Fluorescence Microscopy With 6 Nm Resolution On DNA Origami

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Super-Resolution Imaging by Dual Iterative Structured

used 60 nm DNA origami structures, [38] and a re-usable stable fluorescence slide with linear patterns (Argo-SIM slide) (Figure 2, Figure S1, Supporting Information). The peak-to-peak distance of 60.2±9.4 nm (s.d.) determined for the DNA origamis as well as the distances resolved on the Argo-slides demonstrate unequiv -

Metrology of DNA Arrays by Super-Resolution Microscopy

commercial manufacturing.22-25 Super-resolution fluorescence microscopy has proven to be a powerful tool for biological imaging, and in the case of DNA-based nanostructures, the technique known as DNA-PAINT enables non-destructive, multiplexed optical imaging with resolution down to ~5 nm.26-

DNA-Based Super-Resolution Microscopy: DNA-PAINT

G C A T genes T A C G G C A T Review DNA-Based Super-Resolution Microscopy: DNA-PAINT Daniel J. Nieves 1,2, Katharina Gaus 1,2 and Matthew A. B. Baker 3,4,* 1 EMBL Australia Node in Single

The 2015 super-resolution microscopy roadmap

The prospects of adaptive optics for super-resolution microscopy 9 Correlative super-resolution optical and electron microscopy roadmap 11 Microscopy reference samples produces by DNA nanotechnology 13 Super-resolution microscopy to dissect plasma membrane organization 15 Photoswitchable fluorescent proteins for nanoscopy 17


Preparation of DNA origami scaffolds. Rectangular DNA origami arrays consist of an M13mp18 viral DNA scaffold (New England Biolabs) and 202 ssDNA staples as previously described 1. For all structures assembled here, staples 1-12 and 205-216 were omitted to prevent inter-array base stacking interactions that result in undesirable

DNA‐Barcoded Fluorescence Microscopy for Spatial Omics

tial omics by fluorescence microscopy, the resolution should In DNA origami,[35] a long single-stranded DNA DNA‐Barcoded Fluorescence Microscopy for

Supplementary Materials for

Fluorescence lifetime imaging microscopy of DNA origami pillars with 80 nm nanoparticles. Orangered spots represent ATTO647N dyes on DNA origami pillars - without nanoparticles. The shortened fluorescence lifetime (blue spots) indicates binding of nanoparticles. Commonly, intermediate binding yields were intended to use the

PAINT using proteins: A new brush for super-resolution artists

resulting in bursts of fluorescence, just as in the original small-molecule PAINT experiments. In this implementa-tion of the method, however, the transient interaction is highly specific, dictated by the sequence of the two comple-mentary DNA strands. DNA-PAINT has been widely used to image DNA origami type structures in vitro. 9 20

ORIGINAL ARTICLE Open Access Tip induced fluorescence

separated by 20.7 nm on a DNA origami triangle with 120 nm side length by correlating topography and fluorescence data. With this method, we anticipate applications in nano- and life sciences, such as the determination of the structure of macromolecular assemblies on surfaces, molecular interactions, as well as the

Super-Resolution Fingerprinting Detects Chemical Reactions

KEYWORDS: Chemical imaging, DNA origami, PAINT, points accumulation for imaging in nanoscale topography, single molecule super-resolution fluorescence microscopy D NA nanotechnology1−4 has laid the foundation for a multitude of nanoscale devices that permit control over dynamic chemical or optoelectronic processes.5−10 Many of

Supporting information for lysosomes by fluorescence

6 μL Tube DNA origami nanostructures (10 nM) were incubated with 3 μL YOYO-1 (10 μM) in 50 μL TAE-Mg for 2 hours at 40 oC.2 Then the mixtures were ultrafiltrated to separate spare staple strands and dyes. YOYO-1 labeled origami nanostructures were allowed to adsorb the cleaned cover slip. Then the

Lithographically Driven Nanoscale Assembly of DNA Nanostructures

of triangular DNA origami. Figure 1. EPI-fluorescence image of the nanopatterned dots functionalized with a Cy3 labeled dsDNA: exitation 550nm , emission 568nm. Every fifth sub-50nm dot, a 1mm register dot is clearly visible, and brighter in the fluorescence image. Exposure time: 300ms. Figure 3. Liquid AFM image of DNA origami

Submicrometre geometrically encoded fluorescent barcodes self

resolution is a major challenge in biomedical science. Fluorescence microscopy is a powerful tool, but its multiplexing ability is limited by the number of spectrally distinguishable fluorophores. Here, we used (deoxy)ribonucleic acid (DNA)-origami technology to construct submicrometre nanorods that act as fluorescent barcodes.


