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High-speed multiplexed DNA-PAINT imaging of nuclear organization using an expanded sequence repertoire
Abhinav Banerjee1, Micky Anand1, Mansi Srivastava1,2
1Department of Biochemistry, Indian Institute of Science, Malleswaram, Bangalore, India.
Nature Communications
|April 22, 2026
Summary
This study introduces faster DNA-PAINT imaging sequences for visualizing multiple targets in cells. The enhanced method allows for 12-plex super-resolution imaging, improving nanoscale biological analysis.
Area of Science:
- Biophysics
- Molecular Biology
- Nanotechnology
Background:
- DNA-Points Accumulation for Imaging in Nanoscale Topography (DNA-PAINT) is a super-resolution microscopy technique.
- Multiplexed imaging allows visualization of multiple targets simultaneously.
Purpose of the Study:
- To develop speed-optimized DNA-PAINT sequences for enhanced multiplexed imaging.
- To enable visualization of up to twelve targets sequentially at high resolution.
Main Methods:
- Implementation of the Exchange-PAINT protocol.
- Development of speed-optimized imager sequences for DNA-PAINT.
- Creation of a comprehensive analysis pipeline for nanoscale chromatin organization.
Main Results:
- Demonstrated 12-plex super-resolved imaging of DNA origami nanostructures in four hours with 3-5 nm precision.
- Achieved 9-plex super-resolution imaging of nuclear targets.
- Captured loss of chromatin contacts upon transcription inhibition using multiplexed imaging and the analysis pipeline.
Conclusions:
- Accelerated speed and high spatial resolution are achievable in multiplexed super-resolution imaging.
- The developed sequences and pipeline facilitate in-depth mapping of the nuclear landscape.
- This advancement promotes broader adoption of DNA-PAINT for cellular imaging applications.
