Affymetrix received US Patent No. 6,600,996, “Computer-aided techniques for analyzing biological sequences.” The patent covers computer-aided techniques for ana-lyzing biological sequences such as nucleic acids. The computer system may analyze hybridization intensities indicating hybridization affinity between nucleic acid probes and a sample nucleic acid sequence in order to call bases in the sample sequence. Multiple base calls may be combined to form a single base call. Addition-ally, the computer system may analyze hybridization intensities in order to monitor gene expression or the change in gene expression as compared to a baseline.
The company also received US Patent No. 6,600,031, “Methods of making nucleic acid or oligonucleotide arrays.” The patent covers a synthetic strategy for the creation of large-scale chemical diversity. Solid-phase chemistry, photolabile protecting groups, and photolithography are used to achieve light-directed spatially addressable parallel chemical synthesis. Binary masking techniques are utilized in and example. A reactor system, photoremovable protective groups, and improved data collection and handling techniques are described. A technique for screening linker molecules is also provided.
The University of Iowa Research Foundation received US Patent No. 6,599,703, “Iterative and regenerative DNA sequencing method.” The inventors say this method addresses the need for technology that can sequence thousands of distinct DNA samples in parallel. In the future, it will be possible to apply the invention to the sequencing of large portions of genomes for which there is no prior sequence information without cloning in vivo, according to the inventors. The invention includes a number of practical implementations of novel chip-based support arrays for carrying out the described protocols in an automated manner. This method sequences DNA in discrete intervals starting at one end of a double stranded DNA segment and is designed to overcome problems inherent in other sequencing methods, including the need for gel resolution of DNA fragments and the generation of artifacts caused by single-stranded DNA secondary structures. The invention can be used to create offset collections of DNA segments and sequence the segments in parallel to provide continuous sequence information over long intervals. This method is also suitable for automation and multiplex automation to sequence large sets of segments.
BASF of Ludwigshafen, Germany, received US Patent No. 6,599,755, “Method and device for applying small quantities of liquid.” The invention provides a method of depositing small amounts of liquid — on a range of 500 pl to 10 nl — on a substrate by using a pipette tip, which is connected to a flexible delivery line. Liquid is taken up by expanding the volume in the delivery line, and liquid is ejected by exposing the line to an impulse, provided by a hammer, that is transmitted to the liquid contained within it.
Sangamo BioScience of Richmond, Calif., received US Patent No. 6,599,692, “Functional genomics using zinc finger proteins.”