Patents Assigned to Stratos Genomics, Inc.
-
Patent number: 11708566Abstract: Recombinant DP04-type DNA polymerase variants with amino acid substitutions that confer modified properties upon the polymerase for improved single molecule sequencing applications are provided. Such properties may include enhanced binding and incorporation of bulky nucleotide analog substrates into daughter strands and the like. Also provided are compositions comprising such DP04 variants and nucleotide analogs, as well as nucleic acids which encode the polymerases with the aforementioned phenotypes.Type: GrantFiled: May 3, 2018Date of Patent: July 25, 2023Assignee: Stratos Genomics, Inc.Inventors: Mark Stamatios Kokoris, Marc Prindle, Jack Chase, Robert Busam, Michael Kovarik, Salka Keller, Megan Murt, Greg Thiessen
-
Patent number: 11530392Abstract: Recombinant DPO4-type DNA polymerase variants with amino acid substitutions that confer modified properties upon the polymerase for improved single molecule sequencing applications are provided. Such properties may include enhanced binding and accurate incorporation of bulky nucleotide analog substrates into daughter strands and the like. Also provided are compositions comprising such DPO4 variants and nucleotide analogs, as well as nucleic acids which encode the polymerases with the aforementioned phenotypes.Type: GrantFiled: December 10, 2018Date of Patent: December 20, 2022Assignee: Stratos Genomics, Inc.Inventors: Mark Kokoris, Marc Prindle, Gregory Scott Thiessen, Alexander Isaac Lehmann, Drew Goodman, Aaron Jacobs, John Chase
-
Patent number: 11299725Abstract: Recombinant DPO4-type DNA polymerase variants with amino acid substitutions that confer modified properties upon the polymerase for improved single molecule sequencing applications are provided. Such properties may include enhanced binding and incorporation of bulky nucleotide analog substrates into daughter strands and the like. Also provided are compositions comprising such DPO4 variants and nucleotide analogs, as well as nucleic acids which encode the polymerases with the aforementioned phenotypes.Type: GrantFiled: May 4, 2020Date of Patent: April 12, 2022Assignee: Stratos Genomics, Inc.Inventors: Mark Stamatios Kokoris, Marc Prindle, Melud Nabavi, Craig Ostrander, Taylor Lehmann, Samantha Vellucci, Michael Kovarik, Jack Chase, Robert Busam, Miranda Lahman
-
Patent number: 10996213Abstract: Nanopore-based molecular analysis systems including a disposable well array, methods of analysis of biomolecules using nanopore molecular analysis systems, and methods of fabricating disposable well arrays are provided.Type: GrantFiled: January 12, 2017Date of Patent: May 4, 2021Assignee: STRATOS GENOMICS, INC.Inventors: Robert N. McRuer, Steven Hickman
-
Patent number: 10851405Abstract: Methods and related products are disclosed that improve the probability of interaction between a target molecule and a nanopore by capturing the target molecule on a surface comprising the nanopore. The captured target molecule, the nanopore, or both, are able to move relative to each other along the surface. When the leader of the target molecule is in proximity with the nanopore, interaction of the target portion of the target molecule with the nanopore occurs, thereby permitting sensing of the target portion. Confining the target molecule and nanopore in this manner leads to significantly enhanced interaction with the nanopore.Type: GrantFiled: May 2, 2017Date of Patent: December 1, 2020Assignee: STRATOS GENOMICS, INC.Inventors: Mark Stamatios Kokoris, Robert N. McRuer
-
Patent number: 10774105Abstract: Phosphoramidate esters and related nucleotide analogs useful in polynucleotide sequencing techniques, and synthetic methods for preparing those compounds, are disclosed, including compounds having the following structure: wherein R1, R2, R3 and R4 are as defined herein. These compounds include nucleotide phosphoramidates analogs that are modified on the alpha-phosphate to enable attachment of a variety of application-specific substituents such as tether molecules.Type: GrantFiled: April 10, 2019Date of Patent: September 15, 2020Assignee: STRATOS GENOMICS, INC.Inventors: Mark Stamatios Kokoris, John Tabone, Melud Nabavi, Aaron Jacobs
