Patents by Inventor Peter Crisalli
Peter Crisalli 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: 20240150824Abstract: The present disclosure relates to tagged nucleoside-5?-oligophosphates having a positively charged polymer tag structure and components thereof. Such nucleoside-5?-oligophosphates are useful, for example, in nanopore-based sequencing-by-synthesis applications. Also disclosed herein are nanopore constructs engineered to have additional negatively-charged moieties in the channel of the nanopore. Such nanopores can be useful, for example, for providing a repellant force against template and/or primer nucleic acids inserting into the pore during a nucleic sequence-by-synthesis process. The tagged nucleoside-5?-oligophosphates and nanopores disclosed herein can be used together to provide nanopore-based nucleic acid sequencing-by-synthesis systems and processes having reduced background tag levels and improved throughput.Type: ApplicationFiled: August 9, 2021Publication date: May 9, 2024Inventors: Aruna Ayer, Frank Bergmann, Peter Crisalli, Lars Hillringhaus, Omid Khakshoor, Hannes Kuchelmeister, Rongxin Nie, Marshall W. Porter, Christoph Seidel, Seong-Ho Shin, Meng Taing, Adolfo Vargas
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Publication number: 20240010668Abstract: The present disclosure provides 3? protected nucleotides, including those 3? protected nucleotides having a detectable tag. Systems and methods of sequencing nucleic acids using the 3? protected nucleotides are also disclosed, such as the sequencing of a nucleic acid using a nanopore or the sequencing of a nucleic acid via sequencing-by-synthesis.Type: ApplicationFiled: August 11, 2023Publication date: January 11, 2024Inventors: Frank Bergmann, Peter Crisalli, Dieter Heindl, Omid Khakshoor, Meng Taing
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Patent number: 11802276Abstract: Disclosed are methods for isolating polymerase complexes from a mixture of polymerase complex components. The polymerase complexes can comprise a nanopore to provide isolated nanopore sequencing complexes. The methods relate to the positive and negative isolation of the polymerase complexes and/or nanopore sequencing complexes. Also disclosed is a nucleic acid adaptor for isolating active polymerase complexes, polymerase complexes comprising the nucleic acid adaptor, and methods for isolating active polymerase complexes using the nucleic acid adaptor.Type: GrantFiled: May 24, 2018Date of Patent: October 31, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: Helen Franklin, Cynthia Cech, Timothy Kellogg Craig, Aruna Ayer, Kirti Dhiman, Natalie B. Chechelski Johnston, Joshua N. Mabry, Arkadiusz Bibillo, Peter Crisalli, Randall W. Davis
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Patent number: 11773130Abstract: The present disclosure provides 3? protected nucleotides, including those 3? protected nucleotides having a detectable tag. Systems and methods of sequencing nucleic acids using the 3? protected nucleotides are also disclosed, such as the sequencing of a nucleic acid using a nanopore or the sequencing of a nucleic acid via sequencing-by-synthesis.Type: GrantFiled: July 6, 2022Date of Patent: October 3, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: Frank Bergmann, Peter Crisalli, Dieter Heindl, Omid Khakshoor, Meng Taing
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Patent number: 11746337Abstract: Disclosed are methods for isolating polymerase complexes from a mixture of polymerase complex components. The polymerase complexes can comprise a nanopore to provide isolated nanopore sequencing complexes. The methods relate to the positive and negative isolation of the polymerase complexes and/or nanopore sequencing complexes. Also disclosed is a nucleic acid adaptor for isolating active polymerase complexes, polymerase complexes comprising the nucleic acid adaptor, and methods for isolating active polymerase complexes using the nucleic acid adaptor.Type: GrantFiled: May 11, 2020Date of Patent: September 5, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: Helen Franklin, Cynthia Cech, Timothy Kellogg Craig, Aruna Ayer, Kirti Dhiman, Natalie B. Chechelski Johnston, Joshua N. Mabry, Arkadiusz Bibillo, Peter Crisalli, Randall W. Davis
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Publication number: 20230159999Abstract: This application discloses compositions comprising primer compounds that reduce or block deleterious threading into a nanopore of nucleic acid strands displaced by a nanopore-linked polymerase, for example during the use of a nanopore device for nucleic acid sequencing. Also disclosed are methods for using the compositions to reduce deleterious threading events during nanopore-based nucleic acid detection techniques, such as nanopore sequencing.Type: ApplicationFiled: August 4, 2022Publication date: May 25, 2023Inventors: Aruna Ayer, David Beyer, Peter Crisalli, Kirti Dhiman, Helen Franklin, Swathi Chakravarthy, Omid Khakshoor, Blake Langdon, Meng Taing, Adolfo Vargas
