Abstract: A method any system for performing optical PCR. The method includes binding nucleic acids in a sample fluid bind to a solid-phase substrate. The method also includes flowing the sample fluid in a fluid conduit to a trapping site. The trapping site may include a chamber. The method may further include applying a magnetic field to trap the solid-phase substrate of the sample fluid flowing through the fluid conduit at the trapping site. The method further includes flowing a wash buffer through the fluid conduit to remove impurities from the solid-phase substrate. The method further includes flowing an immiscible fluid through the fluid conduit to remove residual sample fluid and/or wash buffer. The method further includes flowing an elution buffer through the fluid conduit to elute nucleic acids from the solid-phase substrate and performing optical PCR on the eluted nucleic acids.

Abstract: A method for extracting nucleic acids includes mixing a biological sample with a solid-phase substrate to produce a sample fluid. The nucleic acids in the sample fluid bind to the solid-phase substrate. The method also includes flowing the sample fluid in a fluid conduit to a trapping site. The trapping site may include a chamber. The method may further include applying a magnetic field to trap the solid-phase substrate of the sample fluid flowing through the fluid conduit at the trapping site. The method further includes flowing a wash buffer through the fluid conduit to remove impurities from the solid-phase substrate. The method further includes flowing an immiscible fluid through the fluid conduit to remove residual sample fluid and/or wash buffer. The method further includes flowing an elution buffer through the fluid conduit to elute nucleic acids from the solid-phase substrate.

Abstract: Provided herein are methods of nucleic acid sequencing using nucleotides with labels attached to the phosphate group so that incorporation of such nucleotides into a primed template results in formation of a phospho-label. Treatment of the phospho-label with a phophatase generates a free label which can be detected in a variety of ways. The labels can include, e.g., chemiluminescent labels, chemiluminescent substrates and enzyme activators. Also provided are reagents such as nucleotides phospholinked to labels such as enzyme activators.

Abstract: The invention provides methods and apparatuses that allow a protein sample to undergo reduction, alkylation, and digestion in a continuous flow process carried out within a microfluidic device. Methods and apparatuses in accordance with the invention can be employed as part of an automated proteomics analysis carried out in an integrated proteomics system.

Abstract: Methods for screening a compound for enzyme inhibition activity include providing at least one sample mixture to a microfluidic device, applying vacuum pressure to the sample mixture, flowing the sample mixture along a microchannel of the microfluidic device, separating at least two components of the sample mixture based upon a net charge difference between the product and at least one other material to produce separated material, detecting at least one of the separated materials, and determining enzyme inhibition activity based on the detection of the separated material. Kits for screening a compound for enzyme inhibition activity include a first multiwell plate having a specific plurality of enzymes disposed within a first plurality of wells and a second multiwell plate having a plurality of enzyme substrates disposed with a second plurality of wells, a phosphate source and a cofactor disposed within each well of the second plate.

Abstract: A microfluidic device with a filter includes a substrate; a flowpath including a well formed in the substrate in fluid communication with a channel formed in the substrate; and a filter disposed across the flowpath and associated with the channel.

Abstract: The present teachings relate to methods, systems, and apparatus for low cost label-free assay detection. The present teachings, in a variety of embodiments, employ opposing forces to detect signals which depend on the number of charges on and/or the size of a particle. The particle, which can be subjected to opposing forces, can have specific capture probes at its surface. As analytes of interest are captured by the particle, the number of charges on the particle surface and/or the size of the particle is changed. A particle parameter or kinematic property such as the position, velocity, acceleration or force of/on the particle can be measured, and results obtained relating, for example, to the present, absence, quantity, and such, of one or more analytes of interest. Various embodiments are described for efficient, high throughput assays of samples potentially including one or more analytes of interest, such as bioanalytes.

Abstract: A microfluidic device with a filter includes a substrate; a flowpath including a well formed in the substrate in fluid communication with a channel formed in the substrate; and a filter disposed across the flowpath and associated with the channel.

Abstract: The present teachings relate to systems, methods, and the like, for analyzing biological polymers, by use of opposing forces. Among other things, the present teachings can be used to determine sequence information, such as in genetic sequencing and genotyping applications. Various embodiments are described for efficient, high throughput sequencing of nucleic-acid molecules, such as DNA. Various embodiments are described wherein nucleic-acid sequence information is determined without the need or use of extrinsic labels. As well various embodiments of methods, systems, and the like, are described, which can provide long and accurate read lengths for low-cost nucleic acid sequencing.

