Patents by Inventor Pinar Iyidogan
Pinar Iyidogan 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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Publication number: 20240240162Abstract: Provided herein are engineered DNA polymerases comprising modifications improving accuracy and processivity of the polymerase including modifications in the Motif A region, optionally, along with additional modifications in the palm and/or exonuclease domains of the polymerase. Also provided are nucleic acids encoding the engineered DNA polymerases comprising modifications in motif A of the polymerase, optionally, with additional modifications. Methods, vectors, kits, and compositions comprising the nucleic acids and compositions, methods and kits comprising the engineered polymerases are also provided.Type: ApplicationFiled: November 21, 2023Publication date: July 18, 2024Applicant: Pacific Biosciences of California, Inc.Inventors: Pinar IYIDOGAN, Mariam IFTIKHAR, Bridget KIDD, Lewis CHURCHFIELD
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Patent number: 11976323Abstract: Provided are sequencing-by-binding methods of detecting cognate nucleotides using a crippled DNA polymerizing enzyme that possesses the ability to bind the next correct nucleotide downstream of a primer in a template-dependent fashion, but does not possess the activity needed to promote phosphodiester bond formation. Use of the crippled DNA polymerase permits interrogation of one nucleotide at a time, without incorporation of any nucleotide. Labeled nucleotides, such as fluorescently labeled nucleotides, can be used in conjunction with the crippled DNA polymerase to establish cognate nucleotide identity in a rapid manner.Type: GrantFiled: January 7, 2020Date of Patent: May 7, 2024Assignee: PACIFIC BIOSCIENCES OF CALIFORNIA, INC.Inventors: Kandaswamy Vijayan, Pinar Iyidogan
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Patent number: 11913038Abstract: Provided are nucleic acids encoding engineered polymerases comprising at least one modification in a motif A and/or at least one modification in a motif B of the polymerase and engineered polymerases encoded by the nucleic acids. Also provided are engineered DNA polymerases comprising a variant of SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:3, the variant being at least 80% identical to SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3 and comprising an amino acid substitution at one or more positions selected from the group consisting of L408, Y409, P410, R484, A/L485, and I486. Methods, vectors, kits, and compositions comprising the nucleic acids and compositions, methods and kits comprising the engineered polymerases are also provided.Type: GrantFiled: December 29, 2021Date of Patent: February 27, 2024Assignee: PACIFIC BIOSCIENCES OF CALIFORNIA, INC.Inventor: Pinar Iyidogan
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Patent number: 11873516Abstract: Provided herein are engineered DNA polymerases comprising modifications improving accuracy and processivity of the polymerase including modifications in the Motif A region, optionally, along with additional modifications in the palm and/or exonuclease domains of the polymerase. Also provided are nucleic acids encoding the engineered DNA polymerases comprising modifications in motif A of the polymerase, optionally, with additional modifications. Methods, vectors, kits, and compositions comprising the nucleic acids and compositions, methods and kits comprising the engineered polymerases are also provided.Type: GrantFiled: February 8, 2022Date of Patent: January 16, 2024Assignee: PACIFIC BIOSCIENCES OF CALIFORNIA, INC.Inventors: Pinar Iyidogan, Mariam Iftikhar, Bridget Kidd, Lewis Churchfield
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Publication number: 20240011086Abstract: A sensor having a first electrode and a second electrode operably connected by a conduction channel, wherein a polymerase, primed template nucleic acid and nucleotide form a stabilized ternary complex that is immobilized in or on the conduction channel, whereby association and dissociation of the ternary complex is detected due to changes in electrical properties of the sensor. Identification of the nucleotide type that participates in the complex indicates the identity of the next template base in the template. Repeated cycles of extending the primer and detecting stabilized ternary complexes can allow determination of the sequence of nucleotides for the template.Type: ApplicationFiled: September 10, 2019Publication date: January 11, 2024Applicant: OMNIOME, INC.Inventors: Maxim ABASHIN, Pinar IYIDOGAN, John T. MURPHY, Alex NEMIROSKI, Min-Jui Richard SHEN, Michele Elizabeth WISNIEWSKI
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Publication number: 20220290216Abstract: Methods, compositions, kits and apparatuses that include a fluid, the fluid containing a ternary complex and Li+, wherein the ternary complex includes a primed template nucleic acid, a polymerase, and a nucleotide cognate for the next correct base for the primed template nucleic acid molecule. As an alternative or addition to Li+, the fluid can contain betaine or a metal ion that inhibits polymerase catalysis such as Ca2+. In addition to Li+, the fluid can contain polyethylenimine (PEI) with or without betaine.Type: ApplicationFiled: January 4, 2022Publication date: September 15, 2022Applicant: Omniome, Inc.Inventors: Morassa Mohseni MIDDLETON, Mark C. WALLEN, Pinar IYIDOGAN, Michael James SCHMIDT, Brittany A. ROHRMAN, Ying Lin LIU, Fabian BLOCK, Arnold OLIPHANT
