Patents by Inventor Niles A. Pierce
Niles A. Pierce 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: 8962582Abstract: The present application relates to the use of hybridization chain reaction (HCR) to form double stranded RNA polymers in the presence of a target, such as a nucleic acid associated with a disease or disorder. The RNA polymers are preferably able to activate the RNA-dependent kinase PKR. Activation of PKR via RNA-HCR can be used to treat a wide variety of diseases and disorders by specifically targeting diseased cells.Type: GrantFiled: June 7, 2011Date of Patent: February 24, 2015Assignee: California Institute of TechnologyInventors: Robert Dirks, Niles A. Pierce
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Publication number: 20150004615Abstract: The present subject matter relates to the use conditional hairpins, such as, but not limited to shRNAs. The conditional formation of these structures can allow for further events, such as gene silencing (in some embodiments).Type: ApplicationFiled: June 30, 2014Publication date: January 1, 2015Inventors: Niles A. Pierce, Lisa Hochrein
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Publication number: 20140107983Abstract: Described is a system and process for designing the equilibrium base-pairing properties of a test tube of interacting nucleic acid strands. A target test tube is specified as a set of desired ‘on-target’ complexes, each with a target secondary structure and target concentration, and a set of undesired ‘off-target’ complexes, each with vanishing target concentration. Sequence design is performed by optimizing the test tube ensemble defect, corresponding to the concentration of incorrectly paired nucleotides at equilibrium evaluated over the ensemble of the test tube.Type: ApplicationFiled: September 20, 2013Publication date: April 17, 2014Applicant: California Institute of TechnologyInventors: Brian R. Wolfe, Niles A. Pierce
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Patent number: 8658780Abstract: The present invention relates to the use of cross-linking probes to covalently bind probes to nucleic acid targets. In some embodiments, the probe comprises an initiator region that is able to bind to a first portion of a target nucleic acid, a probe region linked too the initiator region that is able to bind to a second region of the target nucleic acid and that comprises one or more cross-linkers, and a blocking region hybridized to the probe region.Type: GrantFiled: January 28, 2011Date of Patent: February 25, 2014Assignee: California Institute of TechnologyInventors: Niles A. Pierce, Jeffrey Robert Vieregg
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Publication number: 20130323838Abstract: The present application relates to methods and compositions for triggering RNAi. Triggered RNAi is highly versatile because the silencing targets are independent of the detection targets. In some embodiments, methods of silencing or modulating the expression of a target gene are provided. The methods generally comprise providing an initiator to a cell comprising a detection target and a silencing target gene, wherein the detection target is different from the silencing target gene, wherein binding of the detection target to the initiator initiates formation of an inactivator double-stranded RNA (inactivator dsRNA). The inactivator dsRNA can silence or modulate the expression of the silencing target gene.Type: ApplicationFiled: May 16, 2013Publication date: December 5, 2013Applicant: CALIFORNIA INSTITUTE OF TECHNOLOGYInventors: Niles A. Pierce, Peng Yin
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Publication number: 20130262071Abstract: Described herein are systems and processes for designing the sequence of one or more interacting nucleic acid strands intended to adopt a target secondary structure at equilibrium. The target secondary structure is decomposed into a binary tree and candidate mutations are evaluated on leaf nodes of the tree. During a process of leaf optimization, defect-weighted mutation sampling is used to select each candidate mutation position with a probability proportional to its contribution to an ensemble defect of the leaf. Subsequences of the tree are then merged, moving up the tree until a final nucleotide sequence of interest is determined that has the target secondary structure at equilibrium.Type: ApplicationFiled: February 28, 2013Publication date: October 3, 2013Applicant: CALIFORNIA INSTITUTE OF TECHNOLOGYInventors: NILES A. PIERCE, BRIAN R. WOLFE, JOSEPH ZADEH
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Patent number: 8507204Abstract: The present invention relates to the use of fluorescently labeled nucleic acid probes to identify and image analytes in a biological sample. In the preferred embodiments, a probe is provided that comprises a target region able to specifically bind an analyte of interest and an initiator region that is able to initiate polymerization of nucleic acid monomers. After contacting a sample with the probe, labeled monomers are provided that form a tethered polymer. Triggered probes and self-quenching monomers can be used to provide active background suppression.Type: GrantFiled: January 31, 2012Date of Patent: August 13, 2013Assignee: California Institute of TechnologyInventors: Niles A. Pierce, Robert Dirks, Scott E. Fraser
