Abstract: The invention provides assay particles useful, for example, for detecting analytes and binding molecule interactions. One type of assay particle includes a core portion encased by a shell portion, wherein the shell portion comprises an inorganic phosphor that binds selectively to a target molecule. Another type of an assay particle includes a core portion encased by a shell portion, and a coat portion covering the shell portion, wherein the coat portion comprises an inorganic phosphor that binds selectively to a target molecule. A further type of assay particle includes a core portion encased by a shell portion, and a coat portion covering the shell portion, wherein the coat portion comprises an inorganic phosphor and a target selective binding moiety, and wherein the assay particle is buoyant in aqueous media.

Abstract: The invention provides methods for detecting and isolating phosphomolecules using phosphoaffinity materials that comprise a hydrated metal oxide. In an embodiment, a method for detecting a phosphomolecule in a sample involves (a) contacting a sample with a phosphoaffinity material comprising a hydrated metal oxide, under conditions wherein a phosphomolecule is capable of binding to the phosphoaffinity material to form a phosphomolecule-phosphoaffinity material complex, and (b) detecting formation of a phosphomolecule-phosphoaffinity material complex, thereby detecting a phosphomolecule in the sample.

Abstract: The invention provides methods for isolating a target molecule from a sample. In an embodiment, the method involves contacting a sample with a capture agent, the agent comprising a siderophore and a transition metal cation, under conditions wherein the agent is capable of binding a target molecule to form a target molecule-capture agent complex, wherein the target molecule is selected from the group consisting of a phosphorylated molecule, a nitrotyrosine-containing molecule and a sulfated molecule, and separating the target molecule-capture agent complex from the sample, thereby isolating the target molecule from the sample. Also provided are methods for determining the presence of a target molecule in a sample, that involve contacting a sample with a capture agent, the agent comprising a siderophore and a transition metal cation.

Abstract: The present invention provides dyes, reactive dyes and labeled reagents that may be used in the detection or quantification of desirable target molecules, such as proteins, nucleic acids and cellular organelles. Dyes are provided that may be used free in solution where the binding of the dye to the target molecule provides signal generation. Dyes are also provided that comprise reactive groups that may be used to attach the dyes to probes that will bind to desirable target molecules. The novel dyes of the present invention have been modified to provide beneficial properties.

Abstract: Novel fluorescent derivitization reagents are described that are suitable for coupling to biomolecules that contain aldehyde or ketone functional groups. In one embodiment is provided reagents that have the following formula: wherein Q is carbonyl, thiocarbonyl, or sulfonyl, and R5 is -L-Z; L is arylene, or a C1-6 perfluoroalkylene, or a single covalent bond; Z is a carbonyl hydrazide, hydrazide, sulfonyl hydrazide, or a thiocarbonyl hydrazide; R11-R14 are independently H, C1-6alkyl, C1-6 alkoxy, C1-6 perfluoroalkyl, C1-6 alkylamino, di(C2-12-alkyl)amino, amino, carboxy, cyano, halogen, hydroxy, nitro, phenyl, or sulfo; and R21-R24 are independently H, C1-6 alkyl, C1-6 alkoxy, C1-6 perfluoroalkyl, C1-6 alkylamino, di(C2-12-alkyl)amino, amino, carboxy, cyano, halogen, hydroxy, nitro, phenyl, sulfo, or -L-Z. The method of treating a sample with the derivativization reagents is described.

Abstract: Embodiments of the present invention provide a staining solution and of method of using the staining solution for selectively detecting proteins that contain two or more ?-helical transmembrane domains. The staining solution comprises a lipophilic dyes and at least about a 30% hydrophobic solvent. The dyes of the present are represented by the general formula A-B-E wherein A is a nitrogen heterocycle, B is a bridge moiety and E is an electron pair accepting moiety that comprises either a carbonyl or nitrogen atom. In one embodiment these lipophilic dyes are merocyanine dye, a cyanine dye, a styryl dye or a carbazolylvinyl dye.

