High-Speed Super-Resolution Imaging Using Protein-Assisted DNA-PAINT

Filius, Mike; Cui, Tao; Ananth, Adithya N.; Docter, M.W.; Hegge, Jorrit W.; Oost, John van der; Joo, Chirlmin

doi:10.1021/acs.nanolett.9b04277

Cited by 52 publications

(38 citation statements)

References 42 publications

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“…Previously, Xu et al applied dual-objective STORM in 3D imaging to enhance image quality by increasing the output of photons in each acquisition [ 55 ]. In chemical control, a specific protein (i.e., Agos [ 56 ]) loading is employed to increase the binding speed of the imager stand to the target site as well as increase the imaging speed up to 30 times using the combination of FRET and DNA-PAINT [ 43 ]. Moreover, the combination of a detection method along with various labeling dyes allows the monitoring of the interaction between dye and DNA molecule, which allows precise structural localization in customizable applications [ 57 ].…”

Section: Discussionmentioning

confidence: 99%

Toward Sub-Diffraction Imaging of Single-DNA Molecule Sensors Based on Stochastic Switching Localization Microscopy

Lee

Batjikh

Kang

2020

Sensors

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The natural characteristics of deoxyribonucleic acid (DNA) enable its advanced applications in nanotechnology as a special tool that can be detected by high-resolution imaging with precise localization. Super-resolution (SR) microscopy enables the examination of nanoscale molecules beyond the diffraction limit. With the development of SR microscopy methods, DNA nanostructures can now be optically assessed. Using the specific binding of fluorophores with their target molecules, advanced single-molecule localization microscopy (SMLM) has been expanded into different fields, allowing wide-range detection at the single-molecule level. This review discusses the recent progress in the SR imaging of DNA nano-objects using SMLM techniques, such as direct stochastic optical reconstruction microscopy, binding-activated localization microscopy, and point accumulation for imaging nanoscale topography. Furthermore, we discuss their advantages and limitations, present applications, and future perspectives.

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Section: Discussionmentioning

confidence: 99%

Toward Sub-Diffraction Imaging of Single-DNA Molecule Sensors Based on Stochastic Switching Localization Microscopy

Lee

Batjikh

Kang

2020

Sensors

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“…Single-molecule flow cells were prepared as previously described. 20,21 In brief, to avoid non-specific binding, quartz slides (G. Finkerbeiner Inc) were acidic piranha etched and passivated twice with polyethylene glycol (PEG). The first round PEGylation was performed with mPEG-SVA (Laysan Bio) and PEG-biotin (Laysan Bio), followed by a second round of PEGylation with MS(PEG)4 (ThermoFisher).…”

Section: Methodsmentioning

confidence: 99%

High-Resolution Single-Molecule FRET via DNA eXchange (FRET X)

Filius

Kim

Severins

et al. 2020

Preprint

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Single-molecule FRET is a versatile tool to study nucleic acids and proteins at the nanometer scale. However, currently, only a couple of FRET pairs can be reliably measured on a single object. The limited number of available FRET pair fluorophores and complicated data analysis makes it challenging to apply single-molecule FRET for structural analysis of biomolecules. Currently, only a couple of FRET pairs can be reliably measured on a single object. Here we present an approach that allows for the determination of multiple distances between FRET pairs in a single object. We use programmable, transient binding between short DNA strands to resolve the FRET efficiency of multiple fluorophore pairs. By allowing only a single FRET pair to be formed at a time, we can determine the FRET efficiency and pair distance with sub-nanometer resolution. We determine the distance between other pairs by sequentially exchanging DNA strands. We name this multiplexing approach FRET X for FRET via DNA eXchange. We envision that our FRET X technology will be a tool for the high-resolution structural analysis of biomolecules and other nano-structures.

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“…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 ].…”

Section: Single-molecule Imaging For Biological Processesmentioning

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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High-Speed Super-Resolution Imaging Using Protein-Assisted DNA-PAINT

Cited by 52 publications

References 42 publications

Toward Sub-Diffraction Imaging of Single-DNA Molecule Sensors Based on Stochastic Switching Localization Microscopy

Toward Sub-Diffraction Imaging of Single-DNA Molecule Sensors Based on Stochastic Switching Localization Microscopy

High-Resolution Single-Molecule FRET via DNA eXchange (FRET X)

DNA Manipulation and Single-Molecule Imaging

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