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Publication number: 20220235336Abstract: Provided are nucleic acids encoding engineered polymerases comprising at least one modification in a motif A and/or at least one modification in a motif B of the polymerase and engineered polymerases encoded by the nucleic acids. Also provided are engineered DNA polymerases comprising a variant of SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:3, the variant being at least 80% identical to SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3 and comprising an amino acid substitution at one or more positions selected from the group consisting of L408, Y409, P410, R484, A/L485, and I486. Methods, vectors, kits, and compositions comprising the nucleic acids and compositions, methods and kits comprising the engineered polymerases are also provided.Type: ApplicationFiled: December 29, 2021Publication date: July 28, 2022Applicant: OMNIOME, INC.Inventor: Pinar IYIDOGAN
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Publication number: 20220235338Abstract: Provided herein are engineered DNA polymerases comprising modifications improving accuracy and processivity of the polymerase including modifications in the Motif A region, optionally, along with additional modifications in the palm and/or exonuclease domains of the polymerase. Also provided are nucleic acids encoding the engineered DNA polymerases comprising modifications in motif A of the polymerase, optionally, with additional modifications. Methods, vectors, kits, and compositions comprising the nucleic acids and compositions, methods and kits comprising the engineered polymerases are also provided.Type: ApplicationFiled: February 8, 2022Publication date: July 28, 2022Applicant: Omniome, LLCInventors: Pinar IYIDOGAN, Mariam IFTIKHAR, Bridget KIDD, Lewis CHURCHFIELD
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Patent number: 11242557Abstract: Methods, compositions, kits and apparatuses that include a fluid, the fluid containing a ternary complex and Li+, wherein the ternary complex includes a primed template nucleic acid, a polymerase, and a nucleotide cognate for the next correct base for the primed template nucleic acid molecule. As an alternative or addition to Li+, the fluid can contain betaine or a metal ion that inhibits polymerase catalysis such as Ca2+. In addition to Li+, the fluid can contain polyethylenimine (PEI) with or without betaine.Type: GrantFiled: July 19, 2019Date of Patent: February 8, 2022Assignee: OMNIOME, INC.Inventors: Morassa Mohseni Middleton, Mark C. Wallen, Pinar Iyidogan, Michael James Schmidt, Brittany A. Rohrman, Ying Lin Liu, Fabian Block, Arnold Oliphant
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Patent number: 11242512Abstract: Provided are nucleic acids encoding engineered polymerases comprising at least one modification in a motif A and/or at least one modification in a motif B of the polymerase and engineered polymerases encoded by the nucleic acids. Also provided are engineered DNA polymerases comprising a variant of SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:3, the variant being at least 80% identical to SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3 and comprising an amino acid substitution at one or more positions selected from the group consisting of L408, Y409, P410, R484, A/L485, and I486. Methods, vectors, kits, and compositions comprising the nucleic acids and compositions, methods and kits comprising the engineered polymerases are also provided.Type: GrantFiled: September 11, 2019Date of Patent: February 8, 2022Assignee: OMNIOME, INC.Inventor: Pinar Iyidogan
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Patent number: 11203779Abstract: Provided are methods and systems for reducing the time needed for sequencing nucleic acids. The approach relies on detecting formation of nucleotide-specific ternary complexes comprising a polymerase (e.g., a DNA polymerizing enzyme), a primed template nucleic acid molecule, and a nucleotide complementary to the templated base of the primed template nucleic acid. The methods and systems facilitate determination of the next correct nucleotide, as well as the subsequent next correct nucleotide from a cycle of examining four different nucleotides without requiring chemical incorporation of any nucleotide into the primer.Type: GrantFiled: August 14, 2019Date of Patent: December 21, 2021Assignee: OMNIONIE, INC.Inventors: Pinar Iyidogan, Kandaswamy Vijayan
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Patent number: 11203778Abstract: Provided are methods and systems for detecting formation of nucleotide-specific ternary complexes comprising a DNA polymerase, a nucleic acid, and a nucleotide complementary to the templated base of the primed template nucleic acid. The methods and systems facilitate determination of the next correct nucleotide without requiring chemical incorporation of the nucleotide into the primer. These results can even be achieved in procedures employing unlabeled, native nucleotides.Type: GrantFiled: March 19, 2020Date of Patent: December 21, 2021Assignee: OMNIOME, INC.Inventors: Pinar Iyidogan, Kandaswamy Vijayan
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Publication number: 20210139867Abstract: Provided herein are engineered DNA polymerases comprising modifications improving accuracy and processivity of the polymerase including modifications in the Motif A region, optionally, along with additional modifications in the palm and/or exonuclease domains of the polymerase. Also provided are nucleic acids encoding the engineered DNA polymerases comprising modifications in motif A of the polymerase, optionally, with additional modifications. Methods, vectors, kits, and compositions comprising the nucleic acids and compositions, methods and kits comprising the engineered polymerases are also provided.Type: ApplicationFiled: November 6, 2020Publication date: May 13, 2021Applicant: Omniome, Inc.Inventors: Pinar IYIDOGAN, Mariam IFTIKHAR, Bridget KIDD, Lewis CHURCHFIELD
