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Nature communications
11 21, 2017;8 (1): 1665.

DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle.

Andrey Mikheikin, Anita Olsen, Kevin Leslie, Freddie Russell-Pavier, Andrew Yacoot, Loren Picco, Oliver Payton, Amir Toor, Alden Chesney, James K Gimzewski, Bud Mishra, Jason Reed
Author Information
  1. Andrey Mikheikin: Department of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA.
  2. Anita Olsen: Department of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA.
  3. Kevin Leslie: Department of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA.
  4. Freddie Russell-Pavier: National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, Middlesex, UK.
  5. Andrew Yacoot: National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, Middlesex, UK.
  6. Loren Picco: Interface Analysis Centre, H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK.
  7. Oliver Payton: Interface Analysis Centre, H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK.
  8. Amir Toor: Department of Internal Medicine, VCU School of Medicine, Richmond, 23284, VA, USA.
  9. Alden Chesney: VCU Massey Cancer Center, Richmond, 23284, VA, USA.
  10. James K Gimzewski: Department of Chemistry and Biochemistry, UCLA, Los Angeles, 90095, CA, USA. ORCID
  11. Bud Mishra: Departments of Computer Science and Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, 10012, NY, USA.
  12. Jason Reed: Department of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA. jcreed@vcu.edu.
PMID: 29162844 DOI: 10.1038/s41467-017-01891-9

Abstract

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.

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Grants

  1. R01 CA185189/NCI NIH HHS
  2. R01 GM094388/NIGMS NIH HHS
  3. P30 CA016059/NCI NIH HHS

MeSH Term

CRISPR-Cas Systems
Chromosome Mapping
DNA
Genomics
High-Throughput Nucleotide Sequencing
Humans
Image Processing, Computer-Assisted
Immunoglobulin Heavy Chains
Lymphoma, Follicular
Microscopy, Atomic Force
Nanoparticles
Nanotechnology
Proto-Oncogene Proteins c-bcl-2
Translocation, Genetic

Chemicals

Immunoglobulin Heavy Chains
Proto-Oncogene Proteins c-bcl-2
DNA
Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

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