title: Toward quantitative fluorescence microscopy with DNA origami nanorulers.
abstract: The dynamic development of fluorescence microscopy has created a large number of new techniques, many of which are able to overcome the diffraction limit. This chapter describes the use of DNA origami nanostructures as scaffold for quantifying microscope properties such as sensitivity and resolution. The DNA origami technique enables placing of a defined number of fluorescent dyes in programmed geometries. We present a variety of DNA origami nanorulers that include nanorulers with defined labeling density and defined distances between marks. The chapter summarizes the advantages such as practically free choice of dyes and labeling density and presents examples of nanorulers in use. New triangular DNA origami nanorulers that do not require photoinduced switching by imaging transient binding to DNA nanostructures are also reported. Finally, we simulate fluorescence images of DNA origami nanorulers and reveal that the optimal DNA nanoruler for a specific application has an intermark distance that is roughly 1.3-fold the expected optical resolution.
authors: Braunschweig University of Technology, Institute for Physical & Theoretical Chemistry and Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany.
authors: Susanne
authors: S
authors: Beater
authors: Braunschweig University of Technology, Institute for Physical & Theoretical Chemistry and Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany.
authors: Mario
authors: M
authors: Raab
authors: Braunschweig University of Technology, Institute for Physical & Theoretical Chemistry and Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany.
authors: Philip
authors: P
authors: Tinnefeld
mesh_terms: D003198:Computer Simulation; D015342:DNA Probes / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D008856:Microscopy, Fluorescence / Q000379:methods / Q000592:standards; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D012015:Reference Standards; D059010:Single-Cell Analysis / Q000379:methods / Q000592:standards*; D013194:Staining and Labeling
chemical_list: D015342:DNA Probes; D005456:Fluorescent Dyes
keywords: DNA origami; Fluorescence microscopy; Nanoruler; Superresolution microscopy