Affymetrix of Santa Clara, Calif., has received US Patent No. 6,965,020, "Nucleic acid labeling compounds." The patent claims nucleic acid labeling compounds that are capable of being enzymatically incorporated into a nucleic acid. The nucleic acids to which the compounds are attached maintain their ability to bind to a complementary nucleic acid sequence nucleic acid labeling. The patent describes these compounds and provides heterocyclic derivatives containing a detectable moiety. The patent also claims methods of making such heterocyclic derivatives and it describes methods of attaching the heterocyclic derivatives to a nucleic acid.
Affymetrix has also received US Patent No. 6,965,704, "System, method, and computer software product for grid alignment of multiple scanned images." The patent claims systems, methods, and computer program products for aligning multiple images of arrays of biological materials. One described method includes aligning a grid with a first image, generating grid alignment data based on the alignment of the grid with the first image, storing the grid alignment data in memory, retrieving the grid alignment data responsive to an indication to align a second image, and analyzing the second image based on the retrieved grid alignment data. In some implementations, the first image and second images are generated by scanning the same array of biological materials, the patent states. The array can be a spotted array, a synthesized array, or other type of parallel biological assay.
Bioarray Solutions of Warren, NJ, has received US Patent No. 6,964,747, "Production of dyed polymer microparticles." The patent describes a method where a dye is incorporated into polymer microparticles using a solvent system. The system comprises a first solvent in which the dye and the microparticle polymer are soluble, a second solvent in which the dye and the microparticle polymer are not or only weakly soluble, and a third solvent, in which the dye and the microparticle polymer are not or only weakly soluble. The formulation provides substantially complete partitioning of the dye to the microparticles and the method may be used to obtain dyed polymer microparticle formed of cross-linked or non-cross-linked polymers. Libraries are also claimed that contain two or more sets of microparticles of different dye loadings. Fluorescent core-shell microparticles are produced from a mixture of microparticle cores incorporating one or more fluorescent dyes, a polymerization mixture comprising at least one polymerizable shell monomer, at least one free radical polymerization initiator comprising a water-insoluble oxidizing agent, and at least one water-soluble reducing agent.
Packard Biosciences of Meriden, Conn., has received US Patent No. 6,964,847, "Derivative nucleic acids and uses thereof." The patent claims a method for multiplexed analysis of a plurality of target nucleic acid sequences in a sample. To accomplish this, a derivative nucleic acid for each target sequence analyzed must be present in the sample. The derivative nucleic acid is a nucleic acid which includes a capture tag sequence at one, or both, of its 3' and 5' termini, the patent states. The derivative sequence is produced only upon the hybridization of a probe or primer which includes the sequence tag as an internal fragment to the target sequence for which it is specific. The sequence tag is analyzed by its ability to bind to a capture probe bound to an insoluble substrate, a bead, or an ordered array of partially duplex capture probes. The presence of the derivative nucleic acid, and its characteristic terminal sequence tag, is diagnostic of the presence of a selected target sequence, the patent claims. The method can be used to evaluate, identify, or quantitate the presence of one, or preferably a plurality, of specific nucleic acid sequences, or the presence of specific sequence variations.
Yeda Research and Development Co. of Rehovot, Israel, has received US Patent No. 6,965,831, "Coupled two-way clustering analysis of data." The patent describes a coupled, two-way clustering approach to gene microarray data analysis, for identifying subsets of the genes and samples, in a way that when one of these items is used to cluster the other, stable and significant partitions emerge. The patent states that the method is suitable for gene microarray data, where the contributions of a variety of biological mechanisms to the gene expression levels are entangled in a large body of experimental data.