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Incyte Genomics, Amersham Pharmacia Biotech, Hitachi Software Engineering, PerkinElmer, Agilent Technologies, CuraGen, Affymetrix

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Incyte Genomics has been awarded US Patent No. 6,448,013, “Duplex probes for hybridization reactions.” The patent refers to methods to count the number of polynucleotides in a particular sample. One of these methods involves using single- or double-stranded probes to contact the targets, then comparing them to a reference hybridization pattern in order to measure the amounts of particular nucleic acids in a sample.

Amersham Pharmacia Biotech (now Amersham Biosciences) has received US Patent No. 6,448,010, “Method for detecting mutations using arrayed primer extension.” The method involves using oligonucleotide primers with a sequence complementary to that of the target sequence, which is organized in order to detect the first base added to them through primer extension — a method for detecting single-base mutations. A sample sequence is then hybridized to the primers, and the primer is extended by this single base using reagents that include labeled ddNTPs. Labeled ddNTPs that do not correspond to the expected base indicate a mutation. The labels can include chemiluminescent reagents, fluorescent dyes, radioactive, or electrically conductive tags. The patent also discloses a kit and an array for mutation detection.

Hitachi Software Engineering has received US Patent No. 6,453,243, “Method for displaying result of hybridization experiment using biochip and method for evaluating experimental error of hybridization experiment.” The patent refers to a method for displaying results of hybridization experiments using a biochip. Data from control spots in sections on a biochip are measured, plotted, and displayed on a single screen, making it possible to skim the whole biochip to find experimental errors.

PerkinElmer has received US Patent No. 6,451,525, “Parallel sequencing method.” The patent refers to a method for obtaining sequence information from a number of target polynucleotides in a sample. In one embodiment, the method involves contacting a plurality of different sequence primers with a polynucleotide sample under conditions effective for the primers to anneal to primer-complementary regions in one or more target polynucleotides, to form one or more target-primer hybrid(s).

Agilent Technologies has received US Patent No. 6,450,047, “Device for high throughput sample processing, analysis and collection, and methods of use thereof.” A microanalysis device with a number of sample processing compartments is described for use in liquid phase analysis. The system comprises a plurality of interconnected microanalysis devices. The device is formed by microfabrication of microstructures in novel support substrates. The invention can be used for the analysis of small and/or macromolecular and/or other solutes in the liquid phase.

CuraGen has received US Patent No. 6,453,245, “Method and apparatus for identifying, classifying, or quantifying protein sequences in a sample without sequencing.” This invention provides methods by which biologically derived DNA sequences in a mixed sample or in an arrayed single sequence clone can be determined and classified without sequencing. The methods make use of information on the presence of carefully chosen target subsequences, typically ranging in length from four to eight base pairs, and preferably the length between target subsequences in a sample DNA sequence together with DNA sequence databases containing lists of sequences likely to be present in the sample to determine a sample sequence. Computer implemented methods are provided to analyze the experimental results and to determine the sample sequences in question and to carefully choose target sub-sequences so that experiments yield a maximum amount of information.

Affymetrix has received US Patent No. 6,451,536, “Products for detecting nucleic acids.” The invention provides methods and apparatus for sequencing, fingerprinting, and mapping biological macromolecules, typically polymers. The methods make use of a plurality of sequence-specific recognition reagents which can also be used for classification of biological samples, and to characterize their sources. The invention relies in part on the ability to synthesize or attach specific recognition reagents at known locations on a substrate, typically a single substrate. In particular, the present invention provides the ability to prepare a substrate having a very high-density matrix pattern of positionally defined specific recognition reagents. The reagents are capable of interacting with their specific targets while attached to the substrate, for example via solid phase interactions, and by appropriate labeling of these targets, the sites of the interactions between the target and the specific reagents may be derived. Because the reagents are positionally defined, the sites of the interactions will define the specificity of each interaction.

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