Super-resolution fingerprinting detects chemical reactions and idiosyncrasies of single DNA pegboards

Alexander Johnson-Buck, Jeanette Nangreave, Do Nyun Kim, Mark Bathe, Hao Yan, Nils G. Walter

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

We employ the single-particle fluorescence nanoscopy technique points accumulation for imaging in nanoscale topography (PAINT) using site-specific DNA probes to acquire two-dimensional density maps of specific features patterned on nanoscale DNA origami pegboards. We show that PAINT has a localization accuracy of ∼10 nm that is sufficient to reliably distinguish dense (>104 features μm-2) sub-100 nm patterns of oligonucleotide features. We employ two-color PAINT to follow enzyme-catalyzed modification of features on individual origami and to show that single nanopegboards exhibit stable, spatially heterogeneous probe-binding patterns, or "fingerprints." Finally, we present experimental and modeling evidence suggesting that these fingerprints may arise from feature spacing variations that locally modulate the probe binding kinetics. Our study highlights the power of fluorescence nanoscopy to perform quality control on individual soft nanodevices that interact with and position reagents in solution.

Original languageEnglish
Pages (from-to)728-733
Number of pages6
JournalNano Letters
Volume13
Issue number2
DOIs
Publication statusPublished - Feb 13 2013

Fingerprint

Topography
Chemical reactions
chemical reactions
topography
DNA
deoxyribonucleic acid
Imaging techniques
probes
Fluorescence
fluorescence
oligonucleotides
Oligonucleotides
DNA Probes
quality control
Quality control
reagents
enzymes
Enzymes
spacing
Color

Keywords

  • Chemical imaging
  • DNA origami
  • PAINT
  • points accumulation for imaging in nanoscale topography
  • single molecule super-resolution fluorescence microscopy

ASJC Scopus subject areas

  • Condensed Matter Physics
  • Bioengineering
  • Chemistry(all)
  • Materials Science(all)
  • Mechanical Engineering

Cite this

Super-resolution fingerprinting detects chemical reactions and idiosyncrasies of single DNA pegboards. / Johnson-Buck, Alexander; Nangreave, Jeanette; Kim, Do Nyun; Bathe, Mark; Yan, Hao; Walter, Nils G.

In: Nano Letters, Vol. 13, No. 2, 13.02.2013, p. 728-733.

Research output: Contribution to journalArticle

Johnson-Buck, A, Nangreave, J, Kim, DN, Bathe, M, Yan, H & Walter, NG 2013, 'Super-resolution fingerprinting detects chemical reactions and idiosyncrasies of single DNA pegboards', Nano Letters, vol. 13, no. 2, pp. 728-733. https://doi.org/10.1021/nl304415b
Johnson-Buck, Alexander ; Nangreave, Jeanette ; Kim, Do Nyun ; Bathe, Mark ; Yan, Hao ; Walter, Nils G. / Super-resolution fingerprinting detects chemical reactions and idiosyncrasies of single DNA pegboards. In: Nano Letters. 2013 ; Vol. 13, No. 2. pp. 728-733.
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