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18 results for “DNA origami”
DNA Origami Raw AFM Data - NanoLocz: Image analysis platform for AFM, high-speed AFM and localization AFM
<p>The data file is in the original ARIS data format as captured on a Cypher VRS1250 AFM (Oxford Instruments)<br><br><br></p>
Tilt-series 4DSTEM dataset of DNA origami with gold nanoparticles
<p>Raw TEM data for the manuscript "Three-dimensional Electron Ptychography of Organic-inorganic Hybrid Nanostructures".</p>
DNA origami book biosensor for multiplex detection of cancer-associated nucleic acids
<p>This dataset contains the raw data that were used for the publication entitled, "DNA origami book biosensor for multiplex detection of cancer-associated nucleic acids" published in Nanoscale.</p> <p> </p> <p>Abstract</p> <p>DNA nanotechnology provides a promising approach for the development of biomedical point-of-care diagnostic nanoscale devices that are easy to use and cost-effective, highly sensitive and thus constitute an alternative to expensive, complex diagnostic devices. Moreover, DNA nanotechnology-based devices are particularly advantageous for applications in oncology, owing to being ideally suited for the detection of cancer-associated nucleic acids, including circulating tumor-derived DNA fragments (ctDNAs), circulating microRNAs (miRNAs) and other RNA species. Here, we present a dynamic DNA origami book biosensor that is precisely decorated with arrays of fluorophores acting as donors and acceptors and also fluorescence quenchers that produce a strong optical readout upon exposure to external stimuli for the single or dual detection of target oligonucleotides and miRNAs. This biosensor allowed the detection of target molecules either through the decrease of Förster resonance energy transfer (FRET) or an increase in the fluorescence intensity profile owing to a rotation of the constituent top layer of the structure. Single-DNA origami experiments showed that detection of two targets can be achieved simultaneously within 10 min with a limit of detection in the range of 1–10 pM. Overall, our DNA origami book biosensor design showed sensitive and specific detection of synthetic target oligonucleotides and natural miRNAs extracted from cancer cells. Based on these results, we foresee that our DNA origami biosensor may be developed into a cost-effective point-of-care diagnostic strategy for the specific and sensitive detection of a variety of DNAs and RNAs, such as ctDNAs, miRNAs, mRNAs, and viral DNA/RNAs in human samples.</p>
Self-Regeneration and Self-Healing in DNA Origami Nanostructures
<p>DNA nanotechnology and advances in the DNA origami technique have enabled facile design and synthesis of complex and<br> functional nanostructures. Molecular devices are, however, prone to rapid functional and structural degradation due to the high proportion of surface atoms at the nanoscale and due to complex working environments. Besides stabilizing mechanisms, approaches for the self-repair of functional molecular devices are desirable. Here we exploit the self-assembly and reconfigurability of DNA origami nanostructures to induce the self-repair of defects of photoinduced and enzymatic damage. We provide examples of repair in DNA nanostructures showing the difference between unspecific self-regeneration and damage-specific self-healing mechanisms. Using DNA origami nanorulers studied by atomic force and superresolution DNA PAINT microscopy, quantitative preservation of fluorescence properties is demonstrated with the direct potential for improving nanoscale calibration samples. Here we demonstrate the data on which our findings based on. </p>
Data for "Controlled mechanochemical coupling of anti-junctions in DNA origami arrays"
<p>We provide the raw data for the paper "Controlled mechanochemical coupling of anti-junctions in DNA origami arrays". The files have .tif files-format.</p> <p>Additionally we provide the python scripts used to analyze these data sets.</p>
Benchmarking Smartphone Fluorescence-Based Microscopy with DNA Origami Nanobeads: Reducing the Gap toward Single-Molecule Sensitivity
<p>Smartphone-based fluorescence microscopy has been rapidly developing over the last few years, enabling point-of-need detection of cells, bacteria, viruses, and biomarkers. These mobile microscopy devices are cost-effective, field-portable, and easy to use, and benefit from economies of scale. Recent developments in smartphone camera technology have improved their performance, getting closer to that of lab microscopes. Here, we report the use of DNA origami nanobeads with predefined numbers of fluorophores to quantify the sensitivity of a smartphone-based fluorescence microscope in terms of the minimum number of detectable molecules per diffraction-limited spot. With the brightness of a single dye molecule as a reference, we compare the performance of color and monochrome sensors embedded in state-of-the-art smartphones. Our results show that the monochrome sensor of a smartphone can achieve better sensitivity, with a detection limit of ∼10 fluorophores per spot. The use of DNA origami nanobeads to quantify the minimum number of detectable molecules of a sensor is broadly applicable to evaluate the sensitivity of various optical instruments.</p>
Quantifying Expansion Microscopy with DNA Origami Expansion Nanorulers
<p>Expansion microscopy evolved as an interesting alternative in the field of super-resolution microscopy by physically expanding the target sample to increase its size by a multiple and to subsequently image the sample by conventional fluorescence microcopy. But the quantitative determination of the expansion factor remains challenging, since microscopic measurement standards are missing. Here we use DNA nanorulers in combination with expansion microscopy to expand the fluorescently marked rulers in 2D and to determine the intermark distances before and after expansion. We compare macroscopic and microscopic expansion factors where we found substantial deviations, which should be considered for the quantitative discussion of expansion microscopy data of biological cells and tissues. The demonstrated proof-of-principle opens a new field with the potential to answer questions with respect to quantitation of microscopic magnification and the introduced expansion nanorulers present a powerful tool to reveal the true origin of anisotropy and heterogeneity in expanded microscopy specimen.</p> <p> </p> <p>Here we show the raw data the publication is based on.</p>
Data set for the replication package of the paper "Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers"
<p>Data set for the replication package of the paper "Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers".</p>
NEOtrap data with cholesterol functionalized DNA origami spheres
<p>Source data used in the manuscript:<br> Orientation-locked DNA origami improves single-protein trapping in the NEOtrap</p> <p>The measurements were implemented in 600 KHM buffer under the bias voltage of 100 mV.<br> Names of these files specify the trapped protein's name with corresponding measurement conditions, i.e.,<br> bare origami sphere, Cholesterol functionalized sphere in vertical configuration, and Cholesterol functionalized sphere in horizontal configuration<br> </p>
Site-directed placement of three-dimensional DNA origami
<p><span>The combination of lithographic methods with 2D DNA origami self-assembly has led, among others, to the development of photonic crystal cavity arrays and the exploration of sensing nanoarrays where molecular devices are patterned on the sub-micron scale. Here we extend this concept to the third dimension by mounting 3D DNA origami onto nano-patterned substrates, followed by silicification to provide mechanical and chemical stability. We created fully addressable, three-dimensional nanopatterns of hybrid DNA-silica structures with heights up to 50 nm and feature size in the sub-10-nm regime. Our versatile and scalable method relying on self-assembly at ambient temperatures offers the potential to 3D-position any inorganic and organic components compatible with DNA origami nanoarchitecture, demonstrated with gold nanoparticles. This way of nanotexturing could provide a route for the low-cost production of complex and 3D-patterned surfaces and integrated devices designed on the molecular level while reaching macroscopic dimensions.</span></p>
Programmable liposome organization via DNA origami templates
Open the record for dataset details and reuse information.