KEY WORDS: superresolution microscopy, MINFLUX, single molecule, DNA origami Superresolution microscopy methods such as STED and PALM/STORM have revolutionized far-field optical fluorescence microscopy by manipulating state transitions of the emitters. In STED, a depleting beam featuring a zero of intensity switches off emitters everywhere except

DNA origami nanorulers and emerging reference structures

fluorescent dyes per DNA origami is limited to roughly 1000 for a maximally labeled DNA origami still avoiding quenching and to about 200 dyes for singly labeled staple strands. For a 12 helix-bundle (12 HB), i.e., a typical DNA origami nanoruler structure that has a length of roughly 200 nm and a diameter of ∼13 nm, this means


Figure 2: The first examples of the versatile DNA Origami technique. DNA structures as imaged by AFM. Scale bars are 100 nm for a, b, d and 1 μm for c. Adapted by permission from MacMillan Publishers Ltd: ref. [1]. Raster fill (page does not exist ) Molecule. Watson-Crick base pair. Electron Microscopy. Atomic force microscopy. Fluorescence

Biophysical characterisation of DNA origami nanostructures

Nov 21, 2019 2.6. Fluorescence microscopy Fluorescence microscopy was performed on a bespoke optical imaging system, built around a commercial microscope body (Nikon Eclipse Ti-S) as previously described [30]. A super-continuum laser (Fianium, SC-400-6, Fianium Ltd) coupled to an acousto-optic tunable filter set to 45% at a central

3D superresolution microscopy by supercritical angle detection

method with DNA origami tetrahedra, and present proof-of-principle data C. Forthmann, and P. Tinnefeld, Fluorescence microscopy with 6 nm resolution on DNA origami, ChemPhysChem 15(12

High Resolution Single Molecule Optical Localization of

Rajulapati, Anuradha, High Resolution Single Molecule Optical Localization of Multiple Fluorophores on DNA Origami Constructs Fluorophores on DNA Origami Constructs (2009).Theses, Dissertations and Capstones.Paper 805.

BIOPHYSICS Copyright © 2020 Programming PAM antennae for

dCas9 was characterized by analyzing the variation of the fluorescence intensity at the target DNA position with time. We found that the occurrence of binding events on origami P (94 ± 1.8%) was consid-erably higher than that on origami B (68 ± 3.5%) (Fig. 2A and fig. S5). The distribution of binding events on individual origami

S uper-Resolution Fingerprinting Detects Chemical Reactions

Fluorescence nanoscopy combines high spatial resolution and tunable chemical specificity with relatively low invasiveness9 14, and therefore holds promise for the spatiotemporal imaging and quality control of functional nanomaterials8,10,12,13,15,16. As targets for fluorescence nanoscopy, 60 x 90 nm rectangular DNA origami tiles1 were

DNA-PAINT Microscopy at Speed - viXra.org

DNA-PAINT Microscopy at Speed Recent advances in fluorescence microscopy allow researchers to study biological processes below the classical diffraction limit of light. [20] Scientists at the U.S. Department of Energy's Ames Laboratory are now able to see greater details of DNA origami nanostructures, which will lead to a greater

Graphene Energy Transfer for Single‐Molecule Biophysics

Using DNA origami nanopositioners, biosensing, single-molecule tracking, and DNA PAINT super-resolution with <3 nm z-resolution are demonstrated. The range of examples shows the potential of graphene-on-glass coverslips as a versatile platform for single-molecule biophysics, biosensing, and super-resolution microscopy. 1. Introduction

A Survey of Smartphone-based Fluorescence Microscopy Technology

c. Super resolution microscopy - Super Resolution Microscopy makes it easy to image the light microscope below the (resolution) diffraction mark. In the transition to a sensor, the wave structure of light can make an insignificantly tiny source of illumination blend into a 200-300 nm region.

Microscope calibration using laser written fluorescence

Cannell, and C. Soeller, 4D Super-Resolution Microscopy with Conventional Fluorophores and Single Wavelength Excitation in Optically Thick Cells and Tissues, PLoS One 6(5), e20645 (2011). 1. Introduction Fluorescence microscopes are essential tools across a wide range of scientific research. The

Single-Molecule Kinetics and Super-Resolution Microscopy by

imaging with <30 nm resolution. The method is demonstrated for flat monomeric DNA structures as well as multimeric, ribbon-like DNA structures. KEYWORDS Nanobiotechnology, biophysics, DNA origami, fluorescence microscopy, super-resolution, single-molecule kinetics R ecently,thefieldofDNAnanotechnology1,2 hasbeen

FRET enhancement close to gold nanoparticles positioned in

the opposite side of the DNA-origami. The four different FRET pair positions (D 1A D 4A) under investigation are shown simultaneously. (b) AFM height image (tapping mode in air; z-scale 10 nm; image size 200 × 200 nm) recorded on a AuNP conjugated DNA origami with a molar ratio (AuNP:DNA origami) = (2:1), deposited on mica surface.