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Patent number: 11525124Abstract: Disclosed are methods for isolating polymerase complexes from a mixture of polymerase complex components. The polymerase complexes can comprise a nanopore to provide isolated nanopore sequencing complexes. The methods relate to the positive and negative isolation of the polymerase complexes and/or nanopore sequencing complexes. Also disclosed is a nucleic acid adaptor for isolating active polymerase complexes, polymerase complexes comprising the nucleic acid adaptor, and methods for isolating active polymerase complexes using the nucleic acid adaptor.Type: GrantFiled: May 11, 2020Date of Patent: December 13, 2022Assignee: Roche Sequencing Solutions, Inc.Inventors: Helen Franklin, Cynthia Cech, Timothy Kellogg Craig, Aruna Ayer, Kirti Dhiman, Natalie B. Chechelski Johnston, Joshua N. Mabry, Arkadiusz Bibillo, Peter Crisalli, Randall W. Davis
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Publication number: 20220348604Abstract: The present disclosure provides 3? protected nucleotides, including those 3? protected nucleotides having a detectable tag. Systems and methods of sequencing nucleic acids using the 3? protected nucleotides are also disclosed, such as the sequencing of a nucleic acid using a nanopore or the sequencing of a nucleic acid via sequencing-by-synthesis.Type: ApplicationFiled: July 6, 2022Publication date: November 3, 2022Inventors: Frank Bergmann, Peter Crisalli, Dieter Hiendl, Omid Khakshoor, Meng Taing
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Patent number: 11440933Abstract: The present disclosure provides 3? protected nucleotides, including those 3? protected nucleotides having a detectable tag. Systems and methods of sequencing nucleic acids using the 3? protected nucleotides are also disclosed, such as the sequencing of a nucleic acid using a nanopore or the sequencing of a nucleic acid via sequencing-by-synthesis.Type: GrantFiled: December 16, 2019Date of Patent: September 13, 2022Assignee: ROCHE SEQUENCING SOLUTIONS, INC.Inventors: Frank Bergmann, Peter Crisalli, Dieter Hiendl, Omid Khakshoor, Meng Taing
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Patent number: 11293060Abstract: The present invention relates to improving the processing rate of a sequencing reaction, for example in a nanopore sequencing reaction, by means of using improved nucleoside-tags. The tags are linked to the nucleoside phosphate via a Pictet Spengler reaction. Exemplary sequencing reactions that are improved by the present methods include nanopore-based nucleic acid sequencing-by-synthesis reactions.Type: GrantFiled: October 8, 2019Date of Patent: April 5, 2022Assignee: Roche Sequencing Solutions, Inc.Inventors: Frank Bergmann, Ian Quang Chau, Peter Crisalli, Hannah Marie Kallewaard-Lum, Hannes Kuchelmeister, Sebastian Johannes Pomplun, Hasham Saqib, Christian Wellner
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Publication number: 20220041642Abstract: The present disclosure provides 3? protected nucleotides, including those 3? protected nucleotides having a detectable tag. Systems and methods of sequencing nucleic acids using the 3? protected nucleotides are also disclosed, such as the sequencing of a nucleic acid using a nanopore or the sequencing of a nucleic acid via sequencing-by-synthesis.Type: ApplicationFiled: December 16, 2019Publication date: February 10, 2022Inventors: Frank Bergmann, Peter Crisalli, Dieter Hiendl, Omid Khakshoor, Meng Taing
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Publication number: 20210317521Abstract: The present disclosure relates to compounds comprising a negatively-charged polymer moiety which is capable of entering a nanopore and upon entering a nanopore in the presence of positive ions results in an increased flow of the positive ions through the nanopore. The present disclosure provides methods of preparing the compounds and for their use as nanopore-detectable tags, in particular, for nanopore-based nucleic acid detection and sequencing.Type: ApplicationFiled: April 13, 2021Publication date: October 14, 2021Applicant: Roche Sequencing Solutions, Inc.Inventors: Dmitriy Gremyachinskiy, Peter Crisalli, Andrew Trans, Ashwini Bhat
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Patent number: 11008613Abstract: The present disclosure relates to compounds comprising a negatively-charged polymer moiety which is capable of entering a nanopore and upon entering a nanopore in the presence of positive ions results in an increased flow of the positive ions through the nanopore. The present disclosure provides methods of preparing the compounds and for their use as nanopore-detectable tags, in particular, for nanopore-based nucleic acid detection and sequencing.Type: GrantFiled: March 20, 2020Date of Patent: May 18, 2021Assignee: Roche Sequencing Solutions, Inc.Inventors: Dmitriy Gremyachinskiy, Peter Crisalli, Andrew Trans, Ashwini Bhat
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Publication number: 20210088511Abstract: Provided are nanopore-based methods, compositions, and systems for assessing analyte-ligand interactions and analyte concentration in a fluid solution. The compositions include an analyte detection complex that is associated with a nanopore to form a nanopore assembly, the analyte detection complex including an analyte ligand. As a first voltage is applied across the nanopore assembly, the analyte ligand is presented to an analyte in the solution. As a second voltage that is opposite in polarity to the first voltage is applied across the nanopore assembly, the analyte binds to the analyte. By comparing the total number of analyte-ligand binding pairs to a control binding count, the concentration of the analyte can be determined. In other examples, further increasing the second voltage can result in dissociation of the analyte-ligand pair, from which a dissociation voltage—and hence a dissociation constant—can be determined.Type: ApplicationFiled: September 30, 2020Publication date: March 25, 2021Applicant: Roche Diagnostics Operations, Inc.Inventors: Peter CRISALLI, Dmitriy GREMYACHINSKIY, Dieter HEINDL, Hannes KUCHELMEISTER, Michael SCHRAEML, Andrew TRANS
