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Updated: Feb 23, 2026

Robust 3D DNA FISH Using Directly Labeled Probes

Robust 3D DNA FISH Using Directly Labeled Probes

Published on: August 15, 2013

Fast, Background-Free DNA-PAINT Imaging Using FRET-Based Probes.

Alexander Auer^1,2, Maximilian T Strauss^1,2, Thomas Schlichthaerle^1,2

¹Department of Physics and Center for Nanoscience, Ludwig Maximilian University , Munich, Germany.

|September 6, 2017

Summary

We developed FRET-PAINT, a super-resolution microscopy technique. This method overcomes DNA-PAINT

Keywords:

DNA nanotechnology DNA-PAINT FRET Super-resolution microscopy fluorogenic probes

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Area of Science:

Super-resolution microscopy
Molecular imaging
Nanotechnology

Background:

DNA-PAINT microscopy achieves sub-5 nm resolution but is limited by slow acquisition due to background fluorescence.
Nonfluorogenic imager strands in DNA-PAINT emit light even when unbound, necessitating low imager concentrations and limiting imaging speed.

Purpose of the Study:

To overcome the speed limitations of DNA-PAINT microscopy.
To enable fast, background-free super-resolution imaging using DNA-PAINT.
To introduce a novel FRET-based approach for enhanced DNA-PAINT imaging.

Main Methods:

Development of FRET-based imaging probes (FRET-PAINT).
Assay of two FRET-PAINT approaches using fixed or transient acceptor dyes with donor-labeled DNA strands.
Application of FRET-PAINT to DNA origami structures and microtubules in a cellular environment.

Main Results:

Achieved high-quality super-resolution imaging on DNA origami structures in tens of seconds.
Demonstrated successful super-resolution imaging of cellular microtubules in under 30 seconds.
Significantly increased imager strand concentrations and reduced background noise.

Conclusions:

FRET-PAINT enables super-resolution imaging at speeds several orders of magnitude faster than conventional DNA-PAINT.
The technique combines the high resolution and multiplexing of DNA-PAINT with rapid image acquisition.
FRET-PAINT facilitates the study of dynamic biological processes using super-resolution microscopy.