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Patent number: 10731141Abstract: Provided are nucleic acids encoding engineered polymerases comprising at least one modification in a motif A and/or at least one modification in a motif B of the polymerase and engineered polymerases encoded by the nucleic acids. Also provided are engineered DNA polymerases comprising a variant of SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:3, the variant being at least 80% identical to SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3 and comprising an amino acid substitution at one or more positions selected from the group consisting of L408, Y409, P410, R484, A/L485, and I486. Methods, vectors, kits, and compositions comprising the nucleic acids and compositions, methods and kits comprising the engineered polymerases are also provided.Type: GrantFiled: September 11, 2019Date of Patent: August 4, 2020Assignee: OMNIOME, INC.Inventor: Pinar Iyidogan
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Publication number: 20200224251Abstract: Provided are methods and systems for detecting formation of nucleotide-specific ternary complexes comprising a DNA polymerase, a nucleic acid, and a nucleotide complementary to the templated base of the primed template nucleic acid. The methods and systems facilitate determination of the next correct nucleotide without requiring chemical incorporation of the nucleotide into the primer. These results can even be achieved in procedures employing unlabeled, native nucleotides.Type: ApplicationFiled: March 19, 2020Publication date: July 16, 2020Applicant: Omniome, Inc.Inventors: Pinar IYIDOGAN, Kandaswamy VIJAYAN
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Publication number: 20200199668Abstract: Provided are sequencing-by-binding methods of detecting cognate nucleotides using a crippled DNA polymerizing enzyme that possesses the ability to bind the next correct nucleotide downstream of a primer in a template-dependent fashion, but does not possess the activity needed to promote phosphodiester bond formation. Use of the crippled DNA polymerase permits interrogation of one nucleotide at a time, without incorporation of any nucleotide. Labeled nucleotides, such as fluorescently labeled nucleotides, can be used in conjunction with the crippled DNA polymerase to establish cognate nucleotide identity in a rapid manner.Type: ApplicationFiled: January 7, 2020Publication date: June 25, 2020Applicant: Omniome, Inc.Inventors: Kandaswamy VIJAYAN, Pinar IYIDOGAN
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Publication number: 20200131486Abstract: Provided are engineered DNA polymerases exhibiting modified functionality, and polynucleotides encoding same. Modified features include: (1) reduced catalytic activity in the presence of magnesium ions and/or (2) reduced affinity for primed template nucleic acid molecules in the absence of cognate nucleotide, and an ability to discriminate between cognate and non-cognate nucleotides under low salt conditions. Sequencing By Binding™ procedures employing the engineered polymerases have certain advantages. The engineered polymerases can have other uses as well.Type: ApplicationFiled: January 9, 2020Publication date: April 30, 2020Applicant: Omniome, inc.Inventors: Pinar IYIDOGAN, Mark C. WALLEN, Ying L. LIU, Kandaswamy VIJAYAN
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Patent number: 10633692Abstract: Provided are methods and systems for detecting formation of nucleotide-specific ternary complexes comprising a DNA polymerase, a nucleic acid, and a nucleotide complementary to the templated base of the primed template nucleic acid. The methods and systems facilitate determination of the next correct nucleotide without requiring chemical incorporation of the nucleotide into the primer. These results can even be achieved in procedures employing unlabeled, native nucleotides.Type: GrantFiled: April 2, 2019Date of Patent: April 28, 2020Assignee: OMNIOME, INC.Inventors: Pinar Iyidogan, Kandaswamy Vijayan
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Patent number: 10597643Abstract: Provided are engineered DNA polymerases exhibiting modified functionality, and polynucleotides encoding same. Modified features include: (1) reduced catalytic activity in the presence of magnesium ions and/or (2) reduced affinity for primed template nucleic acid molecules in the absence of cognate nucleotide, and an ability to discriminate between cognate and non-cognate nucleotides under low salt conditions. Sequencing By Binding™ procedures employing the engineered polymerases have certain advantages. The engineered polymerases can have other uses as well.Type: GrantFiled: January 9, 2018Date of Patent: March 24, 2020Assignee: OMNIOME, INC.Inventors: Pinar Iyidogan, Mark C. Wallen, Ying L. Liu, Kandaswamy Vijayan
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Publication number: 20200087638Abstract: Provided are nucleic acids encoding engineered polymerases comprising at least one modification in a motif A and/or at least one modification in a motif B of the polymerase and engineered polymerases encoded by the nucleic acids. Also provided are engineered DNA polymerases comprising a variant of SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:3, the variant being at least 80% identical to SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3 and comprising an amino acid substitution at one or more positions selected from the group consisting of L408, Y409, P410, R484, A/L485, and I486. Methods, vectors, kits, and compositions comprising the nucleic acids and compositions, methods and kits comprising the engineered polymerases are also provided.Type: ApplicationFiled: September 11, 2019Publication date: March 19, 2020Applicant: OMNIOME, INC.Inventor: Pinar IYIDOGAN