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Publication number: 20200277581Abstract: Disclosed are methods for isolating polymerase complexes from a mixture of polymerase complex components. The polymerase complexes can comprise a nanopore to provide isolated nanopore sequencing complexes. The methods relate to the positive and negative isolation of the polymerase complexes and/or nanopore sequencing complexes. Also disclosed is a nucleic acid adaptor for isolating active polymerase complexes, polymerase complexes comprising the nucleic acid adaptor, and methods for isolating active polymerase complexes using the nucleic acid adaptor.Type: ApplicationFiled: May 11, 2020Publication date: September 3, 2020Applicant: Roche Sequencing Solutions, Inc.Inventors: Helen FRANKLIN, Cynthia CECH, Timothy Kellogg CRAIG, Aruna AYER, Kirti DHIMAN, Natalie B. CHECHELSKI JOHNSTON, Joshua N. MABRY, Arkadiusz BIBILLO, Peter CRISALLI, Randall W. DAVIS
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Publication number: 20200270589Abstract: Disclosed are methods for isolating polymerase complexes from a mixture of polymerase complex components. The polymerase complexes can comprise a nanopore to provide isolated nanopore sequencing complexes. The methods relate to the positive and negative isolation of the polymerase complexes and/or nanopore sequencing complexes. Also disclosed is a nucleic acid adaptor for isolating active polymerase complexes, polymerase complexes comprising the nucleic acid adaptor, and methods for isolating active polymerase complexes using the nucleic acid adaptor.Type: ApplicationFiled: May 11, 2020Publication date: August 27, 2020Applicant: ROCHE SEQUENCING SOLUTIONS, INC.Inventors: Helen FRANKLIN, Cynthia CECH, Timothy Kellogg CRAIG, Aruna AYER, Kirti DHIMAN, Natalie B. CHECHELSKI JOHNSTON, Joshua N. MABRY, Arkadiusz BIBILLO, Peter CRISALLI, Randall W. DAVIS
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Publication number: 20200216894Abstract: The present disclosure relates to compounds comprising a negatively-charged polymer moiety which is capable of entering a nanopore and upon entering a nanopore in the presence of positive ions results in an increased flow of the positive ions through the nanopore. The present disclosure provides methods of preparing the compounds and for their use as nanopore-detectable tags, in particular, for nanopore-based nucleic acid detection and sequencing.Type: ApplicationFiled: March 20, 2020Publication date: July 9, 2020Applicant: Roche Sequencing Solutions, Inc.Inventors: Dmitriy Gremyachinskiy, Peter Crisalli, Andrew Trans, Ashwini Bhat
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Patent number: 10669580Abstract: The present disclosure relates to compounds comprising a negatively-charged polymer moiety which is capable of entering a nanopore and upon entering a nanopore in the presence of positive ions results in an increased flow of the positive ions through the nanopore. The present disclosure provides methods of preparing the compounds and for their use as nanopore-detectable tags, in particular, for nanopore-based nucleic acid detection and sequencing.Type: GrantFiled: August 23, 2017Date of Patent: June 2, 2020Assignee: Roche Sequencing Solutions, Inc.Inventors: Dmitriy Gremyachinskiy, Peter Crisalli, Andrew Trans, Ashwini Bhat
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Publication number: 20200040392Abstract: The present invention relates to improving the processing rate of a sequencing reaction, for example in a nanopore sequencing reaction, by means of using improved nucleoside-tags. The tags are linked to the nucleoside phosphate via a Pictet Spengler reaction. Exemplary sequencing reactions that are improved by the present methods include nanopore-based nucleic acid sequencing-by-synthesis reactions.Type: ApplicationFiled: October 8, 2019Publication date: February 6, 2020Inventors: Frank Bergmann, Ian Quang Chau, Peter Crisalli, Hannah Marie Kallewaard-Lum, Hannes Kuchelmeister, Sebastian Johannes Pomplun, Hasham Saqib, Christian Wellner
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Publication number: 20180340157Abstract: Disclosed are methods for isolating polymerase complexes from a mixture of polymerase complex components. The polymerase complexes can comprise a nanopore to provide isolated nanopore sequencing complexes. The methods relate to the positive and negative isolation of the polymerase complexes and/or nanopore sequencing complexes. Also disclosed is a nucleic acid adaptor for isolating active polymerase complexes, polymerase complexes comprising the nucleic acid adaptor, and methods for isolating active polymerase complexes using the nucleic acid adaptor.Type: ApplicationFiled: May 24, 2018Publication date: November 29, 2018Inventors: Helen FRANKLIN, Cynthia CECH, Timothy Kellogg CRAIG, Aruna AYER, Kirti DHIMAN, Natalie B. CHECHELSKI JOHNSTON, Joshua N. MABRY, Arkadiusz BIBILLO, Peter CRISALLI, Randall W. DAVIS