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A DNA nanoscope via auto-cycling proximity recording

Author

Listed:
  • Thomas E. Schaus

    (Harvard University
    Harvard Medical School)

  • Sungwook Woo

    (Harvard University
    Harvard Medical School)

  • Feng Xuan

    (Harvard University
    Harvard Medical School)

  • Xi Chen

    (Harvard University
    Harvard Medical School)

  • Peng Yin

    (Harvard University
    Harvard Medical School)

Abstract

Analysis of the spatial arrangement of molecular features enables the engineering of synthetic nanostructures and the understanding of natural ones. The ability to acquire a comprehensive set of pairwise proximities between components would satisfy an increasing interest in investigating individual macromolecules and their interactions, but current biochemical techniques detect only a single proximity partner per probe. Here, we present a biochemical DNA nanoscopy method that records nanostructure features in situ and in detail for later readout. Based on a conceptually novel auto-cycling proximity recording (APR) mechanism, it continuously and repeatedly produces proximity records of any nearby pairs of DNA-barcoded probes, at physiological temperature, without altering the probes themselves. We demonstrate the production of dozens of records per probe, decode the spatial arrangements of 7 unique probes in a homogeneous sample, and repeatedly sample the same probes in different states.

Suggested Citation

  • Thomas E. Schaus & Sungwook Woo & Feng Xuan & Xi Chen & Peng Yin, 2017. "A DNA nanoscope via auto-cycling proximity recording," Nature Communications, Nature, vol. 8(1), pages 1-9, December.
  • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_s41467-017-00542-3
    DOI: 10.1038/s41467-017-00542-3
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    Cited by:

    1. Hong Kang & Yuexuan Yang & Bryan Wei, 2024. "Synthetic molecular switches driven by DNA-modifying enzymes," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    2. Sungwook Woo & Sinem K. Saka & Feng Xuan & Peng Yin, 2024. "Molecular robotic agents that survey molecular landscapes for information retrieval," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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