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Modulating transformation of DNA origami nanoarray via sequence design
Dongfang Wang1,2, Fiona Cole3, Martina Pfeiffer3
1School of Biomedical Engineering, University of Science and Technology of China, Hefei, China.
Nature Communications
|July 2, 2025
Summary
Researchers explored DNA domino arrays, finding that base design at four-way junctions controls nanoarray transformations. This work enables predictable modulation of DNA nanostructures for advanced applications.
Area of Science:
- DNA nanotechnology
- Structural DNA nanotechnology
- Biomolecular engineering
Background:
- Four-way DNA junctions are fundamental building blocks in DNA nanotechnology.
- Reconfigurable DNA nanoarrays (domino arrays) utilize these junctions for stepwise transformations.
- Understanding junction design is crucial for controlling nanoarray behavior.
Purpose of the Study:
- To investigate how DNA base design at four-way junctions influences the kinetics and thermodynamics of transformations in DNA domino arrays.
- To establish a platform for studying the designable modulation of DNA nanoarray transformations.
- To explore the coordinated transformation of multiple four-way junctions within a nanoarray.
Main Methods:
- Fabrication of a DNA domino array with uniform sequences at each junction.
- Utilizing Atomic Force Microscopy (AFM) for structural imaging.
- Employing single-molecule Förster resonance energy transfer (smFRET) microscopy for kinetic and thermodynamic analysis.
Main Results:
- Demonstrated that specific DNA base designs at junctions enable predictable modulation of four-way junction configurations.
- Showcased the ability to regulate the energy difference between junction states, controlling transformation pathways.
- Observed coordinated transformations across the DNA domino array.
Conclusions:
- The design of DNA bases at four-way junctions is a key factor in controlling the transformation dynamics of reconfigurable DNA nanoarrays.
- This study provides a foundation for the rational design of complex, stepwise transformations in DNA nanostructures.
- The developed platform facilitates detailed investigation of nanoarray behavior using advanced microscopy techniques.
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