DNA nanoscopy
DNA nanoscopy or DNA microscopy uses DNA-DNA interactions and then using sequencing to form a visual image of the geometry being studied.
- Original APR DNA nanoscope — auto proximity recording using DNA, original publication Nature.
- Scaling up with a “molecular ruler” — bioRxiv preprint from the same lab; distance records calibrated on origami, reconstructing patterns with >100 unique features. bioRxiv, Molecular Systems Lab
- Primer Exchange Reaction (PER) — the isothermal DNA synthesis cascade that underpins several recording schemes. Nature Chemistry (2017). PMC
- DNA microscopy (optics-free) — original Cell paper: encodes proximities into DNA via a stand-alone reaction + computational reconstruction. ScienceDirect
- Volumetric DNA microscopy — 3D, organism-scale extension; Nature Biotechnology (2025). Nature, PMC
- SCOPE — spatial reConstruction via Oligonucleotide Proximity Encoding; an optics-free 2D array demo inspired by DNA microscopy. PMC
- Error-correction/algorithms for DNA microscopy — a 2024 methods paper focused on reconstruction robustness. Nature
- “DNA-GPS” for large-scale optics-free spatial genomics. ScienceDirect
- Review - Microscopy-by-sequencing primer (Trends in Biotechnology, 2019) — great conceptual survey. PMC, marcottelab.org
- Review - Imaging-by-sequencing methods (Nanoscale, 2023) — broader technique landscape & contrasts vs optical ST/PAINT. RSC Publishing
The auto proximity recording paper mentions that probes can be attached via either antibodies or aptamers, which is handy for protein targets you care about. Nature
DNA-PAINT context (optical, but DNA-programmed): If you’re mixing sequencing-based readout with optical benchmarks, these are handy: a recent DNA-PAINT review (2025) and Ångström-resolution DNA-PAINT (2023). RSC Publishing, Nature