensor for detecting Human Papillomavirus (HPV)-16 DNA.

Keywords:
DNA origamiDNAzymeG‐quadruplexmechanochemical sensornano‐template

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Area of Science:

  • Biotechnology and Nanotechnology
  • Molecular Biology and Biochemistry

Background:

  • Biomacromolecule crowding influences cellular processes and requires optimization on artificial interfaces for enhanced activity.
  • Achieving optimal density and activity of target molecules on artificial surfaces remains a significant challenge.

Purpose of the Study:

  • To utilize DNA origami as a precise template for regulating the density and crowding of DNAzyme (G-quadruplex-hemin complex).
  • To investigate the impact of crowding on DNAzyme catalytic efficiency and explore its application in biosensing.

Main Methods:

  • Employing DNA origami as a scaffold to control the spatial arrangement and density of G-quadruplex-hemin DNAzyme.
  • Characterizing the catalytic efficiency of the DNAzyme at varying crowding levels.
  • Designing and constructing a DNA origami-based mechanochemical sensor.

Main Results:

  • DNA origami enabled precise regulation of DNAzyme density, achieving high catalytic efficiency at moderate crowding.
  • Increased crowding beyond optimal levels led to DNAzyme inactivation and reduced catalytic performance.
  • DNA origami served as an isotropic scaffold for creating nanoenzyme ensembles with tunable catalytic efficiencies.

Conclusions:

  • DNA origami is a versatile tool for optimizing nanoenzyme activity through controlled crowding.
  • The developed DNA origami-DNAzyme system successfully detected Human Papillomavirus (HPV)-16 DNA fragments, demonstrating its potential in disease diagnostics.