Browse
Submit Data
Databases
API
Help

Dataset Information

26 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

All-in-One Optofluidic Chip for Molecular Biosensing Assays

ABSTRACT: Integrated biosensor platforms have become subjects of high interest for consolidated assay preparation and analysis to reduce sample-to-answer response times. By compactly combining as many biosensor processes and functions as possible into a single lab-on-chip device, all-in-one point-of-care devices can aid in the accessibility and speed of deployment due to their compact size and portability. Biomarker assay preparation and sensing are functionalities that are often carried out on separate devices, thus increasing opportunity of contamination, loss of sample volume, and other forms of error. Here, we demonstrate a complete lab-on-chip system combining sample preparation, on-chip optofluidic dye laser, and optical detection. We first show the integration of an on-chip distributed feedback dye laser for alignment-free optical excitation of particles moving through a fluidic channel. This capability is demonstrated by using Rhodamine 6G as the gain medium to excite single fluorescent microspheres at 575 nm. Next, we present an optofluidic PDMS platform combining a microvalve network (automaton) for sample preparation of nanoliter volumes, on-chip distributed feedback dye laser for target excitation, and optical detection. We conduct concurrent capture and fluorescence tagging of Zika virus nucleic acid on magnetic beads in 30 min. Target-carrying beads are then optically excited using the on-chip laser as they flow through an analysis channel, followed by highly specific fluorescence detection. This demonstration of a complete all-in-one biosensor is a tangible step in the development of a rapid, point-of-care device that can assist in limiting the severity of future outbreaks.

SUBMITTER: Sano T

PROVIDER: S-EPMC9313335 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Molecular sentinel-on-chip for SERS-based biosensing.

Project description:The development of DNA detection techniques on large-area plasmonics-active platforms is critical for many medical applications such as high-throughput screening, medical diagnosis and systems biology research. Here, we report for the first time a unique "molecular sentinel-on-chip" (MSC) technology for surface-enhanced Raman scattering (SERS)-based DNA detection. This unique approach allows label-free detection of DNA molecules on chips developed on a wafer scale using large area nanofabrication methodologies. To develop plasmonics-active biosensing platforms in a repeatable and reproducible manner, we employed a combination of deep UV lithography, atomic layer deposition, and metal deposition to fabricate triangular-shaped nanowire (TSNW) arrays having controlled sub-10 nm gap nanostructures over an entire 6 inch wafer. The detection of a DNA sequence of the Ki-67 gene, a critical breast cancer biomarker, on the TSNW substrate illustrates the usefulness and potential of the MSC technology as a novel SERS-based DNA detection method.

| S-EPMC4022304 | biostudies-literature

Integrated Optofluidic Chip for Oscillatory Microrheology.

Project description:We propose and demonstrate an on-chip optofluidic device allowing active oscillatory microrheological measurements with sub-μL sample volume, low cost and high flexibility. Thanks to the use of this optofluidic microrheometer it is possible to measure the viscoelastic properties of complex fluids in the frequency range 0.01-10 Hz at different temperatures. The system is based on the optical forces exerted on a microbead by two counterpropagating infrared laser beams. The core elements of the optical part, integrated waveguides and an optical modulator, are fabricated by fs-laser writing on a glass substrate. The system performance is validated by measuring viscoelastic solutions of aqueous worm-like micelles composed by Cetylpyridinium Chloride (CPyCl) and Sodium Salicylate (NaSal).

| S-EPMC7118116 | biostudies-literature

Optofluidic tweezer on a chip.

Project description:A novel method to realize an optical tweezer involving optofluidic operation in a microchannel is proposed. To manipulate the optical tweezer, light from an optical fiber is passed through both PDMS (polydimethylsiloxane)-air surface lenses and an optofluidic region, which is located in a control channel. Two liquids with different refractive indices (RIs) are introduced into the control channel to form two different flow patterns (i.e., laminar and segmented flows), depending on the liquid compositions, the channel geometry, and the flow rates. By altering the shapes of the interface of the two liquids in the optofluidic region, we can continuously or intermittently control the optical paths of the light. To demonstrate the functionality of the proposed method, optical tweezer operations on a chip are performed. Changing the flow pattern of two liquids with different RIs in the optofluidic region results in successful trapping of a 25 μm diameter microsphere and its displacement by 15 μm.

| S-EPMC3026034 | biostudies-other

Optical particle sorting on an optofluidic chip.

Project description:We report size-based sorting of micro- and sub-micron particles using optical forces on a planar optofluidic chip. Two different combinations of fluid flow and optical beam directions in liquid-core waveguides are demonstrated. These methods allow for tunability of size selection and sorting with efficiencies as high as 100%. Very good agreement between experimental results and calculated particle trajectories in the presence of flow and optical forces is found.

| S-EPMC3926539 | biostudies-other

Backscattering-Based Discrimination of Microparticles Using an Optofluidic Multiangle Scattering Chip.