-
Patent number: 10745685Abstract: Recombinant DPO4-type DNA polymerase variants with amino acid substitutions that confer modified properties upon the polymerase for improved single molecule sequencing applications are provided. Such properties may include enhanced binding and incorporation of bulky nucleotide analog substrates into daughter strands and the like. Also provided are compositions comprising such DPO4 variants and nucleotide analogs, as well as nucleic acids which encode the polymerases with the aforementioned phenotypes.Type: GrantFiled: November 11, 2016Date of Patent: August 18, 2020Assignee: Stratos Genomics, Inc.Inventors: Mark Stamatios Kokoris, Marc Prindle, Melud Nabavi, Craig Ostrander, Taylor Lehmann, Samantha Vellucci, Michael Kovarik, Jack Chase, Robert Busam, Miranda Lahman
-
Patent number: 10676782Abstract: Translocation control for sensing by a nanopore, as well as methods and products related to the same, are provided. Such methods optimize duplex stability to provide high fill rate (of the hybridization sites) but do not prevent rapid dissociation required for high read rates, as well as controlling the translocation of a target molecule for sensing by a nanopore by use of a selective pulsed voltage. Products related to the same include a reporter construct comprising two or more phosphoramidites.Type: GrantFiled: September 12, 2019Date of Patent: June 9, 2020Assignee: STRATOS GENOMICS, INC.Inventors: Robert N. McRuer, Mark Stamatios Kokoris
-
Patent number: 10457979Abstract: Translocation control for sensing by a nanopore, as well as methods and products related to the same, are provided. Such methods optimize duplex stability to provide high fill rate (of the hybridization sites) but do not prevent rapid dissociation required for high read rates, as well as controlling the translocation of a target molecule for sensing by a nanopore by use of a selective pulsed voltage. Products related to the same include a reporter construct comprising two or more phosphoramidites.Type: GrantFiled: May 14, 2015Date of Patent: October 29, 2019Assignee: STRATOS GENOMICS, INC.Inventors: Robert N. McRuer, Mark Stamatios Kokoris
-
Patent number: 10407714Abstract: Methods and related products are disclosed that improve the probability of interaction between a target molecule and a nanopore by capturing the target molecule on a surface comprising the nanopore. The captured target molecule, the nanopore, or both, are able to move relative to each other along the surface. When the leader of the target molecule is in proximity with the nanopore, interaction of the target portion of the target molecule with the nanopore occurs, thereby permitting sensing of the target portion. Confining the target molecule and nanopore in this manner leads to significantly enhanced interaction with the nanopore.Type: GrantFiled: May 2, 2017Date of Patent: September 10, 2019Assignee: STRATOS GENOMICS, INC.Inventors: Mark Stamatios Kokoris, Robert N. McRuer
-
Patent number: 10301345Abstract: Phosphoramidate esters and related nucleotide analogs useful in polynucleotide sequencing techniques, and synthetic methods for preparing those compounds, are disclosed, including compounds having the following structure: wherein R1, R2, R3 and R4 are as defined herein.Type: GrantFiled: November 20, 2015Date of Patent: May 28, 2019Assignee: STRATOS GENOMICS, INC.Inventors: Mark Stamatios Kokoris, John Tabone, Melud Nabavi, Aaron Jacobs
-
Patent number: 9920386Abstract: Nucleic acid sequencing methods and related products are disclosed. Methods for sequencing a target nucleic acid comprise providing a daughter strand produced by a template-directed synthesis, the daughter strand comprising a plurality of subunits coupled in a sequence corresponding to a contiguous nucleotide sequence of all or a portion of the target nucleic acid, wherein the individual subunits comprise a tether, at least one probe or nucleobase residue, and at least one selectively cleavable bond. The selectively cleavable bond(s) is/are cleaved to yield an Xpandomer of a length longer than the plurality of the subunits of the daughter strand, the Xpandomer comprising the tethers and reporter elements for parsing genetic information in a sequence corresponding to the contiguous nucleotide sequence of all or a portion of the target nucleic acid. Reporter elements of the Xpandomer are then detected.Type: GrantFiled: July 6, 2015Date of Patent: March 20, 2018Assignee: Stratos Genomics, Inc.Inventors: Mark Stamatios Kokoris, Robert N. McRuer