Abstract: Kits including novel fluorescent derivitization reagents for labeling an aldehyde- and/or ketone-containing target substance in a sample are described. In one embodiment kits are provided the novel fluorescent derivitization reagents of which have the following formula: wherein Q is carbonyl, thiocarbonyl, or sulfonyl, and R5 is -L-Z; L is arylene, or a C1-6 perfluoroalkylene; Z is a carbonyl hydrazide, hydrazide, sulfonyl hydrazide, or a thiocarbonyl hydrazide; R11-R14 are independently H, C1-16 alkyl, C1-6 alkylamino, amino, or halogen; and R21-R24 are independently H, C 1-6 alkyl, C 1-6 alkoxy, C1-6 perfluoroalkyl, C1-6 alkylamino, di(C2-12-alkyl)amino, amino, carboxy, cyano, halogen, hydroxy, nitro, phenyl, sulfo, or -L-Z. The kits and reagents described are particularly useful for labeling glycoproteins or glycopeptides, nucleic acids, and lipopolysaccharides in electrophoresis gels.

Abstract: The present invention relates to phosphate-binding compounds that find use in binding, detecting and isolating phosphorylated target molecules including the subsequent identification of target molecules that interact with phosphorylated target molecules or molecules capable of being phosphorylated. A binding solution is provide that comprises a phosphate-binding compound, an acid and a metal ion wherein the metal ion simultaneously interacts with an exposed phosphate group on a target molecule and the metal chelating moiety of the phosphate-binding compound forming a bridge between the phosphate-binding compound and a phosphorylated target molecule resulting in a ternary complex. The binding solution of the present invention finds use in binding and detecting immobilized and solubilized phosphorylated target molecules, isolation of phosphorylated target molecules from a complex mixture and aiding in proteomic analysis wherein kinase and phosphatase substrates and enzymes can be identified.

Abstract: The invention provides assay particles useful, for example, for detecting analytes and binding molecule interactions. One type of assay particle includes a core portion encased by a shell portion, wherein the shell portion comprises an inorganic phosphor that binds selectively to a target molecule. Another type of an assay particle includes a core portion encased by a shell portion, and a coat portion covering the shell portion, wherein the coat portion comprises an inorganic phosphor that binds selectively to a target molecule. A further type of assay particle includes a core portion encased by a shell portion, and a coat portion covering the shell portion, wherein the coat portion comprises an inorganic phosphor and a target selective binding moiety, and wherein the assay particle is buoyant in aqueous media.

Abstract: The inventions relates to methods and kits for capture and/or analysis of kinases and/or phosphatases in one or more samples. In some embodiments, a kinase inhibitor, e.g. staurosporine or its derivative, is used to capture kinases from a sample. In some embodiments, a phosphatase inhibitor, e.g. microcystin or its derivative, is used to capture phosphatases from a sample. Methods for quantitative analysis of captured kinases and/or proteases are also provided. In some embodiments, quantitative analysis is accomplished using mass spectrometry. In addition, the invention provides kits related to same.

Abstract: The present invention provides dyes, reactive dyes and labeled reagents that may be used in the detection or quantification of desirable target molecules, such as proteins, nucleic acids and cellular organelles. Dyes are provided that may be used free in solution where the binding of the dye to the target molecule provides signal generation. Dyes are also provided that comprise reactive groups that may be used to attach the dyes to probes that will bind to desirable target molecules. The novel dyes of the present invention have been modified to provide beneficial properties.

Abstract: Disclosed are methods and reagents for detecting the presence of and/or activity of one or more phospho-transfer activities such as kinase, phosphatase, nucleotide cyclase, or phosphodiesterase activities.