Quantifying Protein Copy Number in Super-Resolution Using an

super-resolution microscopy. 21-23 In particular, we recently developed a versatile approach that uses a well-defined DNA origami structure as a calibration standard for super-resolution microscopy. 24. In this approach, we functionalized the DNA-origami with a defined number of

Sub 100-nm metafluorophores with digitally tunable optical

organic fluorophores, organized in a spatially controlled fashion in a compact sub 100-nm architecture using a DNA nanostructure scaffold. Using DNA origami with a size of 90 × 60 nm2, substantially smaller than the optical diffraction limit, we constructed small fluorescent probes with digitally tunable brightness, color, and

multiplexed 3d cellular super-resolution imaging with dnA

16.6 nm 0 10 20 Position (nm) Counts Counts 30 40 (ii) 15.8 nm 0 10 20 Position (nm) 30 40 40 120 20 0 60. Figure 1 DNA-PAINT. (a) A microtubule-like DNA origami polymer (cylinders represent DNA double helices) is decorated with single-stranded extensions (docking strands) on two opposite faces (red) spaced ~16 nm apart. Complementary

A bio-hybrid DNA rotor stator nanoengine that moves along

e, High-resolution atomic force microscopy images of the catenane T7RNAP-ZIF nanoengine in tapping mode in liquid. f,g, Fluorescence kinetics of the RCT performed by the catenane (blue), the control catenane lacking the Zif268 binding site (red), a positive control double-stranded 126 bp ring (green) and a negative control 126 bp ring

DNA-Origami-Based Fluorescence Brightness Standards for

Sep 20, 2020 DNA origami15 18 is ideal for the creation of such a standard. DNA origami has been used to engineer standards for fluorescence microscopy, but existing quantification methods either rely on super-resolution techniques or only demonstrate applications for counting organic dyes.12,19 Here, we present DNA-origami-based brightness standards

Angular reconstitution-based 3D reconstructions of

Superresolution Imaging of Model DNA Origami. DNA origami were labeled by DNA-PAINT (13, 14). Equally spaced docking strands were placed to provide high-density labeling using Atto647n- or Alexa488-labeled imager strands (Fig. 1A and SI Appendix, Figs. S1, S3, and Materials and Methods). Two distinct DNA origami structures were used

DNA-barcoded labeling probes for highly multiplexed Exchange

over 50 and assay their orthogonality in a novel DNA origami-based crosstalk assay. Using our optimized conjugation and labeling strategies, we demonstrate nine-color super-resolution imaging in situ in fixed cells. Introduction Fluorescence microscopy has become a standard method for in situ characterization of molecular details in both

Quantifying Expansion Microscopy with DNA Origami Expansion

In the past decade super-resolution microscopy1,2 developed rapidly and allowed seeing new structural details in fluorescence microscopy, especially in the field of bioimaging3-6. Most of the evolving techniques like (d)STORM7,8, STED9 or SIM10 just to name a few focused on overcoming the diffraction

Angular reconstitution-based 3D reconstructions of

153 nm Fig. 1. Self-assembly of DNA origami and single-particle averaging. ( A)Sche-matic representation of DNA origami and DNA-PAINT strategy. Docking strands were positioned on the surface of the orig ami at regular spacings; imager strands were localized with nanometer precision. ( B) Single, surface-bound DNA origami

Photobleaching of YOYO-1 in super-resolution single DNA

microscopy at ≈250 nm [21]. This is important in visualizing the conformation of DNA molecules, such as DNA looping by proteins, a necessary process for gene regulation and expres-sion [22], characterizing DNA origami [23,24], and imaging the unpacking of DNA [25]. Two main categories of super-

Introducing Lattice SIM for ZEISS Elyra 7 Structured

Figure 5 shows an image of 120 nm DNA-origami (GATTA-SIM Nanoruler 120B, Gattaquant Germany) imaged at a wavelength of 488 nm with a ZEISS Plan-APOCHROMAT 63× 1.4 oil lens on ZEISS Elyra 7. Molecules at different lateral orientations have been measured and angles are shown. 120 nm resolution in all major lateral directions using the

Correlative AFM and Super-Resolution STED Analysis of DNA

Fig. 5: High-speed AFM images of R80 DNA Origami. Both images (256 x 256 pixels) were recorded at 400 lines/s, resulting in a temporal resolution of ~1.6 frames/s. Z-scale in both images is 2 nm. The resulting AFM images show that it is possible to non-invasively study the molecular structures of the NRO at a