Project description:In this research, we designed and fabricated an optofluidic chip for the detection and differentiation of single particles via the combination of backscattered (BSC) and forward-scattered (FSC) or side-scattered (SSC) light intensity. The high sensitivity of BSC light to the refractive index of the particles enabled an effective approach for the differentiation of individual particles based on the type of material. By recording BSC as well as FSC and SSC light intensities from single particles, transiting through the illumination zone in a microfluidic channel, the size and type of material could be detected simultaneously. The analysis of model samples of polystyrene (PS), as a primary microplastic particle, and silica microspheres showed substantially higher BSC signal values of PS because of a larger refractive index compared to the silica. The scatter plots correlating contributions of BSC (FSC-BSC and SSC-BSC) allowed a clear differentiation of PS and silica particles. To demonstrate the great potential of this methodology, two "real-life" samples containing different types of particles were tested as application examples. Commercial toothpaste and peeling gel products, as primary sources of microplastics into effluents, were analyzed via the optofluidic chip and compared to results from scanning electron microscopy. The scattering analysis of the complex samples enabled the detection and simultaneous differentiation of particles such as microplastics according to their differences in the refractive index via distinctive areas of high and low BSC signal values. Hence, the contribution of BSC light measurements in multiangle scattering of single particles realized in an optofluidic chip opens the way for the discrimination of single particles in a liquid medium in manifold fields of application ranging from environmental monitoring to cosmetics.

| S-EPMC9161266 | biostudies-literature

Simplified ChIP-exo assays.

Project description:ChIP-seq and ChIP-exo identify where proteins bind along any genome in vivo. Although ChIP-seq is widely adopted in academic research, it has inherently high noise. In contrast, ChIP-exo has relatively low noise and achieves near-base pair resolution. Consequently, and unlike other genomic assays, ChIP-exo provides structural information on genome-wide binding proteins. Construction of ChIP-exo libraries is technically difficult. Here we describe greatly simplified ChIP-exo methods, each with use-specific advantages. This is achieved through assay optimization and use of Tn5 tagmentation and/or single-stranded DNA ligation. Greater library yields, lower processing time, and lower costs are achieved. In comparing assays, we reveal substantial limitations in other ChIP-based assays. Importantly, the new ChIP-exo assays allow high-resolution detection of some protein-DNA interactions in organs and in as few as 27,000 cells. It is suitable for high-throughput parallelization. The simplicity of ChIP-exo now makes it a highly appropriate substitute for ChIP-seq, and for broader adoption.

| S-EPMC6054642 | biostudies-literature

Multi-mode mitigation in an optofluidic chip for particle manipulation and sensing.

Project description:A new waveguide design for an optofluidic chip is presented. It mitigates multi-mode behavior in solid and liquid-core waveguides by increasing fundamental mode coupling to 82% and 95%, respectively. Additionally, we demonstrate a six-fold improvement in lateral confinement of optically guided dielectric microparticles and double the detection efficiency of fluorescent particles.

| S-EPMC2860178 | biostudies-literature

Comparison of sample preparation methods for ChIP-chip assays.

Project description:A single chromatin immunoprecipitation (ChIP) sample does not provide enough DNA for hybridization to a genomic tiling array. A commonly used technique for amplifying the DNA obtained from ChIP assays is ligation-mediated PCR (LM-PCR). However; using this amplification method, we could not identify Oct4 binding sites on genomic tiling arrays representing 1% of the human genome (ENCODE arrays). In contrast, hybridization of a pool of 10 ChIP samples to the arrays produced reproducible binding patterns and low background signals. However the pooling method would greatly increase the number of ChIP reactions needed to analyze the entire human genome. Therefore, we have adapted the GenomePlex whole genome amplification (WGA) method for use in ChIP-chip assays; detailed ChIP and amplification protocols used for these analyses are provided as supplementary material. When applied to ENCODE arrays, the products prepared using this new method resulted in an Oct4 binding pattern similar to that from the pooled Oct4 ChIP samples. Importantly, the signal-to-noise ratio using the GenomePlex WGA method is superior to the LM-PCR amplification method.

| S-EPMC2268903 | biostudies-literature

Ultralow power trapping and fluorescence detection of single particles on an optofluidic chip.

Project description:The development of on-chip methods to manipulate particles is receiving rapidly increasing attention. All-optical traps offer numerous advantages, but are plagued by large required power levels on the order of hundreds of milliwatts and the inability to act exclusively on individual particles. Here, we demonstrate a fully integrated electro-optical trap for single particles with optical excitation power levels that are five orders of magnitude lower than in conventional optical force traps. The trap is based on spatio-temporal light modulation that is implemented using networks of antiresonant reflecting optical waveguides. We demonstrate the combination of on-chip trapping and fluorescence detection of single microorganisms by studying the photobleaching dynamics of stained DNA in E. coli bacteria. The favorable size scaling facilitates the trapping of single nanoparticles on integrated optofluidic chips.

| S-EPMC2863329 | biostudies-literature

Multiplexed Biosensing of Proteins and Virions with Disposable Plasmonic Assays.

Project description:Our growing ability to tailor healthcare to the needs of individuals has the potential to transform clinical treatment. However, the measurement of multiple biomarkers to inform clinical decisions requires rapid, effective, and affordable diagnostics. Chronic diseases and rapidly evolving pathogens in a larger population have also escalated the need for improved diagnostic capabilities. Current chemical diagnostics are often performed in centralized facilities and are still dependent on multiple steps, molecular labeling, and detailed analysis, causing the result turnaround time to be over hours and days. Rapid diagnostic kits based on lateral flow devices can return results quickly but are only capable of detecting a handful of pathogens or markers. Herein, we present the use of disposable plasmonics with chiroptical nanostructures as a platform for low-cost, label-free optical biosensing with multiplexing and without the need for flow systems often required in current optical biosensors. We showcase the detection of SARS-CoV-2 in complex media as well as an assay for the Norovirus and Zika virus as an early developmental milestone toward high-throughput, single-step diagnostic kits for differential diagnosis of multiple respiratory viruses and any other emerging diagnostic needs. Diagnostics based on this platform, which we term "disposable plasmonics assays," would be suitable for low-cost screening of multiple pathogens or biomarkers in a near-point-of-care setting.

| S-EPMC10521139 | 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