Patents by Inventor Glenn H. McGall
Glenn H. McGall has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 6881836Abstract: Novel compounds are provided which are useful 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 which can be removed by photolysis to unmask a reactive group. The protecting group has the general formula Ar—C(R1)(R2)—O—C(O)— wherein: Ar is an optionally substituted fused polycyclic aryl or heteroaromatic group or a vinylogous derivative thereof; R1 and R2 are independently H, optionally substituted alkyl, alkenyl or alkynyl, optionally substituted aryl or optionally substituted heteroaromatic, or a vinylogous derivative of the foregoing; and X is a leaving group, a chemical fragment linked to Ar—C(R1)(R2)—O—C(O)— via a heteroatom, or a solid support; provided that when Ar is 1-pyrenyl and R1 and R2 are H, X is not linked to Ar—C(R1)(R2)—O—C(O)— via a nitrogen atom.Type: GrantFiled: January 22, 2003Date of Patent: April 19, 2005Assignee: Affymetrix, IncInventors: Glenn H. McGall, Ngo Q. Nam, Richard P. Rava
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Patent number: 6858711Abstract: The present invention provides a simplified method for identifying differences in nucleic acid abundances (e.g., expression levels) between two or more samples. The methods involve providing an array containing a large number (e.g. greater than 1,000) of arbitrarily selected different oligonucleotide probes where the sequence and location of each different probe is known. Nucleic acid samples (e.g. mRNA) from two or more samples are hybridized to the probe arrays and the pattern of hybridization is detected. Differences in the hybridization patterns between the samples indicates differences in expression of various genes between those samples. This invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves providing a nucleic acid, providing a labeled oligonucleotide and then enzymatically ligating the oligonucleotide to the nucleic acid. Thus, for example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase.Type: GrantFiled: June 13, 2001Date of Patent: February 22, 2005Assignee: Affymetrix, Inc.Inventors: Glenn H. McGall, Anthony D. Barone
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Publication number: 20040248162Abstract: Methods are provided for fabricating an array of polymers wherein the polymers may be released from the surface of the array by activation of a cleavable moiety. Also provided are arrays of polymers having of polymers wherein the polymers can be released from the surface of the array by activation of a releasable group. Arrays of nucleic acids wherein a nucleic acid probe may be released from the array by activation of a releasable groups and methods for fabrication of such arrays are also disclosed.Type: ApplicationFiled: March 2, 2004Publication date: December 9, 2004Applicant: Affymetrix, INC.Inventors: Andrea Cuppoletti, Glenn H. McGall
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Publication number: 20040203056Abstract: Radiation-activated catalysts (RACs), autocatalytic reactions, and protective groups are employed to achieve a. highly sensitive, high resolution, radiation directed combinatorial synthesis of pattern arrays of diverse polymers. When irradiated, RACs produce catalysts that can react with enhancers, such as those involved in autocatalytic reactions. The autocatalytic reactions produce at least one product that removes protecting groups from synthesis intermediates. This invention has a wide variety of applications and is particularly useful for the solid phase combinatorial synthesis of polymers.Type: ApplicationFiled: May 7, 2004Publication date: October 14, 2004Applicant: Affymetrix, Inc.Inventors: Jody E. Beecher, Martin J. Goldberg, Glenn H. McGall
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Publication number: 20040185473Abstract: Methods are provided for fabricating an array of polymers wherein the polymers may be released from the surface of the array by activation of a releasable group. Also provided are methods for fabricating an array of polymers wherein the polymers can be released from the surface of the array by activation of a releasable group. Arrays of nucleic acids wherein a nucleic acid probe may be released from the array by activation of a releasable groups and methods for fabrication of such arrays are also disclosed.Type: ApplicationFiled: December 16, 2003Publication date: September 23, 2004Applicant: Affymetrix, INC.Inventors: Andrea Cuppoletti, Glenn H. McGall
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Publication number: 20040180368Abstract: Methods are provided for fabricating high density oligonucleotide arrays with activators. According to the disclosed methods for preparing high density oligonucleotide arrays on a solid support, the following steps are provided: a) providing a solid support having a surface comprising functional groups; b) attaching an activated nucleotide to a functional group in the presence of an activator; c) repeating the step of attaching an activated nucleotide to form an oligonucleotide array having at least 100 different oligonucleotides/cm2.Type: ApplicationFiled: December 18, 2003Publication date: September 16, 2004Applicant: Affymetrix, INC.Inventor: Glenn H. McGall
