Patents by Inventor Anthony D. Barone
Anthony D. Barone 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: 7282327Abstract: Compounds of the following structure: are useful as nucleic labeling compounds.Type: GrantFiled: August 15, 2003Date of Patent: October 16, 2007Assignee: Affymetrix, Inc.Inventors: Glenn H. McGall, Anthony D. Barone
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Patent number: 7179905Abstract: 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: GrantFiled: June 2, 2003Date of Patent: February 20, 2007Assignee: Affymetrix, Inc.Inventors: Glenn McGall, Anthony D. Barone
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Patent number: 7060443Abstract: Methods for testing oligonucleotide arrays are disclosed including methods for testing the efficiency of nucleotide coupling; methods for testing amounts of deprotected oligonucleotides; methods for determining amounts of depurinated oligonucleotides; and methods of detecting the presence of cleavable structural features, such as double-stranded nucleic acids.Type: GrantFiled: June 10, 2003Date of Patent: June 13, 2006Assignee: Affymetrix, Inc.Inventors: Glenn McGall, Anthony D. Barone, Martin Diggelmann, David J. Lockhart, Ann Maria Caviani Pease, Mark Chee
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Patent number: 7026114Abstract: VLSIPS™ manufacturing processes are of increasing commercial importance. The present invention provides methods and compositions for monitoring the efficiency and quality of polymer synthesis in VLSIPS™ arrays. Methods for monitoring polymer synthesis in an array on a substrate are provided. Monoisomeric labels for the labeling of synthetic polymer arrays are provided. Methods and compositions for post-synthetically labeling polymers in polymer arrays are also provided.Type: GrantFiled: November 30, 1995Date of Patent: April 11, 2006Assignee: Affymetrix, Inc.Inventors: Anthony D. Barone, Glenn H. Mc Gall, Evelyn Chai, Nam Quoc Ngo
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Patent number: 6965020Abstract: 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: GrantFiled: September 11, 2001Date of Patent: November 15, 2005Assignee: Affymetrix, Inc.Inventors: Glenn McGall, Anthony D. Barone
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Patent number: 6864059Abstract: Nucleic acid labeling compounds including the following structure are disclosed: wherein A is a triphosphate group with apporpriate counterions, said counterions selected from the group consisting of H+, Na+, Li+, K+, and NH4+; X is O; Y is OH; Z is OH; L is selected from the group consisting of —CH?CH—C(O)—NH—CH2—CH2—NH—C(O)— and —CH2—CH2—C(O)—NH—CH2—CH2—NH—C(O); M is —(CH2)45—NH—, n is 1 and Q is biotin having the structure: 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: GrantFiled: December 5, 2002Date of Patent: March 8, 2005Assignee: Affymetrix, Inc.Inventors: Glenn McGall, Anthony D. Barone
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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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Patent number: 6844433Abstract: 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: GrantFiled: June 2, 2003Date of Patent: January 18, 2005Assignee: Affymetrix, Inc.Inventors: Glenn McGall, Anthony D. Barone
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Publication number: 20040210045Abstract: 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: May 11, 2004Publication date: October 21, 2004Inventors: Glenn McGall, Anthony D. Barone
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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: 20040076987Abstract: Methods for testing oligonucleotide arrays are disclosed including methods for testing the efficiency of nucleotide coupling; methods for testing amounts of deprotected oligonucleotides; methods for determining amounts of depurinated oligonucleotides; and methods of detecting the presence of cleavable structural features, such as double-stranded nucleic acidsType: ApplicationFiled: June 10, 2003Publication date: April 22, 2004Applicant: Affymetrix, Inc.Inventors: Glenn McGall, Anthony D. Barone, Martin Diggelmann, David J. Lockhart, Ann Maria Caviani Pease, Mark Chee
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Publication number: 20040002595Abstract: 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: June 2, 2003Publication date: January 1, 2004Applicant: Affymetrix, Inc.Inventors: Glenn McGall, Anthony D. Barone
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Publication number: 20030232979Abstract: 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: June 2, 2003Publication date: December 18, 2003Inventors: Glenn McGall, Anthony D. Barone
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Publication number: 20030180757Abstract: 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: December 5, 2002Publication date: September 25, 2003Applicant: Affymetrix, INC.Inventors: Glenn McGall, Anthony D. Barone
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Patent number: 6596856Abstract: 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: GrantFiled: February 9, 2001Date of Patent: July 22, 2003Assignee: Affymetrix, Inc.Inventors: Glenn McGall, Anthony D. Barone
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Patent number: 6576425Abstract: Methods for testing oligonucleotide arrays are disclosed including methods for testing the efficiency of nucleotide coupling; methods for testing amounts of deprotected oligonucleotides; methods for determining amounts of depurinated oligonucleotides; and methods of detecting the presence of cleavable structural features, such as double-stranded nucleic acids.Type: GrantFiled: February 8, 2001Date of Patent: June 10, 2003Assignee: Affymetrix, Inc.Inventors: Glenn McGall, Anthony D. Barone, Martin Diggelmann, David J. Lockhart, Ann Maria Caviani Pease, Mark Chee
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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: 20020182625Abstract: Nucleic acid labeling compounds are disclosed. The 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: March 12, 2002Publication date: December 5, 2002Inventors: Glenn McGall, Anthony D. Barone