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Patent number: 8497364Abstract: The present application relates to methods and compositions for triggering RNAi. Triggered RNAi is highly versatile because the silencing targets are independent of the detection targets. In some embodiments, methods of silencing or modulating the expression of a target gene are provided. The methods generally comprise providing an initiator to a cell comprising a detection target and a silencing target gene, wherein the detection target is different from the silencing target gene, wherein binding of the detection target to the initiator initiates formation of an inactivator double-stranded RNA (inactivator dsRNA). The inactivator dsRNA can silence or modulate the expression of the silencing target gene.Type: GrantFiled: February 27, 2009Date of Patent: July 30, 2013Assignee: California Institute of TechnologyInventors: Niles A. Pierce, Peng Yin
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Patent number: 8478543Abstract: Described herein are systems and processes for designing the sequence of one or more interacting nucleic acid strands intended to adopt a target secondary structure at equilibrium. The target secondary structure is decomposed into a binary tree and candidate mutations are evaluated on leaf nodes of the tree. During a process of leaf optimization, defect-weighted mutation sampling is used to select each candidate mutation position with a probability proportional to its contribution to an ensemble defect of the leaf. Subsequences of the tree are then merged, moving up the tree until a final nucleotide sequence of interest is determined that has the target secondary structure at equilibrium.Type: GrantFiled: April 4, 2011Date of Patent: July 2, 2013Assignee: California Institute of TechnologyInventors: Niles A. Pierce, Brian R. Wolfe, Joseph Zadeh
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Patent number: 8318921Abstract: The present application relates to methods and compositions for triggering RNAi. Triggered RNAi is highly versatile because the silencing targets are independent of the detection targets. In some embodiments, a method of silencing a target gene is provided.Type: GrantFiled: February 29, 2008Date of Patent: November 27, 2012Assignee: California Institute of TechnologyInventors: Niles A. Pierce, Peng Yin
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Patent number: 8241854Abstract: The present application relates to methods and compositions for triggering RNAi. Triggered RNAi is highly versatile because the silencing targets are independent of the detection targets. In some embodiments, methods of silencing or modulating the expression of a marker gene are provided. The methods generally comprise providing an initiator to a cell comprising a detection target and a silencing target gene, wherein the detection target is different from the silencing target gene, wherein binding of the detection target to the initiator initiates formation of an inactivator double-stranded RNA (inactivator dsRNA). The inactivator dsRNA can silence the silencing target gene to modulate the expression of a marker gene.Type: GrantFiled: May 22, 2009Date of Patent: August 14, 2012Assignee: California Institute of TechnologyInventors: Peng Yin, Niles A. Pierce
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Publication number: 20120190835Abstract: The present invention relates to the use of fluorescently labeled nucleic acid probes to identify and image analytes in a biological sample. In the preferred embodiments, a probe is provided that comprises a target region able to specifically bind an analyte of interest and an initiator region that is able to initiate polymerization of nucleic acid monomers. After contacting a sample with the probe, labeled monomers are provided that form a tethered polymer. Triggered probes and self-quenching monomers can be used to provide active background suppression.Type: ApplicationFiled: January 31, 2012Publication date: July 26, 2012Applicant: CALIFORNIA INSTITUTE OF TECHNOLOGYInventors: Niles A. Pierce, Robert Dirks, Scott E. Fraser
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Patent number: 8124751Abstract: The present invention relates to the use of fluorescently labeled nucleic acid probes to identify and image analytes in a biological sample. In the preferred embodiments, a probe is provided that comprises a target region able to specifically bind an analyte of interest and an initiator region that is able to initiate polymerization of nucleic acid monomers. After contacting a sample with the probe, labeled monomers are provided that form a tethered polymer. Triggered probes and self-quenching monomers can be used to provide active background suppression.Type: GrantFiled: May 28, 2010Date of Patent: February 28, 2012Assignee: California Institute of TechnologyInventors: Niles A. Pierce, Robert Dirks, Scott E. Fraser
