DNA origami nanorulers and emerging reference structures

Abstract

The DNA origami technique itself is considered a milestone of DNA nanotechnology and DNA origami nanorulers represent the first widespread application of this technique. DNA origami nanorulers are used to demonstrate the capabilities of techniques and are valuable training samples. They have meanwhile been developed for a multitude of microscopy methods including optical microscopy, atomic force microscopy, and electron microscopy, and their unique properties are further exploited to develop point-light sources, brightness references, nanophotonic test structures, and alignment tools for correlative microscopy. In this perspective, we provide an overview of the basics of DNA origami nanorulers and their increasing applications in fields of optical and especially super-resolution fluorescence microscopy. In addition, emerging applications of reference structures based on DNA origami are discussed together with recent developments.

Self‐Regeneration and Self‐Healing in DNA Origami Nanostructures

“…To establish exemplary self‐repair mechanisms within functional nanodevices, we focused on DNA origami nanostructures with a controlled number and position of fluorescent labels acting as nanorulers. Such nanorulers can serve as distance reference structures for emerging super‐resolution microscopy applications as well as brightness reference standards to determine, for example, the sensitivity of a smartphone microscope [28–32] . While bright point light sources are highly desired for calibration purposes, [33] nanoscale brightness references suffer from molecular device degradation under wear conditions, for example, by photobleaching of the labels and photoinduced damage to the nanostructure during the measurement so that a brightness reference is only providing reliable data for a short period of time.…”

“…To establish exemplary self-repair mechanisms within functional nanodevices,w ef ocused on DNAo rigami nanostructures with ac ontrolled number and position of fluores-cent labels acting as nanorulers.Such nanorulers can serve as distance reference structures for emerging super-resolution microscopy applications as well as brightness reference standards to determine,f or example,t he sensitivity of as martphone microscope. [28][29][30][31][32] While bright point light sources are highly desired for calibration purposes, [33] nanoscale brightness references suffer from molecular device degradation under wear conditions,f or example,b yp hotobleaching of the labels and photoinduced damage to the nanostructure during the measurement so that ab rightness reference is only providing reliable data for ashort period of time.F irst, we studied the possibility to maintain the DNA device by regenerating the brightness functionality by refreshing with non-bleached units.The 12-helix bundle (12HB) DNAo rigami shown in Figure 1A was labeled with fluorescent dyes by hybridizing protruding single-stranded DNA extensions (called docking strands) with an excess of complementary dye-labeled strands (called imager strands) in solution (experimental procedures,m ethods and materials are provided in Supporting Information). [29] Fort he 12HB shown in Figure 1A,labeling of 100 docking sites was ensured by saturating the docking sites with a5 nM solution of 20 nucleotide (nt) long complementary fluorescent imager strands ( Figure 1B).…”

Selbstregeneration und Selbstheilung in DNA‐Origami‐Nanostrukturen

“…Solche Nanolineale können als Distanzstandards für moderne Superauflösungsmikroskopie verwendet werden sowie als Helligkeitsstandards, um z. B. die Empfindlichkeit eines Smartphone‐Mikroskops zu bestimmen [28–32] . Während helle punktförmige Lichtquellen für Kalibrierzwecke sehr begehrt sind, [33] leiden nanoskalige Helligkeitsstandards während einer Messung an molekularer Degradierung, z.…”

“…Solche Nanolineale kçnnen als Distanzstandards fürm oderne Superauflçsungsmikroskopie verwendet werden sowie als Helligkeitsstandards,u mz .B.d ie Empfindlichkeit eines Smartphone-Mikroskops zu bestimmen. [28][29][30][31][32] Während helle punktfçrmige Lichtquellen fürK alibrierzwecke sehr begehrt sind, [33] leiden nanoskalige Helligkeitsstandards während einer Messung an molekularer Degradierung,z .B.d urch Photobleichen der Markierungen und durch photoinduzierte Schäden an der Nanostruktur,sodass ein Helligkeitsstandard nur fürkurze Zeit zuverlässige Daten liefert. Zunächst haben wir die Mçglichkeit untersucht, ein DNA-Nanogerätdadurch zu stabilisieren, dass die Helligkeitsfunktion durch Auffrischen mit nicht geblichenen Bausteinen regeneriert wird.…”

DNA Manipulation and Single-Molecule Imaging

“…DNA nanostructures with single binding sites spaced 5 nm apart were observed as the “MPI” and “LMU” logos [ 204 ]. Thus, DNA-PAINT has provided new insight into the design analysis of DNA-origami nanostructures [ 205 , 206 , 207 , 208 , 209 ].…”