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Superresolution Microscopy Enhances DNA Nanostructures

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A method of superresolution microscopy, called DNA-PAINT, allows all of the strands within DNA-based nanostructures to be visualized individually, with a high degree of spatial resolution. Using DNA-PAINT, researchers can directly visualize all components of the DNA origami structure and determine how well the DNA strands have self-assembled. The technique can quantify both incorporation and accessibility of all individual strands in DNA origami with molecular resolution.

DNA-PAINT superresolution microscopy technique, LMU.
With DNA-PAINT it is possible to visualize all the strands in DNA nanostructures individually. Courtesy of Maximilian Strauss, Max Planck Institute for Biochemistry.

DNA origami structures are essentially assembled by allowing one long single-stranded DNA molecule (the “scaffold” strand) to interact in a controlled, predefined manner with a set of shorter “staple” strands. The staple strands bind to specific stretches of the scaffold strand, progressively folding it into the desired form.

The DNA-PAINT technique, developed by researchers at Ludwig Maximilian University (LMU), makes use of the specificity of DNA-DNA interactions. Short “imager” strands, linked to dye molecules that pair up with complementary sequences, are used to identify sites that are accessible for binding. Imager strands interact with their target sites, producing a blinking signal.

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“By comparing the information in the individual fluorescence images, we are able to attain a higher resolution, so that we can inspect the whole structure in detail,” said Maximilian Strauss, researcher at the Max Planck Institute for Biochemistry at LMU.

“This phenomenon can be understood as follows," Strauss explained. "Let’s say we’re looking at a house with two illuminated windows. Seen from a certain distance, it appears as if the light is coming from one source. However, one can readily distinguish between the positions of the two windows if the lights are alternately switched on and off.”

In a similar way, the DNA-PAINT technique allows researchers to determine the positions of the bound staple strands precisely. The blinking signal emitted by imager strands reveals sites that are available for binding.

Use of DNA-PAINT revealed that strand incorporation strongly correlated with the position in the structure.

The DNA-PAINT method offers direct feedback for the rational refinement of the design and assembly process of DNA nanostructures and provides a quantitative explanation for efficiencies of DNA-based nanomachines.

According to researchers, the method can be applied to virtually any DNA-nanostructure geometry. Researchers believe that DNA-PAINT also could be used to characterize the labeling efficiency of antibodies or cellular proteins and nucleic acids, making it of interest for superresolution microscopy in general and quantitative structural biology in particular.

The research was published in Nature Communications (doi:10.1038/s41467-018-04031-z).

Published: June 2018
Glossary
nanopositioning
Nanopositioning refers to the precise and controlled movement or manipulation of objects or components at the nanometer scale. This technology enables the positioning of objects with extremely high accuracy and resolution, typically in the range of nanometers or even sub-nanometer levels. Nanopositioning systems are employed in various scientific, industrial, and research applications where ultra-precise positioning is required. Key features and aspects of nanopositioning include: Small...
nano
An SI prefix meaning one billionth (10-9). Nano can also be used to indicate the study of atoms, molecules and other structures and particles on the nanometer scale. Nano-optics (also referred to as nanophotonics), for example, is the study of how light and light-matter interactions behave on the nanometer scale. See nanophotonics.
superresolution
Superresolution refers to the enhancement or improvement of the spatial resolution beyond the conventional limits imposed by the diffraction of light. In the context of imaging, it is a set of techniques and algorithms that aim to achieve higher resolution images than what is traditionally possible using standard imaging systems. In conventional optical microscopy, the resolution is limited by the diffraction of light, a phenomenon described by Ernst Abbe's diffraction limit. This limit sets a...
Research & TechnologyeducationEuropeImagingMicroscopyNanopositioningnanoOpticssuperresolutionBiophotonicsnanostructureDNA origamifluorescent imagingDNA nanostructuresBioScan

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