Abstract: Disclosed herein are conjugates comprising a biomolecule linked to a label that have biological activity and are useful in a wide variety of biological applications. For example, provided herein are labeled polymerase conjugates including a polymerase linked to one or more labels, wherein the conjugate has polymerase activity. Such conjugates can exhibit enhanced biological activity and/or superior detectability as compared to conventional labeled polymerases. Also disclosed herein are improved methods for preparing such conjugates, and methods and systems for using such conjugates in biological applications such as nucleotide incorporation, primer extension and single molecule sequencing.

Abstract: Provided herein are compositions, systems, methods and kits useful for obtaining sequence information from a nucleic acid molecule. In some embodiments, the compositions, systems, methods and kits are useful for sequencing of natural or modified nucleic acids. In some embodiments, the compositions, systems, methods and kits relate to bi-directional sequencing of nucleic acids. In some embodiments, the compositions, systems, methods and kits relate to sequencing of nucleic acids linked to a solid support. In some embodiments, the methods useful for obtaining sequence information from a nucleic acid molecule include label-free or ion-based sequencing methods.

Abstract: Provided herein are systems and methods for nucleotide incorporation reactions. The systems comprise polymerases having altered nucleotide incorporation kinetics and are linked to an energy transfer donor moiety, and nucleotide molecules linked with at least one energy transfer acceptor moiety. The donor and acceptor moieties undergo energy transfer when the polymerase and nucleotide are proximal to each other during nucleotide binding and/or nucleotide incorporation. As the donor and acceptor moieties undergo energy transfer, they generate an energy transfer signal which can be associated with nucleotide binding or incorporation. Detecting a time sequence of the generated signals, or the change in the signals, can be used to determine the order of the incorporated nucleotides, and can therefore be used to deduce the sequence of the target molecule.

Abstract: Provided herein are methods and compositions for real time single molecule sequencing of a polymeric molecule, such as a polynucleotide, by isolating the polymeric molecule in a nanofluidic device, subjecting it in situ to a polymerase reaction wherein various components of the polymerase reaction mixture are labeled, and determining the time-sequence of incorporation of monomeric subunits during the polymerization process.

Abstract: Disclosed herein are conjugates comprising a biomolecule linked to a label that have biological activity and are useful in a wide variety of biological applications. For example, provided herein are polymerase-nanoparticle conjugates including a polymerase linked to a nanoparticle, wherein the conjugate has polymerase activity. Such conjugates can exhibit reduced aggregation and improved stochiometries wherein the average biomolecule:nanoparticle ratio approaches or equals 1:1. Also disclosed herein are improved methods for preparing such conjugates, and methods and systems for using such conjugates in biological applications such as nucleotide incorporation, primer extension and single molecule sequencing.

Abstract: Provided herein are compositions and systems for use in polymerase-dependent, nucleotide transient-binding methods. The methods are useful for deducing the sequence of a template nucleic acid molecule and single nucleotide polymorphism (SNP) analyses. The methods rely on the fact that the polymerase transient-binding time for a complementary nucleotide is longer compared to that of a non-complementary nucleotide. The labeled nucleotides transiently-binds the polymerase in a template-dependent manner, but does not incorporate. The methods are conducted under any reaction condition that permits transient binding of a complementary or non-complementary nucleotide to a polymerase, and inhibits nucleotide incorporation.

Abstract: Disclosed herein are conjugates comprising a biomolecule linked to a label that have biological activity and are useful in a wide variety of biological applications. For example, provided herein are labeled polymerase conjugates including a polymerase linked to one or more labels, wherein the conjugate has polymerase activity. Such conjugates can exhibit enhanced biological activity and/or superior detectability as compared to conventional labeled polymerases. Also disclosed herein are improved methods for preparing such conjugates, and methods and systems for using such conjugates in biological applications such as nucleotide incorporation, primer extension and single molecule sequencing.

