DNA Separation and Fluorescence Monitoring by Integrated Waveguides in an Optofluidic Chip (original) (raw)
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ELECTROPHORESIS, 2010
By applying integrated-waveguide laser excitation to an optofluidic chip, fluorescently labeled DNA molecules of 12 or 17 different sizes are separated by CE with high operating speed and low sample consumption of 600pL.WhendetectingthefluorescencesignalsofmigratingDNAmoleculeswithaPMT,theLODisaslowas2.1pM.Inthediagnosticallyrelevantsizerange(600 pL. When detecting the fluorescence signals of migrating DNA molecules with a PMT, the LOD is as low as 2.1 pM. In the diagnostically relevant size range (600pL.WhendetectingthefluorescencesignalsofmigratingDNAmoleculeswithaPMT,theLODisaslowas2.1pM.Inthediagnosticallyrelevantsizerange(150-1000 base-pairs) the molecules are separated with reproducibly high sizing accuracy (499%) and the plug broadening follows Poissonian statistics. Variation of the power dependence of migration time on base-pair size -probably with temperature and condition of the sieving gel matrix -indicates that the capillary migration cannot be described by a simple physical law. Integrated-waveguide excitation of a 12-mm narrow microfluidic segment provides a spatio-temporal resolution that would, in principle, allow for a 20-fold better accuracy than the currently supported by state-of-the-art electrophoretic separation in microchips, thereby demonstrating the potential of this integrated optical approach to fulfill the resolution demands of future electrophoretic microchips.
2008
Femtosecond-laser-written optical waveguides were monolithically integrated into a commercial lab-on-a-chip to intersect a microfluidic channel. Laser excitation through these waveguides confines the excitation window to a width of 12 μm, enabling high-spatial-resolution monitoring of different fluorescent analytes, during their migration/separation in the microfluidic channel by capillary electrophoresis. Wavelength-selective monitoring of the on-chip separation of fluorescent dyes is implemented as a proof-of-principle. We envision well-controlled microfluidic plug formation, waveguide excitation, and a low limit of detection to enable monitoring of extremely small quantities with high spatial resolution.
Dual-point dual-wavelength fluorescence monitoring of DNA separation in a lab on a chip
2010
We present a simple approach in electrophoretic DNA separation and fluorescent monitoring that allows to identify the insertion or deletion of base-pairs in DNA probe molecules from genetic samples, and to perform intrinsic calibration/referencing for highly accurate DNA analysis. The principle is based on dual-point, dual-wavelength laser-induced fluorescence excitation using one or two excitation windows at the intersection of integrated waveguides and microfluidic channels in an optofluidic chip and a single, color-blind photodetector, resulting in a limit of detection of ~200 pM for single-end-labeled DNA molecules. The approach using a single excitation window is demonstrated experimentally, while the option exploiting two excitation windows is proposed theoretically.
Polymer Microfluidic Chips with Integrated Waveguides for Reading Microarrays
Analytical Chemistry, 2007
A microfluidic chip with an integrated planar waveguide was fabricated in poly(methyl methacrylate), PMMA, using a single-step, double-sided hot-embossing approach. The waveguide was embedded in air on three sides and the solution being interrogated on the fourth. DNA probes were covalently attached to the waveguide surface by plasma activating the PMMA and the use of carbodiimide coupling chemistry. Successful hybridization events were read using evanescent excitation monitored by an imaging microscope, which offered high spatial resolution (2 μm) and a large field-of-view (20-mm-diameter field-of-view), providing imaging of the entire array without scanning. The application of the microfluidic/waveguide assembly was demonstrated by detecting low abundant point mutations; insertion C mutations in BRCA1 genes associated with breast cancer were analyzed using a universal array coupled to an allele-specific ligation assay. DNA probes consisting of amine-terminated oligonucleotides were printed inside the microfluidic channel using a non-contact micro-spotter. Mutant and wide-type genomic DNAs of BRCA1 were PCR amplified, with the amplicons subjected to ligation detection reactions (LDRs). LDR solutions were allowed to flow over the microarray positioned on the polymer waveguide with successful ligation events discerned through fluorescence signatures present at certain locations of the array. The microfluidic/ waveguide assembly could detect polymorphisms present at <1% of the total DNA content.
SPIE Proceedings, 2007
In order to solve the drawbacks of sensitivity and portability in optical biosensors we have developed ultrasensitive and miniaturized photonic silicon sensors able to be integrated in a "lab-on-a-chip" microsystem platform. The sensors are integrated Mach-Zehnder interferometers based on TIR optical waveguides (Si/SiO 2 /Si 3 N 4) of micro/nanodimensions. We have applied this biosensor for DNA testing and for detection of single nucleotide polymorphisms at BRCA-1 gene, involved in breast cancer development, without target labeling. The oligonucleotide probe is immobilized by covalent attachment to the sensor surface through silanization procedures. The hybridization was performed for different DNA target concentrations showing a lowest detection limit at 10 pM. Additionally, we have detected the hybridization of different concentrations of DNA target with two mismatching bases corresponding to a mutation of the BRCA-1 gene. Following the way of the lab-on-a-chip microsystem, integration with the microfluidics has been achieved by using a novel fabrication method of 3-D embedded microchannels using the polymer SU-8 as structural material. The optofluidic chip shows good performances for biosensing.
