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
Iterative DNA proximity ligation
"We extend the concept of DNA proximity ligation from a single readout per oligonucleotide pair to multiple reversible, iterative ligations re-using the same oligonucleotide molecules. Using iterative proximity ligation (IPL), we can in principle capture multiple ligation events between each oligonucleotide and its various neighbors and thus recover a far richer knowledge about their relative positions than single, irreversible ligation events. IPL would thus act to sample and record local molecular neighborhoods. By integrating a unique DNA barcode into each participating oligonucleotide, we can catalog the individual ligation events and thus capture the positional information contained therein in a high throughput manner using next-generation DNA sequencing. We propose that by interpreting IPL sequencing results in the context of graph theory and by applying spring layout algorithms, we can recover geometric patterns of objects labeled by DNA. Using simulations, we demonstrate that we can in principle recover letter patterns photolithographed onto slide surfaces using only IPL sequencing data, illustrating how our technique maps complex spatial configurations into DNA sequences and then – using only this sequence information – recovers them. We complement our theoretical work with an experimental proof-of-concept of iterative proximity ligation on an oligonucleotide population."