Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Visible/near-infrared subdiffraction imaging reveals the stochastic nature of DNA walkers.

ABSTRACT: DNA walkers are designed with the structural specificity and functional diversity of oligonucleotides to actively convert chemical energy into mechanical translocation. Compared to natural protein motors, DNA walkers' small translocation distance (mostly <100 nm) and slow reaction rate (<0.1 nm s^-1) make single-molecule characterization of their kinetics elusive. An important indication of single-walker kinetics is the rate-limiting reactions that a particular walker design bears. We introduce an integrated super-resolved fluorescence microscopy approach that is capable of long-term imaging to investigate the stochastic behavior of DNA walkers. Subdiffraction tracking and imaging in the visible and second near-infrared spectra resolve walker structure and reaction rates. The distributions of walker kinetics are analyzed using a stochastic model to reveal reaction randomness and the rate-limiting biochemical reaction steps.

SUBMITTER: Pan J

PROVIDER: S-EPMC5249260 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Visible/near-infrared subdiffraction imaging reveals the stochastic nature of DNA walkers.

Pan Jing J Cha Tae-Gon TG Li Feiran F Chen Haorong H Bragg Nina A NA Choi Jong Hyun JH

Science advances 20170120 1

DNA walkers are designed with the structural specificity and functional diversity of oligonucleotides to actively convert chemical energy into mechanical translocation. Compared to natural protein motors, DNA walkers' small translocation distance (mostly <100 nm) and slow reaction rate (<0.1 nm s<sup>-1</sup>) make single-molecule characterization of their kinetics elusive. An important indication of single-walker kinetics is the rate-limiting reactions that a particular walker design bears. We ...[more]

PMID: 28116353

Similar Datasets

Lanthanide-Based Peptide-Directed Visible/Near-Infrared Imaging and Inhibition of LMP1.

Project description:A lanthanide-based peptide-directed bioprobe LnP19 (Ln = Eu or Yb) is designed as an impressive example of a small molecule-based dual-functional probe for the EBV oncoprotein LMP1. The peptide P19 (Pra-KAhx-K-LDLALK-FWLY-K-IVMSDKW-K-RrRK) is designed to selectively bind to LMP1 by mimicking its TM1 region during oligomerization in lipid rafts while signal transduction is significantly suppressed. Immunofluorescence imaging and Western blotting results reveal that P19 can effectively inactivate the oncogenic cellular pathway nuclear factor κB (NF-κB) and contribute to a selective cytotoxic effect on LMP1-positive cells. By conjugation with cyclen-based europium(III) and ytterbium(III) complexes, EuP19 and YbP19 were constructed to offer visible and near-infrared LMP1-targeted imaging and cancer monitoring. In addition to the ability to target and inhibit LMP1 and to selective inhibit LMP1-positive cells, selective growth inhibition toward the LMP1-positive tumor by LnP19 is also demonstrated.

| S-EPMC8395644 | biostudies-literature

Preprocessing Ground-Based Visible/Near Infrared Imaging Spectroscopy Data Affected by Smile Effects.

Project description:A data set of very high-resolution visible/near infrared hyperspectral images of young Pinus contorta trees was recorded to study the effects of herbicides on this invasive species. The camera was fixed on a frame while the potted trees were moved underneath on a conveyor belt. To account for changing illumination conditions, a white reference bar was included at the edge of each image line. Conventional preprocessing of the images, i.e., dividing measured values by values from the white reference bar in the same image line, failed and resulted in bad quality spectra with oscillation patterns that are most likely due to wavelength shifts across the sensor's field of view (smile effect). An additional hyperspectral data set of a Spectralon white reference panel could be used to characterize and correct the oscillations introduced by the division, resulting in a high quality spectra that document the effects of herbicides on the reflectance characteristics of coniferous trees. While the spectra of untreated trees remained constant over time, there were clear temporal changes in the spectra of trees treated with both herbicides. One herbicide worked within days, the other one within weeks. Ground-based imaging spectroscopy with meaningful preprocessing proved to be an appropriate tool for monitoring the effects of herbicides on potted plants.

| S-EPMC6480459 | biostudies-literature

SAVI: Synthetic apertures for long-range, subdiffraction-limited visible imaging using Fourier ptychography.

