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NGK Insulators, Nisshinbo Industries, Molecular Staging, Sangamo Biosciences, XenoPort, Zyomyx, Nanogen, Third Wave Technologies, ViaLogy, Sangamo Biosciences, Nuvelo, Regents of the University of Minnesota

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NGK Insulators of Nagoya, Japan, received US Patent No. 6,776,960, “Method for producing DNA chip.” The patent covers a method comprising a pretreatment step of forming a poly-L-lysine layer on a surface of a base plate, a sample preparation step of preparing a sample containing a DNA fragment, a dilution step of diluting the concentration of the obtained sample, and a step of supplying a diluted sample solution onto the base plate to produce a DNA chip. The sample preparation includes an amplification step of PCR-amplifying the DNA fragment to prepare a PCR product, a powder formation step of drying the obtained PCR product to form DNA powder, and a mixing step of dissolving the obtained DNA powder in a buffer solution.


Nisshinbo Industries of Tokyo received US Patent No. 6,777,181, “Method for separating and collecting nucleic acids.” The patent covers a method for separating and collecting nucleic acids, which comprises a step of bringing a sample nucleic acid solution into contact with a nucleic acid-immobilized substrate comprising a substrate and two or more kinds of single-stranded nucleic acids separately immobilized on the substrate, allowing hybridization of the immobilized single-stranded nucleic acids and single-stranded nucleic acids complementary to the immobilized single-stranded nucleic acids. It also includes a step of separating the hybridized single-stranded nucleic acids according to immobilized portions of the immobilized nucleic acids, to collect the hybridized single-stranded nucleic acids without disassembling the nucleic acid-immobilized substrate.


Molecular Staging of New Haven, Conn., received US Patent No. 6,777,183, “Process for allele discrimination utilizing primer extension.” Disclosed are methods for allele discrimination involving the use of rolling circle amplification coupled with primer extension and utilizing exonuclease deficient polymerases to distinguish matched and unmated single nucleotide sites, such as in the case of a SNP.


Sangamo Biosciences of Richmond, Calif., received US Patent No. 6,777,185, “Functional genomics using zinc finger proteins.” The patent covers methods of regulating gene expression using recombinant zinc finger proteins for functional genomics and target validation applications.


XenoPort of Santa Clara, Calif., received US Patent No. 6,777,239, “Epitope-captured antibody display.” Reagents and methods for detecting target proteins in a sample are provided in the patent. The reagents include a replicable genetic package, a protein displayed on an exterior surface of the package that is expressed from a heterologous nucleic acid borne by the package, and one or more antibodies complexed with the expressed protein and which have an open binding site for a target protein. Thus, a segment of the nucleic acid encodes for an epitope that is shared by the expressed polypeptide and the target protein. The reagents can be utilized individually or as part of a library or an array to bind target proteins within protein samples to form one or more complexes. By determining the sequence of the segment of the heterologous nucleic acid of a package within a complex, one can identify the target protein since the segment encodes for an epitope that is shared by the expressed and target proteins.


Zyomyx of Hayward, Calif., received US Patent No. 6,780,582, “Arrays of protein-capture agents and methods of use thereof.” Arrays of protein-capture agents useful for the simultaneous detection of a plurality of proteins which are the expression products, or fragments thereof, of a cell or population of cells in an organism are provided. A variety of antibody arrays, in particular, are described. Methods of both making and using the arrays of protein-capture agents are also disclosed. The invention arrays are particularly useful for various proteomics applications including assessing patterns of protein expression and modification in cells.


Nanogen of San Diego, received US Patent No. 6,780,584, “Electronic systems and component devices for macroscopic and microscopic molecular biological reactions, analyses and diagnostics.” The patent pertains to the design, fabrication, and uses of an electronic system that can actively carry out and control multi-step and multiplex reactions in macroscopic or microscopic formats. In particular, these reactions include molecular biological reactions, such as nucleic acid hybridizations, nucleic acid amplification, sample preparation, antibody/antigen reactions, clinical diagnostics, combinatorial chemistry and selection, drug screening, oligonucleotide and nucleic acid synthesis, peptide synthesis, biopolymer synthesis, and catalytic reactions. A key feature of the present invention is the ability to control the localized concentration of two or more reaction-dependent molecules and their reaction environment in order to greatly enhance the rate and specificity of the molecular biological reaction.


Third Wave Technologies of Madison, Wis., received US Patent No. 6,780,585, “Polymorphism analysis by nucleic and acid structure probing.” The invention relates to methods and compositions for analyzing nucleic acids. In particular, the present invention provides methods and compositions for the detection and characterization of nucleic acid sequences and sequence changes. The methods of the present invention permit the detection and/or identification of genetic polymorphism such as those associated with human disease and permit the identification of pathogens (e.g., viral and bacterial strain identification).


ViaLogy of Altadena, Calif., received US Patent No. 6,780,589, “Method and system using active signal processing for repeatable signal amplification in dynamic noise backgrounds.” The patent covers a technique that is useful for determining the presence of specific hybridization expression within an output pattern generated from a digitized image of a biological sample applied to an arrayed platform. The output pattern includes signals associated with noise, and signals associated with the biological sample, some of which are degraded or obscured by noise. The output pattern is first segmented using tessellation. Signal processing, such as interferometry, or more specifically, resonance interferometry, and even more specifically quantum resonance interferometry or stochastic resonance interferometry, is then used to amplify signals associated with the biological sample within the segmented output pattern having an intensity lower than the intensity of signals associated with noise so that they may be clearly distinguished from background noise. The improved detection technique allows repeatable, rapid, reliable, and inexpensive measurements of arrayed platform output patterns.


Sangamo Biosciences of Richmond, Calif., received US Patent No. 6,780,590, “Gene identification.” The patent provides methods and compositions for identifying a particular genomic sequence as a gene and/or a coding region, once that sequence has been tentatively identified as a gene based on genomic analysis using one or more gene prediction algorithms. The methods include the use of exogenous molecules such as zinc finger proteins, which are capable of binding to and modulating expression of gene transcription, targeted to putative gene sequences, followed by assay for one or more selected phenotypes.


Nuvelo of Sunnyvale, Calif., has received US Patent No. 6,783,969, “CathepsinV-like polypeptides.” The present invention provides novel nucleic acids, novel polypeptide sequences encoded by these nucleic acids, and uses thereof.


Regents of the University of Minnesota, Minneapolis, have received US Patent No. 6,784,982, “Direct mapping of DNA chips to detector arrays.” The patent covers a device for detecting the pattern of polynucleic acid hybridization to a surface. The device includes a positioning device for receiving a nucleic acid chip and keeping the chip in a sampling position. The nucleic acid chip is an object with a flat sample surface and an opposed surface that is joined to the sample surface by a thickness, with the sample surface having sequences of nucleic acids immobilized thereto, with each sequence being immobilized to a particular chip address. The device also includes an electronic light detector array comprising detector pixels, which are sensors located at particular detector pixel addresses, wherein the sampling position places the sample surface of the chip at a well-defined position relative to the electronic light detector array.