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Patent number: 6770436Abstract: Radiation-activated catalysts (RACs), autocatalytic reactions, and protective groups are employed to achieve a highly sensitive, high resolution, radiation directed combinatorial synthesis of pattern arrays of diverse polymers. When irradiated, RACs produce catalysts that can react with enhancers, such as those involved in autocatalytic reactions. The autocatalytic reactions produce at least one product that removes protecting groups from synthesis intermediates. This invention has a wide variety of applications and is particularly useful for the solid phase combinatorial synthesis of polymers.Type: GrantFiled: May 25, 2000Date of Patent: August 3, 2004Assignee: Affymetrix, Inc.Inventors: Jody E. Beecher, Martin J. Goldberg, Glenn H. McGall
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Publication number: 20040106728Abstract: New compounds, compositions and methods which find application in solid phase synthesis including the preparation of high-density arrays of diverse polymer sequences such as diverse peptides and oligonucleotides as well as in preparation of arrays of small ligand molecules. The compounds of the present invention are those which are typically referred to as linking groups, linkers or spacers and include unsymmetrical disulfide linking groups, and 1,3-diol derivatives capable of providing a triggered release of an attached compound from a solid support under mild conditions. Additional new compounds are labels which can be incorporated into either the 3′ or 5′ terminus of a DNA oligomer.Type: ApplicationFiled: July 14, 2003Publication date: June 3, 2004Applicant: Affymetrix, Inc.Inventors: Glenn H. McGall, Anthony D. Barone, Martin Diggelmann
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Publication number: 20040101892Abstract: Nucleic acid labeling compounds containing heterocyclic derivatives are disclosed. The heterocyclic derivative containing compounds are synthesized by condensing a heterocyclic derivative with a cyclic group (e.g. a ribofuranose derivative). The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.Type: ApplicationFiled: August 15, 2003Publication date: May 27, 2004Applicant: Affymetrix, INC.Inventors: Glenn H. McGall, Anthony D. Barone
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Publication number: 20040086914Abstract: In one aspect of the invention, a method is provided for end-labeling RNA (total RNA, mRNA, cRNA or fragmented RNA). In one embodiment, T4 RNA ligase is used to attach a 3′-biotinylated AMP or CMP donor to an RNA acceptor molecule. In another embodiment, a pyrophosphate molecule 3′-AppN-3′-linker-biotin is used as donor molecule.Type: ApplicationFiled: July 11, 2003Publication date: May 6, 2004Applicant: Affymetrix, INC.Inventors: Kyle B. Cole, Vivi Truong, Glenn H. McGall, Anthony D. Barone
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Publication number: 20030235824Abstract: The present invention provides an array of polymers and methods of forming arrays of polymers by providing a substrate having a first layer including one or more dielectric coatings on a solid support and a second layer including a plurality of polymers disposed on the first layer. The invention also provides methods for forming an array of polymers on a substrate using light-directed synthesis by providing a substrate having a first layer including one or more dielectric coatings on a solid support; derivatizing the first layer by contacting the first layer with a silanation reagent, and a second layer disposed on said first layer wherein the second layer includes functional groups protected with a photolabile protecting group.Type: ApplicationFiled: June 20, 2002Publication date: December 25, 2003Applicant: Affymetrix, INC.Inventors: Mark Trulson, Glenn H. McGall, Bei-Shen Sywe, Lisa T. Kajisa, Dana Truong
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Publication number: 20030194715Abstract: In one aspect of the invention, photoactivatable silane compounds and methods for their synthesis and use are provided. In one embodiment, the photoactivatable silane compounds synthesized are represented by a formula: PG-LS—SN, wherein PG is a photoactivatable group, LS is a linkage and spacer group, and SN is a silane group. The silanes allow the photoactivatable silane compounds to be covalently bound to the surface of a substrate such as silica. The photoactivatable group forms a hydrophobic layer that can be photochemically cross-linked with a layer of hydrophilic functional polymers. In another embodiment, a method is disclosed to synthesize a substrate of hydrophobic layers and hydrophilic functional polymer layers thereafter onto glass surfaces. An array of biopolymers such as nucleic acids and peptides may then be covalently attached to the substrate using photolithography and biopolymer synthesis.Type: ApplicationFiled: July 9, 2002Publication date: October 16, 2003Applicant: Affymetrix, INC.Inventors: Handong Li, Glenn H. McGall
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Publication number: 20030144499Abstract: Novel compounds are provided which are useful 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 which can be removed by photolysis to unmask a reactive group.Type: ApplicationFiled: January 22, 2003Publication date: July 31, 2003Applicant: Affymetrix, Inc.Inventors: Glenn H. McGall, Ngo Q. Nam, Richard P. Rava
