Single molecule characterization of DNA binding and strand displacement reactions on lithographic DNA origami microarrays

Max B. Scheible, Günther Pardatscher, Anton Kuzyk, Friedrich C. Simmel*

*Corresponding author for this work

Research output: Contribution to journalArticleScientificpeer-review

35 Citations (Scopus)

Abstract

The combination of molecular self-assembly based on the DNA origami technique with lithographic patterning enables the creation of hierarchically ordered nanosystems, in which single molecules are positioned at precise locations on multiple length scales. Based on a hybrid assembly protocol utilizing DNA self-assembly and electron-beam lithography on transparent glass substrates, we here demonstrate a DNA origami microarray, which is compatible with the requirements of single molecule fluorescence and super-resolution microscopy. The spatial arrangement allows for a simple and reliable identification of single molecule events and facilitates automated read-out and data analysis. As a specific application, we utilize the microarray to characterize the performance of DNA strand displacement reactions localized on the DNA origami structures. We find considerable variability within the array, which results both from structural variations and stochastic reaction dynamics prevalent at the single molecule level.

Original languageEnglish
Pages (from-to)1627-1633
Number of pages7
JournalNano Letters
Volume14
Issue number3
DOIs
Publication statusPublished - 12 Mar 2014
MoE publication typeA1 Journal article-refereed

Keywords

  • DNA origami
  • DNA strand displacement reactions
  • Dynamic DNA nanotechnology
  • e-beam lithography
  • single molecule fluorescence

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