Integrated optical microfluidic lab-on-a-chip
Photonics North 2008, 2008
Bio-security for health monitoring and diagnosis are the needs of the hour, for rapid detection of biological and chemical species. This calls for a necessity to develop a cost effective miniaturized and portable biosensor device for in-situ biomedical applications and Point-of-Care Testing (POCT). While portability of the biosensor is required for in-situ medical detections, miniaturization is essential for handling smaller sample volumes and high throughput. Thus, the above mentioned concerns cannot be addressed unless a fully integrated biosensor system is developed. In this work, an integrated opto microfluidic based Lab-on-a-chip device is proposed for carrying out fluorescence based biodetection. The input and output fibers were integrated with the microfluidic channel so as to make a robust setup. Fluorescence detection was carried out using Alexafluor 647 tagged antibody particles and the output was measured with a Spectrometer-on-Chip, integrated with the device. The experimental results prove that the proposed device is highly suitable for Lab-on-a-Chip applications.
The next major challenges for lab-on-a-chip (LoC) technology are 1) the integration of microfluidics with optical detection technologies and 2) the large-scale production of devices at a low cost. In this paper the fabrication and characterisation of a simple optical LoC platform comprising integrated multimode waveguides and microfluidic channels based on a photo-patternable acrylate based polymer is reported. The polymer can be patterned into both waveguides and microfluidic channels using photolithography. Devices are therefore both quick and cost-effective to fabricate, resulting in chips that are potentially disposable. The devices are designed to be highly sensitive, using an in-plane direct excitation configuration in which waveguides intersect the microfluidic channel orthogonally. The waveguides are used both to guide the excitation light and to collect the fluorescence signal from the analyte. The potential of the device to be used for fluorescence measurements is demonstrated using an aqueous solution of sodium fluorescein. A detection limit of 7 nM is achieved. The possibilities offered by such a device design, in providing a cost-effective and disposable measurement system based on the integration of optical waveguides with LoC technology is discussed.
Integrated microfluidic biophotonic chip for laser induced fluorescence detection
Biomedical microdevices, 2010
Integrated Lab-on-a-Chip or Micro-Total Analysis Systems offer several advantages for the detection of active chemical and biological species. In this work, an integrated microfluidic biophotonic chip is proposed for carrying out laser induced fluorescence detection. A Spectrometer-on-Chip device, specifically designed for multiple fluorescence detections at different emission wavelengths is integrated with the opto-microfluidic chip fabricated on Silicon-Polymer hybrid platform. The input fiber from the laser source, and output fiber coupled with a Spectrometer-on-Chip were integrated with the microfluidic channel so as to make a robust setup. Fluorescence detection was carried out using Alexafluor 647 tagged antibody particles. The experimental results show that the proposed biophotonic microfluidic device is highly suitable for high throughput detection of chemical and biological specimens.
Polymer waveguide backplanes for optical sensor interfaces in microfluidics
Lab on a Chip, 2007
A polymer optical backplane capable of generic luminescence detection within microfluidic chips is demonstrated using large core polymer waveguides and vertical couplers. The waveguides are fabricated through a new process combining mechanical machining and vapor polishing with elastomer microtransfer molding. A backplane approach enables general optical integration with planar array microfluidics since optical backplanes can be independently designed but still integrated with planar fluidic circuits. Fabricated large core waveguides exhibit a loss of 0.1 dB cm 21 at 626 nm, a measured numerical aperture of 0.50, and a collection efficiency of 2.86% in an n = 1.459 medium, comparable to a 0.50 NA microscope objective. In addition to vertical couplers for out-of-plane collection and excitation, polymer waveguides are doped with organic dyes to provide wavelength selective filtering within waveguides, further improving optical device integration. With large core low loss waveguides, luminescence collection is improved and measurements can be performed with simple LEDs and photodetectors. Fluorescein detection via fluorescence intensity with a limit of detection (3s) of 200 nM in a 1 mL volume is demonstrated. Phosphorescence lifetime based oxygen detection in water in an oxygen controllable microbial cell culture chip with a limit of detection (3s) of 0.08% or 35 ppb is also demonstrated utilizing the waveguide backplane. Single waveguide luminescence collection performance is equivalent to a back collection geometry fiber bundle consisting of nine 500 mm diameter collection fibers.
Lab on a Chip, 2012
One of the main limitations for achieving truly lab-on-a-chip (LOC) devices for point-of-care diagnosis is the incorporation of the "onchip" detection. Indeed, most of the state-of-the-art LOC devices usually require complex read-out instrumentation, losing the main advantages of portability and simplicity. In this context, we present our last advances towards the achievement of a portable and labelfree LOC platform with highly sensitive "on-chip" detection by using nanophotonic biosensors. Bimodal waveguide interferometers fabricated by standard silicon processes have been integrated with sub-micronic grating couplers for efficient light in-coupling, showing a sensitivity of 3.3•10-7 refractive index unit (RIU) in bulk. A 3D network of SU-8 polymer microfluidics monolithically assembled at the wafer-level was included, ensuring a perfect sealing and a compact packaging. To overcome some of the drawbacks inherent to interferometric read-outs, a novel all-optical wavelength modulation system has been implemented, providing a linear response and a direct read-out of the phase variation. Sensitivity, specificity and reproducibility of the wavelength modulated BiMW sensor has been demonstrated through the label-free immunodetection of the human hormone hTSH at picomolar level using a reliable biofunctionalization process.