DNA origami signal amplification in lateral flow immunoassays
Open the record for dataset details and reuse information.
Site-directed placement of three-dimensional DNA origami
Open the record for dataset details and reuse information.
Fluorophore photostability and saturation in the hotspot of DNA origami nanoantennas
<p>Fluorescent dyes used for single-molecule spectroscopy can undergo millions of excitation-emission<br> cycles before photobleaching. Due to the upconcentration of light in a plasmonic hotspot, the<br> conditions for fluorescent dyes are even more demanding inDNAorigami nanoantennas. Here, we<br> briefly review the current state of fluorophore stabilization for single-molecule imaging and reveal<br> additional factors relevant in the context of plasmonic fluorescence enhancement. Weshow that<br> despite the improved photostability of single-molecule fluorophores byDNAorigami nanoantennas,<br> their performance in the intense electric fields in plasmonic hotspots is still limited by the underlying<br> photophysical processes, such as formation of dim states and photoisomerization. These photophysical<br> processes limit the photon count rates, increase heterogeneity and aggravate quantification of<br> fluorescence enhancement factors. These factors also reduce the time resolution that can be achieved<br> in biophysical single-molecule experiments. Finally, we show how the photophysics of aDNAhairpin<br> assay with a fluorophore-quencher pair can be influenced by plasmonicDNAorigami nanoantennas<br> leading to implications for their use in fluorescence-based diagnostic assays. Especially, we show that<br> such assays can produce false positive results by premature photobleaching of the dark quencher. Here we demonstrate the raw data on which our findings based on.</p>
Data for "Estimation of microtubule-generated forces using a DNA origami nanospring"
<p>Data in support of the publication "Estimation of microtubule-generated forces using a DNA origami nanospring"</p>
Using DNA origami nanorulers as traceable distance measurement standards and nanoscopic benchmark structures
<p>In recent years, DNA origami nanorulers for superresolution (SR) fluorescence microscopy have been developed from fundamental proof-of-principle experiments to commercially available test structures. The self-assembled nanostructures allow placing a defined number of fluorescent dye molecules in defined geometries in the nanometer range. Besides the unprecedented control over matter on the nanoscale, robust DNA origami nanorulers are reproducibly obtained in high yields. The distances between their fluorescent marks can be easily analysed yielding intermark distance histograms from many identical structures. Thus, DNA origami nanorulers have become excellent reference and training structures for superresolution microscopy. In this work, we go one step further and develop a calibration process for the measured distances between the fluorescent marks on DNA origami nanorulers. The superresolution technique DNA-PAINT is used to achieve nanometrological traceability of nanoruler distances following the guide to the expression of uncertainty in measurement (GUM). We further show two examples how these nanorulers are used to evaluate the performance of TIRF microscopes that are capable of single-molecule localization microscopy (SMLM).</p> <p>Here we show the raw data the publication is based on.</p>
Fine tuning of CpG spatial distribution with DNA origami for improved cancer vaccination
GEO Series GSE251850. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Interchromophoric Interactions Determine the Maximum Brightness Density in DNA Origami Structures
<p>An ideal point light source is as small and as bright as possible. For fluorescent point light sources, homogeneity of the light sources is important as well as that the fluorescent units inside the light source maintain their photophysical properties, which is compromised by dye aggregation. Here we propose DNA origami as a rigid scaffold to arrange dye molecules in a dense pixel array with high control of stoichiometry and dye–dye interactions. In order to find the highest labeling density in a DNA origami structure without influencing dye photophysics, we alter the distance of two ATTO647N dyes in single base pair steps and probe the dye–dye interactions on the single-molecule level. For small distances strong quenching in terms of intensity and fluorescence lifetime is observed. With increasing distance, we observe reduced quenching and molecular dynamics. However, energy transfer processes in the weak coupling regime still have a significant impact and can lead to quenching by singlet-dark-state-annihilation. Our study fills a gap of studying the interactions of dyes relevant for superresolution microscopy with dense labeling and for single-molecule biophysics. Incorporating these findings in a 3D DNA origami object will pave the way to bright and homogeneous DNA origami nanobeads.</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.