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Affymetrix, Merck, California Institute of Technology, Imaging Research, Able Signal


Affymetrix earned US Patent No. 6,566,515, “Photocleavable protecting groups and methods for their use.” The patent covers novel compounds for use as linking groups in chemical synthesis, preferably in the solid-phase synthesis of oligonucleotides and polypeptides. These compounds are generally photolabile and comprise protecting groups that may be removed by photolysis to unmask a reactive group. Also provided is a method of forming, from component molecules, a number of compounds on a support, each compound occupying a separate predefined region of the support, using the compounds described.

The company also received US Patent No. 6,566,495, “Very large scale immobilized polymer synthesis.” 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 one method. A reactor system, photoremovable protective groups, and improved data collection and handling techniques are also described as is a technique for screening linker molecules.

Affymetrix also earned US Patent No. 6,567,540, “Method and apparatus for providing a bioinformatics database.” The patent covers a database system for organizing information relating to polymer probe array chips including oligonucleotide array chips.


Merck received US Patent No. 6,565,813, “Virtual wells for use in high-throughput screening assays.” The patent covers a system of microtiter-like plates containing virtual wells formed by an arrangement of relatively hydrophilic domains within relatively hydrophobic fields. Assay mixtures are confined to the hydrophilic domains of the virtual wells by the edges of the hydrophobic fields. The use of virtual wells allows one to perform homogeneous and capture-and-wash high throughput screening assays with assay mixtures having volumes on the order of about 100 nanoliters to 10 microliters. Virtual wells also provide a means of easily moving fluids, which is particularly useful for simultaneous additions needed for kinetic studies and flash detection and washing. Methods for controlling evaporation during the dispensing of reagents as well as during incubation are also described. The invention also provides an inexpensive, disposable device for transferring small volumes of an entire array of compounds from a first microtiter-like plate to a second microtiter-like plate, preserving the spatial arrangement of the compounds. Methods of manufacturing and using the device are included.

The California Institute of Technology received US Patent No. 6,555,692, “Preparation and use of bifunc-tional molecules having DNA sequence binding specificity.” The patent covers novel small molecule polyamides that specifically bind with subnanomolar affinity to a predetermined site. The compounds that target the minor groove of B-form double-helical DNA offer a general approach for the control of gene-expression. Simple rules are disclosed that provide for rational control of the DNA-binding sequence specificity of synthetic polyamides containing N-methylpyrrole and N-methylimidazole amino acids. A series of molecular templates for polyamide design are disclosed that provide for small molecules that recognize predetermined DNA sequences with affinities and specificities compar-able to sequence-specific DNA-binding proteins. The pyrrole-imidazole polyamides described represent a class of designed small molecules that can bind any predetermined sequence of double helical DNA.

Imaging Research of St. Catharines, Ontario, Canada, received US Patent No. 6,567,750, “Process for evaluating chemical and biological assays.” The patent covers an analytical process for discriminating data acquired from samples with overlapping distributions, and for im-proving and assessing the statistical validity of hybridization signal in arrays of assays. The process includes a method of convolving data into two or more discrete probability density functions representing signal and non-signal, discrete fluors, or other convolved independent variables. The system uses the probability density functions to assign hybridization signals, objectively, to one of the modeled distributions. Subsequent processes assess variability inherent to the arrays, and use this assessed variation to establish reliability scores and confidence limits for complete hybridization arrays, and for discrete hybridization assays within arrays.

Able Signal of Madison, Wisc., received US Patent No. 6,567,163, “Microarray detector and synthesizer.” The patent covers a system of spatial light modulators for use in the reading and synthesis of microarrays using micromirror systems for synthesizing and acquiring data from nucleic acid microarrays, and systems for collecting, processing, and analyzing data obtained from a microarray.


The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.