Project description:Synthetic aperture radar is a well-known technique for improving resolution in radio imaging. Extending these synthetic aperture techniques to the visible light domain is not straightforward because optical receivers cannot measure phase information. We propose to use macroscopic Fourier ptychography (FP) as a practical means of creating a synthetic aperture for visible imaging to achieve subdiffraction-limited resolution. We demonstrate the first working prototype for macroscopic FP in a reflection imaging geometry that is capable of imaging optically rough objects. In addition, a novel image space denoising regularization is introduced during phase retrieval to reduce the effects of speckle and improve perceptual quality of the recovered high-resolution image. Our approach is validated experimentally where the resolution of various diffuse objects is improved sixfold.

| S-EPMC5392025 | biostudies-literature

Visible and near infrared fluorescence spectral flow cytometry.

Project description:There is a long standing interest in measuring complete emission spectra from individual cells in flow cytometry. We have developed flow cytometry instruments and analysis approaches to enable this to be done routinely and robustly. Our spectral flow cytometers use a holographic grating to disperse light from single cells onto a CCD for high speed, wavelength-resolved detection. Customized software allows the single cell spectral data to be displayed and analyzed to produce new spectra-derived parameters. We show that familiar reference and calibration beads can be employed to quantitatively assess instrument performance. We use microspheres stained with six different quantum dots to compare a virtual bandpass filter approach with classic least squares (CLS) spectral unmixing, and then use antibody capture beads and CLS unmixing to demonstrate immunophenotyping of peripheral blood mononuclear cells using spectral flow cytometry. Finally, we characterize and evaluate several near infrared (NIR) emitting fluorophores for use in spectral flow cytometry. Spectral flow cytometry offers a number of attractive features for single cell analysis, including a simplified optical path, high spectral resolution, and streamlined approaches to quantitative multiparameter measurements. The availability of robust instrumentation, software, and analysis approaches will facilitate the development of spectral flow cytometry applications.

| S-EPMC3594514 | biostudies-literature

Identification of pesticide varieties by testing microalgae using Visible/Near Infrared Hyperspectral Imaging technology.

Project description:In our study, the feasibility of using visible/near infrared hyperspectral imaging technology to detect the changes of the internal components of Chlorella pyrenoidosa so as to determine the varieties of pesticides (such as butachlor, atrazine and glyphosate) at three concentrations (0.6 mg/L, 3 mg/L, 15 mg/L) was investigated. Three models (partial least squares discriminant analysis combined with full wavelengths, FW-PLSDA; partial least squares discriminant analysis combined with competitive adaptive reweighted sampling algorithm, CARS-PLSDA; linear discrimination analysis combined with regression coefficients, RC-LDA) were built by the hyperspectral data of Chlorella pyrenoidosa to find which model can produce the most optimal result. The RC-LDA model, which achieved an average correct classification rate of 97.0% was more superior than FW-PLSDA (72.2%) and CARS-PLSDA (84.0%), and it proved that visible/near infrared hyperspectral imaging could be a rapid and reliable technique to identify pesticide varieties. It also proved that microalgae can be a very promising medium to indicate characteristics of pesticides.

| S-EPMC4829843 | biostudies-other

Shape memory polymers with visible and near-infrared imaging modalities: Synthesis, characterization and in vitro analysis.

Project description:Shape memory polymers (SMPs) are promising for non-invasive medical devices and tissue scaffolds, but are limited by a lack of visibility under clinical imaging. Fluorescent dyes are an alternative to radiocontrast agents in medical applications, they can be utilized in chemical sensors and monitors and may be anti-microbial agents. Thus, a fluorescent SMP could be a highly valuable biomaterial system. Here, we show that four fluorescent dyes (phloxine B (PhB), eosin Y (Eos), indocyanine green(IcG), and calcein (Cal)) can be crosslinked into the polymer backbone to enhance material optical properties without alteration of shape memory and thermomechanical properties. Examinations of the emission wavelengths of the materials compared with the dye solutions showed a slight red shift in the peak emissions, indicative of crosslinking of the material. Quantitative analysis revealed that PhB enabled visibility through 1 cm of blood and through soft tissue. We also demonstrate the utility of these methods in combination with radio-opaque microparticle additives and the use of laser-induced shape recovery to allow for rapid shape recovery below the glass transition temperature. The crosslinking of fluorescent dyes into the SMP enables tuning of physical properties and shape memory and independently of the fluorescence functionality. This fluorescent SMP biomaterial system allows for use of multiple imaging modalities with potential application in minimally invasive medical devices.

| S-EPMC6168213 | biostudies-literature

Near-infrared and visible light dual-mode organic photodetectors.