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Patent number: 6566515Abstract: Novel compounds are provided which are useful 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 which can be removed by photolysis to unmask a reactive group. The protecting group has the general formula Ar—C(R1)(R2)—O—C(O)— wherein: Ar is an optionally substituted fused polycyclic aryl or heteroaromatic group or a vinylogous derivative thereof; R1 and R2 are independently H, optionally substituted alkyl, alkenyl or alkynyl, optionally substituted aryl or optionally substituted heteroaromatic, or a vinylogous derivative of the foregoing; and X is a leaving group, a chemical fragment linked to Ar—C(R1)(R2)—O—C(O)— via a heteroatom, or a solid support; provided that when Ar is 1-pyrenyl and R1 and R2 are H, X is not linked to Ar—C(R1)(R2)—O—C(O)— via a nitrogen atom.Type: GrantFiled: March 14, 2000Date of Patent: May 20, 2003Assignee: Affymetrix, Inc.Inventors: Glenn H. McGall, Ngo Q. Nam, Richard P. Rava
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Publication number: 20030064364Abstract: The present invention provides a simplified method for identifying differences in nucleic acid abundances (e.g., expression levels) between two or more samples. The methods involve providing an array containing a large number (e.g. greater than 1,000) of arbitrarily selected different oligonucleotide probes where the sequence and location of each different probe is known. Nucleic acid samples (e.g. mRNA) from two or more samples are hybridized to the probe arrays and the pattern of hybridization is detected. Differences in the hybridization patterns between the samples indicates differences in expression of various genes between those samples. This invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves providing a nucleic acid, providing a labeled oligonucleotide and then enzymatically ligating the oligonucleotide to the nucleic acid. Thus, for example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase.Type: ApplicationFiled: April 11, 2002Publication date: April 3, 2003Inventors: David J. Lockhart, Mark Chee, Kevin Gunderson, Chaoqiang Lai, Lisa Wodicka, Maureen T. Cronin, Danny H. Lee, Huu M. Tran, Hajime Matsuzaki, Glenn H. McGall, Anthony D. Barone
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Publication number: 20030040618Abstract: Novel compounds are provided which are useful 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 which can be removed by photolysis to unmask a reactive group. The protecting group has the general formula Y, wherein: Y is a chemical structure as shown in FIG. 1. Also provided is a method of forming, from component molecules, a plurality of compounds on a support, each compound occupying a separate predefined region of the support, using the protected compounds described above.Type: ApplicationFiled: September 12, 2001Publication date: February 27, 2003Applicant: Affymetrix, Inc.Inventors: Anthony Barone, Glenn H. McGall
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Publication number: 20030017451Abstract: Methods are provided for analyzing a large number of RNAs. In one embodiment of the invention, RNAs are hybridized with a nucleic acid probe (primer) array. The primers are extended using reverse transcriptase with the RNAs as templated. The resulting primer extension products are detected. The methods are useful for gene expression monitoring, sequence variation detection and transcriptional mapping/annotation.Type: ApplicationFiled: December 21, 2000Publication date: January 23, 2003Inventors: Hui Wang, Steven Smeekens, Glenn H. McGall, Yanxiang Cao
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Publication number: 20010018514Abstract: Nucleic acid labeling compounds containing heterocyclic derivatives are disclosed. The heterocyclic derivative containing compounds are synthesized by condensing a heterocyclic derivative with a cyclic group (e.g. a ribofuranose derivative). The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.Type: ApplicationFiled: July 31, 1998Publication date: August 30, 2001Inventors: GLENN H. MCGALL, ANTHONY D. BARONE
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Patent number: 6150147Abstract: The present invention provides modified methods and apparatus for the preparation of arrays of material wherein each array includes a preselected collection of polymers, small molecules or inorganic materials associated with a surface of a substrate. The methods of the invention provide for modifications to general apparatus, flow cell geometries and solutions used in array fabrication.Type: GrantFiled: February 6, 1998Date of Patent: November 21, 2000Assignee: Affymetrix, Inc.Inventors: Martin J. Goldberg, Mel Yamamoto, Glenn H. McGall, Steven J. Woodman, Eric Spence, Lisa T. Kajisa
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Patent number: 6147205Abstract: Novel compounds are provided which are useful 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 which can be removed by photolysis to unmask a reactive group. The protecting group has the general formula Ar--C(R.sub.1)(R.sub.2)--O--C(O)-- wherein:Ar is an optionally substituted fused polycyclic aryl or heteroaromatic group or a vinylogous derivative thereof;R.sub.1 and R.sub.2 are independently H, optionally substituted alkyl, alkenyl or alkynyl, optionally substituted aryl or optionally substituted heteroaromatic, or a vinylogous derivative of the foregoing; andX is a leaving group, a chemical fragment linked to Ar--C(R.sub.1)(R.sub.2)--O--C(O)-- via a heteroatom, or a solid support; provided that when Ar is 1-pyrenyl and R.sub.1 and R.sub.2 are H, X is not linked to Ar--C(R.sub.1)(R.sub.2)--O--C(O)-- via a nitrogen atom.Type: GrantFiled: March 5, 1997Date of Patent: November 14, 2000Assignee: Affymetrix, Inc.Inventors: Glenn H. McGall, Ngo Q. Nam, Richard P. Rava