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

28 Citations (Scopus)


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
Issue number2
Publication statusPublished - Feb 13 2013



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

ASJC Scopus subject areas

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

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