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, Bhubaneswar Mishra, Jason Reed

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number1665
JournalNature Communications
Volume8
Issue number1
DOIs
StatePublished - Dec 1 2017

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Clustered Regularly Interspaced Short Palindromic Repeats
sequencing
Nanoparticles
deoxyribonucleic acid
nanoparticles
DNA
atomic force microscopy
Follicular Lymphoma
Nanotechnology
Molecules
Videodisks
Patents
Biopsy
high speed
Genomics
Labeling
patents
genome
lymphatic system
Optics

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Mikheikin, A., Olsen, A., Leslie, K., Russell-Pavier, F., Yacoot, A., Picco, L., ... Reed, J. (2017). DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle. Nature Communications, 8(1), [1665]. https://doi.org/10.1038/s41467-017-01891-9

DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle. / Mikheikin, Andrey; Olsen, Anita; Leslie, Kevin; Russell-Pavier, Freddie; Yacoot, Andrew; Picco, Loren; Payton, Oliver; Toor, Amir; Chesney, Alden; Gimzewski, James K.; Mishra, Bhubaneswar; Reed, Jason.

In: Nature Communications, Vol. 8, No. 1, 1665, 01.12.2017.

Research output: Contribution to journalArticle

Mikheikin, A, Olsen, A, Leslie, K, Russell-Pavier, F, Yacoot, A, Picco, L, Payton, O, Toor, A, Chesney, A, Gimzewski, JK, Mishra, B & Reed, J 2017, 'DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle', Nature Communications, vol. 8, no. 1, 1665. https://doi.org/10.1038/s41467-017-01891-9
Mikheikin A, Olsen A, Leslie K, Russell-Pavier F, Yacoot A, Picco L et al. DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle. Nature Communications. 2017 Dec 1;8(1). 1665. https://doi.org/10.1038/s41467-017-01891-9
Mikheikin, Andrey ; Olsen, Anita ; Leslie, Kevin ; Russell-Pavier, Freddie ; Yacoot, Andrew ; Picco, Loren ; Payton, Oliver ; Toor, Amir ; Chesney, Alden ; Gimzewski, James K. ; Mishra, Bhubaneswar ; Reed, Jason. / DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle. In: Nature Communications. 2017 ; Vol. 8, No. 1.
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