Abstract: The invention provides methods for detecting and isolating phosphomolecules using phosphoaffinity materials that comprise a hydrated metal oxide. In an embodiment, a method for detecting a phosphomolecule in a sample involves (a) contacting a sample with a phosphoaffinity material comprising a hydrated metal oxide, under conditions wherein a phosphomolecule is capable of binding to the phosphoaffinity material to form a phosphomolecule-phosphoaffinity material complex, and (b) detecting formation of a phosphomolecule-phosphoaffinity material complex, thereby detecting a phosphomolecule in the sample.

Abstract: The invention describes methods for labeling or detecting of immobilized poly(amino acids), including peptides, polypeptides and proteins, on membranes and other solid supports, using fluorescent dipyrrometheneboron difluoride dyes. Such immobilized poly(amino acids) are labeled or detected on blots or on arrays of poly(amino acids), or are attached to immobilized aptamers.

Abstract: The invention describes methods for labeling or detecting of immobilized poly(amino acids), including peptides, polypeptides and proteins, on membranes and other solid supports, using fluorescent dipyrrometheneboron difluoride dyes. Such immobilized poly(amino acids) are labeled or detected on blots or on arrays of poly(amino acids), or are attached to immobilized aptamers.

Abstract: Novel fluorescent derivitization reagents are described that are suitable for coupling to biomolecules that contain aldehyde or ketone functional groups. In one embodiment is provided reagents that have the following formula: wherein Q is carbonyl, thiocarbonyl, or sulfonyl, and R5 is -L-Z; L is arylene, or a C1-6 perfluoroalkylene, or a single covalent bond; Z is a carbonyl hydrazide, hydrazide, sulfonyl hydrazide, or a thiocarbonyl hydrazide; R11-R14 are independently H, C1-6 alkyl, C1-6 alkoxy, C1-6 perfluoroalkyl, C1-6 alklyamino, di(C2-12alkyl)amino, amino, carboxy, cyano, halogen, hydroxy, nitro, phenyl, or sulfo; and R21-R24 are independently H, C1-6 alkyl, C1-6 alkoxy, C1-6 perfluoroalkyl, C1-6 alklyamino, di(C2-12-alkyl)amino, amino, carboxy, cyano, halogen, hydroxy, nitro, phenyl, sulfo, or -L-Z. The method of treating a sample with the derivativization reagents is described.

Abstract: Methods for enhancing separation and analysis of biological molecules, particularly proteins, and for characterizing tissue, cell, and subcellular (e.g., organelle) expressed protein profiles (proteomes or protein fingerprints) are disclosed. Multi-dimensional diagrams that illustrate the characteristics of the proteins in a sample, based at least in part on interactions between proteins in the system can be produced. In certain embodiments, the diagrams are three-dimensional and incorporate information on protein-protein interactions, protein charge, and protein size for substantially all of the protein species in the sample. Also described are methods of using the provided multi-dimensional diagrams to detect changes in biological systems that are for instance due to disease, drug treatment, environmental condition, and so forth. Methods are provided for correlating changes in three-dimensional proteomic diagrams to disease diagnosis and prognosis, toxicology, therapeutic compound (e.g.

Abstract: The present invention describes a variety of substituted and unsubstituted carbazolylvinyl dyes and their use for detecting and quantifying poly(amino acids), including peptides, polypeptides and proteins. The labeled proteins or peptides are highly colored, but are also detected by their strong fluorescence enhancement. Poly(amino acids) are detected in solution, in electrophoretic gels, and on solid supports, including blots and dipsticks. The present method of staining is highly sensitive, extremely facile, and relatively non-selective and can be accomplished without the use of organic solvent additives.

Abstract: Novel fluorescent derivitization reagents are described that are suitable for coupling to biomolecules that contain aldehyde or ketone functional groups. The method of treating a sample with the derivativization reagents is described. The reagents are particularly useful for labeling glycoproteins or glycopeptides, nucleic acids, and lipopolysaccharides in electrophoresis gels.

Abstract: The invention relates to the staining of amine-containing polymers, including including peptides, polypeptides, and proteins, in gels and on solid supports, using complexes of europium (3+).