Project description:We report a dual-mode organic photodetector (OPD) that has a trilayer visible light absorber/optical spacer/near-infrared (NIR) light absorber configuration. In the presence of NIR light, photocurrent is produced in the NIR light-absorbing layer due to the trap-assisted charge injection at the organic/cathode interface at a reverse bias. In the presence of visible light, photocurrent is produced in the visible light-absorbing layer, enabled by the trap-assisted charge injection at the anode/organic interface at a forward bias. A high responsivity of >10 A/W is obtained in both short and long wavelengths. The dual-mode OPD exhibits an NIR light response operated at a reverse bias and a visible light response operated at a forward bias, with a high specific detectivity of ~1013 Jones in both NIR and visible light ranges. A bias-switchable spectral response OPD offers an attractive option for applications in environmental pollution detection, bioimaging process, wellness, and security monitoring in two distinct bands.

| S-EPMC6994203 | biostudies-literature

Near-Infrared Intraoperative Chemiluminescence Imaging.

Project description:Intraoperative imaging technologies recently entered the operating room, and their implementation is revolutionizing how physicians plan, monitor, and perform surgical interventions. In this work, we present a novel surgical imaging reporter system: intraoperative chemiluminescence imaging (ICI). To this end, we have leveraged the ability of a chemiluminescent metal complex to generate near-infrared light upon exposure to an aqueous solution of Ce(4+) in the presence of reducing tissue or blood components. An optical camera spatially resolves the resulting photon flux. We describe the construction and application of a prototype imaging setup, which achieves a detection limit as low as 6.9 pmol cm(-2) of the transition-metal-based ICI agent. As a proof of concept, we use ICI for the in vivo detection of our transition metal tracer following both systemic and subdermal injections. The very high signal-to-noise ratios make ICI an interesting candidate for the development of new intraoperative imaging technologies.

| S-EPMC5061038 | biostudies-literature

In situ printing of liquid superlenses for subdiffraction-limited color imaging of nanobiostructures in nature.

Project description:The nanostructures and patterns that exist in nature have inspired researchers to develop revolutionary components for use in modern technologies and our daily lives. The nanoscale imaging of biological samples with sophisticated analytical tools, such as scanning electron microscopy (SEM) and transmission electron microscopy (TEM), has afforded a precise understanding of structures and has helped reveal the mechanisms contributing to the behaviors of the samples but has done so with the loss of photonic properties. Here, we present a new method for printing biocompatible "superlenses" directly on biological objects to observe subdiffraction-limited features under an optical microscope in color. We demonstrate the nanoscale imaging of butterfly wing scales with a super-resolution and larger field-of-view (FOV) than those of previous dielectric microsphere techniques. Our approach creates a fast and flexible path for the direct color observation of nanoscale biological features in the visible range and enables potential optical measurements at the subdiffraction-limited scale.

| S-EPMC6330505 | biostudies-literature

Dynamic near-infrared imaging reveals transient phototropic change in retinal rod photoreceptors.

Project description:Stiles-Crawford effect (SCE) is exclusively observed in cone photoreceptors, but why the SCE is absent in rod photoreceptors is still a mystery. In this study, we employed dynamic near infrared light imaging to monitor photoreceptor kinetics in freshly isolated frog and mouse retinas stimulated by oblique visible light flashes. It was observed that retinal rods could rapidly (onset: ?10 ms for frog and 5 ms for mouse; time-to-peak: ?200 ms for frog and 30 ms for mouse) shift toward the direction of the visible light, which might quickly compensate for the loss of luminous efficiency due to oblique illumination. In contrast, such directional movement was negligible in retinal cones. Moreover, transient rod phototropism could contribute to characteristic intrinsic optical signal (IOS). We anticipate that further study of the transient rod phototropism may not only provide insight into better understanding of the nature of vision but also promise an IOS biomarker for functional mapping of rod physiology at high resolution.

| S-EPMC3809571 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data