3D super-resolution microscopy performance and quantitative analysis assessment using DNA-PAINT and DNA origami test samples

Lin, Ruey‐Mo; Clowsley, Alexander H.; Lutz, Tobias; Baddeley, David; Soeller, Christian

doi:10.1016/j.ymeth.2019.05.018

Cited by 27 publications

(20 citation statements)

References 58 publications

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“…To improve the reproducibility of SMLM systems, test and calibration procedures are required prior to starting a new experiment, to ensure optimal system performance and quantitative analysis. 95 NPs such as microspheres, and commercially available origami test samples such as GATTAquant slides are used for SRM 2D and 3D validation procedures. [95][96][97][98][99][100][101] Similarly, software packages that allow analysis, visualization and quantification of SMLM images must also be validated.…”

Section: Robust and Reproduciblementioning

confidence: 99%

“…95 NPs such as microspheres, and commercially available origami test samples such as GATTAquant slides are used for SRM 2D and 3D validation procedures. [95][96][97][98][99][100][101] Similarly, software packages that allow analysis, visualization and quantification of SMLM images must also be validated. These systems can influence data output, and generally use different parameters and terminology, making the selection of an optimal software difficult for the end user.…”

Section: Robust and Reproduciblementioning

confidence: 99%

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Can super-resolution microscopy become a standard characterization technique for materials chemistry?

et al. 2022

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Section: Robust and Reproduciblementioning

confidence: 99%

Section: Robust and Reproduciblementioning

confidence: 99%

Can super-resolution microscopy become a standard characterization technique for materials chemistry?

et al. 2022

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“…The dark time τ D obtained by fitting this CDF to experimental dark time distributions was used to conduct qPAINT analysis. To calculate the number of binding sites uncalibrated qPAINT indices were determined as the inverse of dark times 6,31 . The qPAINT indices were pooled for 6 and 5 spot containing tiles, respectively.…”

Section: Dna-paint Experimentsmentioning

confidence: 99%

Repeat DNA-PAINT suppresses background and non-specific signals in optical nanoscopy

et al. 2021

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DNA-PAINT is a versatile optical super-resolution technique relying on the transient binding of fluorescent DNA ‘imagers’ to target epitopes. Its performance in biological samples is often constrained by strong background signals and non-specific binding events, both exacerbated by high imager concentrations. Here we describe Repeat DNA-PAINT, a method that enables a substantial reduction in imager concentration, thus suppressing spurious signals. Additionally, Repeat DNA-PAINT reduces photoinduced target-site loss and can accelerate sampling, all without affecting spatial resolution.

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“…For this reason, instead of the stochastic photoactivation of a permanently bound fluorophore, PAINT depends exclusively on the stochastic/temporary binding of a fluorescent ligand. Using the characteristics of PAINT, DNA-PAINT, which is an extension of PAINT, has been used as a powerful tool in the characterization of DNA-origami nanostructures (e.g., including tetrahedrons, triangular prisms, cubes, pentagonal prisms, and hexagonal prisms) [201][202][203]. In DNA-PAINT imaging, the stochastic blinking of targets is achieved by the transient hybridization of short, dye-labeled DNA oligonucleotides to a complementary target DNA molecule.…”

Section: Single-molecule Imaging For Dna Origamimentioning

confidence: 99%

DNA Manipulation and Single-Molecule Imaging

2021

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DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. In this review, we provide an overview of the unique studies on DNA manipulation and single-molecule imaging to analyze the dynamic interaction between DNA and protein.

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3D super-resolution microscopy performance and quantitative analysis assessment using DNA-PAINT and DNA origami test samples

Cited by 27 publications

References 58 publications

Can super-resolution microscopy become a standard characterization technique for materials chemistry?

Can super-resolution microscopy become a standard characterization technique for materials chemistry?

Repeat DNA-PAINT suppresses background and non-specific signals in optical nanoscopy

DNA Manipulation and Single-Molecule Imaging

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