Abstract: Methods for highly parallel Sanger sequencing are discussed. In particular, provided herein are methods using particles to clonally amplify templates and to introduce the amplified nucleic acids into many parallel channels with a single template per channel. Once in the channels, the nucleic acids are separated by size using electrophoresis to produce long read length sequencing information. Methods involving optical detection of the size-separated nucleic acids and analysis of the resulting electropherograms to yield the sequences are disclosed.

Abstract: Devices and methods are described for detecting and quantifying nucleic acids using a sealed system that minimizes contamination. In particular, provided herein are devices for and methods using nucleic acid amplification that permit multiple sampling of an amplification reaction mixture and quantitation and identification of amplicons during the course of an amplification reaction. Methods involving the transfer of samples from an amplification reaction mixture into a separation network, separation of nucleic acids based on size, and identification and quantitation of nucleic acids are disclosed.

Abstract: Devices and methods are described for detecting and quantifying nucleic acids using a sealed system that minimizes contamination. In particular, provided herein are devices for and methods using nucleic acid amplification that permit multiple sampling of an amplification reaction mixture and quantitation and identification of amplicons during the course of an amplification reaction. Methods involving the transfer of samples from an amplification reaction mixture into a separation network, separation of nucleic acids based on size, and identification and quantitation of nucleic acids are disclosed.

Abstract: Methods for screening a compound for enzyme inhibition activity include providing at least one sample mixture to a microfluidic device, applying vacuum pressure to the sample mixture, flowing the sample mixture along a microchannel of the microfluidic device, separating at least two components of the sample mixture based upon a net charge difference between the product and at least one other material to produce separated material, detecting at least one of the separated materials, and determining enzyme inhibition activity based on the detection of the separated material. Kits for screening a compound for enzyme inhibition activity include a first multiwell plate having a specific plurality of enzymes disposed within a first plurality of wells and a second multiwell plate having a plurality of enzyme substrates disposed with a second plurality of wells, a phosphate source and a cofactor disposed within each well of the second plate.

Abstract: A microfluidic device with a filter includes a substrate; a flowpath including a well formed in the substrate in fluid communication with a channel formed in the substrate; and a filter disposed across the flowpath.

Abstract: The invention provides methods and apparatuses that allow a protein sample to undergo reduction, alkylation, and digestion in a continuous flow process carried out within a microfluidic device. Methods and apparatuses in accordance with the invention can be employed as part of an automated proteomics analysis carried out in an integrated proteomics system.

Abstract: The present invention provides methods and reagents for targeting probes to selected cellular locations, through the expression of specific binding partners to that probe within the cell. In one embodiment, the probes may comprise spectroscopic probe that can be used in a method for localizing a specific binding partner within a cell, and for creating assays for post-translational activities. The invention allows the monitoring of the location of such intracellular specific binding partners over time and in response to stimuli, such as test chemicals. The spectroscopic probes can be used for screening a test chemical for activity. The present invention also includes cells and transgenic organisms comprising the intracellular specific binding partner, wherein the specific binding partner can bind with the spectroscopic probe/ligand conjugate.

Abstract: Intracellular binding reactions, and particularly DNA/DNA binding protein reactions are detected in situ, using intracellular fluorescence polarization detection. The methods comprise providing a biological cell having at least a first component of a binding reaction disposed therein. The cell is contacted with a second component of the binding reaction whereby the second component is internalized within the biological cell. At least one of the first and second components has a fluorescent label. The amount of binding between the first and second components within the cell is determined by measuring a level of polarized and/or depolarized fluorescence emitted from within the biological cell.

Abstract: Methods for chromatographically separating materials, including the separation of materials in kinase or phosphatase assays, in microfluidic devices under positive or negative fluid pressure. Devices and integrated systems for performing chromatographic separations are also provided.

Abstract: Compositions for monitoring transmembrane potential across cellular membranes. The compositions typically comprise a cell having a plasma membrane that comprises a first leaflet and a second leaflet, the membrane comprising first and second membrane associated components which, when placed adjacent each other either produce or quench a fluorescent signal, wherein. The first membrane associated component translocates from a first leaflet of the membrane to a second leaflet of the membrane in response to an electrical potential gradient across the membrane, the first membrane associated component being selected from a non-fluorescent cationic fluorescence quencher a non-fluorescent anionic fluorescence quencher and a cationic fluorophore.

Abstract: Intracellular binding reactions, and particularly DNA/DNA binding protein reactions are detected in situ, using intracellular fluorescence polarization detection. The methods comprise providing a biological cell having at least a first component of a binding reaction disposed therein. The cell is contacted with a second component of the binding reaction whereby the second component is internalized within the biological cell. At least one of the first and second components has a fluorescent label. The amount of binding between the first and second components within the cell is determined by measuring a level of polarized and/or depolarized fluorescence emitted from within the biological cell.