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Patent number: 8105778Abstract: The present invention relates to the use of nucleic acid probes to identify analytes in a sample. In the preferred embodiments, metastable nucleic acid monomers are provided that associate in the presence of an initiator nucleic acid. Upon exposure to the initiator, the monomers self-assemble in a hybridization chain reaction. The initiator nucleic acid may be, for example, a portion of an analyte to be detected or may be part of an initiation trigger such that it is made available in the presence of a target analyte.Type: GrantFiled: November 3, 2009Date of Patent: January 31, 2012Assignee: California Institute of TechnologyInventors: Robert Dirks, Niles A. Pierce
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Publication number: 20120022243Abstract: The present invention relates generally to programming of biomolecular self-assembly pathways and related methods and constructs for self-assembly of prescribed two and three-dimensional structures.Type: ApplicationFiled: July 19, 2011Publication date: January 26, 2012Inventors: Peng Yin, Niles A. Pierce
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Publication number: 20120021410Abstract: The present embodiments relate to engineering imaging probes based on “triggered molecular geometry.” Upon detection of a molecular signal, nucleic acid hairpin monomers assemble an imageable molecular shape with prescribed geometry. In some embodiments the prescribed shape can be imaged directly. In some embodiments, the prescribed shape can serve as a spatial organizer or amplification scheme for other imaging entities, such as fluorophore and fluorescent proteins.Type: ApplicationFiled: July 19, 2011Publication date: January 26, 2012Inventors: Peng Yin, Niles A. Pierce
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Publication number: 20110313030Abstract: The present application relates to the use of hybridization chain reaction (HCR) to form double stranded RNA polymers in the presence of a target, such as a nucleic acid associated with a disease or disorder. The RNA polymers are preferably able to activate the RNA-dependent kinase PKR. Activation of PKR via RNA-HCR can be used to treat a wide variety of diseases and disorders by specifically targeting diseased cells.Type: ApplicationFiled: June 7, 2011Publication date: December 22, 2011Applicant: California Institute of TechnologyInventors: Robert Dirks, Niles A. Pierce
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Publication number: 20110288148Abstract: The present invention relates to the use of cross-linking probes to covalently bind probes to nucleic acid targets. In some embodiments, the probe comprises an initiator region that is able to bind to a first portion of a target nucleic acid, a probe region linked too the initiator region that is able to bind to a second region of the target nucleic acid and that comprises one or more cross-linkers, and a blocking region hybridized to the probe region.Type: ApplicationFiled: January 28, 2011Publication date: November 24, 2011Inventors: Niles A. Pierce, Jeff Robert Vieregg
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Publication number: 20110288832Abstract: Described herein are systems and processes for designing the sequence of one or more interacting nucleic acid strands intended to adopt a target secondary structure at equilibrium. The target secondary structure is decomposed into a binary tree and candidate mutations are evaluated on leaf nodes of the tree. During a process of leaf optimization, defect-weighted mutation sampling is used to select each candidate mutation position with a probability proportional to its contribution to an ensemble defect of the leaf. Subsequences of the tree are then merged, moving up the tree until a final nucleotide sequence of interest is determined that has the target secondary structure at equilibrium.Type: ApplicationFiled: April 4, 2011Publication date: November 24, 2011Applicant: CALIFORNIA INSTITUTE OF TECHNOLOGYInventors: Niles A. Pierce, Brian R. Wolfe, Joseph Zadeh
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Patent number: 7960357Abstract: The present application relates to the use of hybridization chain reaction (HCR) to form double stranded RNA polymers in the presence of a target, such as a nucleic acid associated with a disease or disorder. The RNA polymers are preferably able to activate the RNA-dependent kinase PKR. Activation of PKR via RNA-HCR can be used to treat a wide variety of diseases and disorders by specifically targeting diseased cells.Type: GrantFiled: October 6, 2006Date of Patent: June 14, 2011Assignee: California Institute of TechnologyInventors: Robert Dirks, Niles A. Pierce