Abstract: Provided herein are systems and methods for nucleotide incorporation reactions. The systems comprise polymerases having altered nucleotide incorporation kinetics and are linked to an energy transfer donor moiety, and nucleotide molecules linked with at least one energy transfer acceptor moiety. The donor and acceptor moieties undergo energy transfer when the polymerase and nucleotide are proximal to each other during nucleotide binding and/or nucleotide incorporation. As the donor and acceptor moieties undergo energy transfer, they generate an energy transfer signal which can be associated with nucleotide binding or incorporation. Detecting a time sequence of the generated signals, or the change in the signals, can be used to determine the order of the incorporated nucleotides, and can therefore be used to deduce the sequence of the target molecule.

Abstract: A seed layer is formed on a substrate using a first biological agent. The seed layer may comprise densified nanoparticles which are bound to the biological agent. The seed layer is then used for a deposition of a metal layer, such as a barrier layer, an interconnect layer, a cap layer and/or a bus line for a solid state device.

Abstract: Provided herein are methods and compositions for real time single molecule sequencing of short nucleotide sequences using nucleotide fluorescent semiconductor nanocrystals-conjugated nucleotide primers.

Abstract: An aqueous substrate surface treatment composition includes cysteine and an acidic solution having a pH of about 7 or less. The composition enables a selective deposition of a metal ion sensitizer and a subsequent selective plating of a metallic cap layer. Various CoWP plating bath compositions are also provided which may be used to form the cap layer.

Abstract: Methods, systems, kits for carrying out a wide variety of different assays that comprise providing a first reagent mixture which comprises a first reagent having a fluorescent label. A second reagent is introduced into the first reagent mixture to produce a second reagent mixture, where the second reagent reacts with the first reagent to produce a fluorescently labeled product having a substantially different charge than the first reagent. A polyion is introduced into at least one of the first and second reagent mixtures, and the fluorescent polarization in the second reagent mixture relative to the first reagent mixture is determined, this fluorescent polarization being indicative of the rate or extent of the reaction.

Abstract: Nucleotides and nucleotide analogs are used in various sequencing by incorporation/sequencing by synthesis methods. Nucleotide analogs comprising 3?-blocking groups are used to provide reversible chain-termination for sequencing by synthesis. Typical blocking groups include phosphate groups and carbamate groups. Fluorescent nucleotides are used to perform sequencing by synthesis with detection by incorporation of the fluorescently labeled nucleotide, optionally followed by photobleaching and intercalating dyes are used to detect addition of a non-labeled nucleotide in sequencing by synthesis with detection by intercalation. Microfluidic devices, including particle arrays, are used in the sequencing methods.

Abstract: A seed layer is formed on a substrate using a first biological agent. The seed layer may comprise densified nanoparticles which are bound to the biological agent. The seed layer is then used for a deposition of a metal layer, such as a barrier layer, an interconnect layer, a cap layer and/or a bus line for a solid state device.

Abstract: An aqueous substrate surface treatment composition includes cysteine and an acidic solution having a pH of about 7 or less. The composition enables a selective deposition of a metal ion sensitizer and a subsequent selective plating of a metallic cap layer. Various CoWP plating bath compositions are also provided which may be used to form the cap layer.

Abstract: Methods and systems of monitoring reactions, e.g., assays, that filter out background signal from substrate, in detecting the product. The methods and systems controllably move detectable reaction product from a first location to a second location at which the product is detected while controllably moving potentially interfering substrate materials away from or not toward the second location. Controllable movement of the different species is accomplished through the controlled combination of bulk fluid flow and differential electrophoresis of substrate and product to move the product, but not the substrate past the detection region.

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: The present invention provides a method of assaying for kinase activity, comprising contacting a fluorescently labeled phosphorylatable peptide substrate with an ATP analog in the presence of a kinase enzyme to yield a first product; contacting the first product with a reactant that comprises a biotin derivative to yield a second product; contacting the second product with a biotin-binding protein; and detecting a difference in a fluorescence polarization level from the second product as compared to a fluorescence polarization of the peptide substrate.

Abstract: Methods, systems and assays are provided for FP detection of nucleic acid hybridization.