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Single-Molecule Kinetics and Super-Resolution Microscopy by Fluorescence Imaging of Transient Binding on DNA Origami

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Ralf Jungmann†§^#, Christian Steinhauer‡§^#, Max Scheible†, Anton Kuzyk†, Philip Tinnefeld*‡§

, and Friedrich C. Simmel*†§

^† Lehrstuhl für Bioelektronik, Physik-Department, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany

^‡ Angewandte Physik−Biophysik, Ludwig-Maximilians-Universität, Amalienstrasse 54, 80799 München, Germany

^§ Center for NanoScience, Ludwig-Maximilians-Universität, Schellingstrasse 4, 80799 München, Germany

Physikalische und Theoretische Chemie - NanoBioScience, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106 Braunschweig, Germany

Nano Lett., 2010, 10 (11), pp 4756–4761

DOI: 10.1021/nl103427w

Publication Date (Web): October 19, 2010

* To whom correspondence should be addressed, (F.C.S.) simmel@ph.tum.de or (P.T.) philip.tinnefeld@physik.uni-muenchen.de., #

These authors contributed equally to this work.

Section:

Biochemical Methods

Abstract

DNA origami is a powerful method for the programmable assembly of nanoscale molecular structures. For applications of these structures as functional biomaterials, the study of reaction kinetics and dynamic processes in real time and with high spatial resolution becomes increasingly important. We present a single-molecule assay for the study of binding and unbinding kinetics on DNA origami. We find that the kinetics of hybridization to single-stranded extensions on DNA origami is similar to isolated substrate-immobilized DNA with a slight position dependence on the origami. On the basis of the knowledge of the kinetics, we exploit reversible specific binding of labeled oligonucleotides to DNA nanostructures for PAINT (points accumulation for imaging in nanoscale topography) imaging with <30 nm resolution. The method is demonstrated for flat monomeric DNA structures as well as multimeric, ribbon-like DNA structures.

Keywords:

Nanobiotechnology; biophysics; DNA origami; fluorescence microscopy; super-resolution; single-molecule kinetics

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This article has been cited by 3 ACS Journal articles (3 most recent appear below).

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Single-Molecule Four-Color FRET Visualizes Energy-Transfer Paths on DNA Origami
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