DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle

Andrey Mikheikin, Oliver Payton, Loren Picco, Freddie Russell-Pavier, Andrew Yacoot, Anita Olsen, Kevin Leslie, A Toor, A Chesney, JK Gimzewski, Bud Mishra, Jason Reed

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Progress in whole-genome sequencing using short-read (e.g., <150 bp), next-generation sequencing technologies has reinvigorated interest in high-resolution physical mapping to fill technical gaps that are not well addressed by sequencing. Here, we report two technical advances in DNA nanotechnology and single-molecule genomics: (1) we describe a labeling technique (CRISPR-Cas9 nanoparticles) for high-speed AFM-based physical mapping of DNA and (2) the first successful demonstration of using DVD optics to image DNA molecules with high-speed AFM. As a proof of principle, we used this new “nanomapping” method to detect and map precisely BCL2–IGH translocations present in lymph node biopsies of follicular lymphoma patents. This HS-AFM “nanomapping” technique can be complementary to both sequencing and other physical mapping approaches.
Original languageEnglish
Pages (from-to)1665-1674
Number of pages9
JournalNature Communications
Publication statusPublished - 21 Nov 2017


  • DNA
  • CRISPR–Cas
  • AFM
  • high-speed AFM
  • High-speed atomic force microscopy

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    Mikheikin, A., Payton, O., Picco, L., Russell-Pavier, F., Yacoot, A., Olsen, A., Leslie, K., Toor, A., Chesney, A., Gimzewski, JK., Mishra, B., & Reed, J. (2017). DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle. Nature Communications, 8, 1665-1674. https://doi.org/10.1038/s41467-017-01891-9