-
Patent number: 9771614Abstract: A method for detecting an analyte employing a nanopore substrate positioned between first and second reservoirs by providing an indicator molecule not associated with the analyte and detecting a change in an optical signal emitted from the indicator moiety as the analyte translocates through a nanopore channel of the nanopore substrate.Type: GrantFiled: January 6, 2015Date of Patent: September 26, 2017Assignee: Stratos Genomics Inc.Inventors: Mark Stamatios Kokoris, Robert N. McRuer
-
Patent number: 9670526Abstract: Methods and related products are disclosed that improve the probability of interaction between a target molecule and a nanopore by capturing the target molecule on a surface comprising the nanopore. The captured target molecule, the nanopore, or both, are able to move relative to each other along the surface. When the leader of the target molecule is in proximity with the nanopore, interaction of the target portion of the target molecule with the nanopore occurs, thereby permitting sensing of the target portion. Confining the target molecule and nanopore in this manner leads to significantly enhanced interaction with the nanopore.Type: GrantFiled: November 8, 2013Date of Patent: June 6, 2017Assignee: Stratos Genomics, Inc.Inventors: Mark Stamatios Kokoris, Robert N. McRuer
-
Publication number: 20140141989Abstract: A method for the rapid identification of a target nucleic acid sequence is provided, as well as corresponding devices, products and kits. Such methods are useful for the rapid detection, identification and/or quantification of target nucleic acid sequences associated with, for example, a pathogen.Type: ApplicationFiled: October 28, 2013Publication date: May 22, 2014Applicant: Stratos Genomics, Inc.Inventors: Mark Stamatios Kokoris, Robert N. McRuer
-
Patent number: 8592182Abstract: Nucleic acid sequencing methods and related devices, products and kits are disclosed. Methods for sequencing a target nucleic acid comprise providing a daughter strand produced by a template-directed synthesis, the daughter strand comprising a plurality of subunits coupled in a sequence corresponding to a contiguous nucleotide sequence of all or a portion of the target nucleic acid, wherein the individual subunits comprise a probe and a reporter construct. The subunit encodes sequence information in its reporter construct that is less than sequence information in the corresponding portion of the target nucleic acid. The reduced information allows for reduced resolution requirements on the detection system and for increased size of resolvable reporter groups.Type: GrantFiled: October 23, 2008Date of Patent: November 26, 2013Assignee: Stratos Genomics Inc.Inventors: Mark Stamatios Kokoris, Robert N. McRuer
-
Patent number: 8586301Abstract: A method for the rapid identification of a target nucleic acid sequence is provided, as well as corresponding devices, products and kits. Such methods are useful for the rapid detection, identification and/or quantification of target nucleic acid sequences associated with, for example, a pathogen.Type: GrantFiled: June 30, 2011Date of Patent: November 19, 2013Assignee: Stratos Genomics, Inc.Inventors: Mark Stamatios Kokoris, Robert N. McRuer
-
Publication number: 20130172197Abstract: Nucleic acid sequencing methods and related products are disclosed. Methods for sequencing a target nucleic acid comprise providing a daughter strand produced by a template-directed synthesis, the daughter strand comprising a plurality of subunits coupled in a sequence corresponding to a contiguous nucleotide sequence of all or a portion of the target nucleic acid, wherein the individual subunits comprise a tether, at least one probe or nucleobase residue, and at least one selectively cleavable bond. The selectively cleavable bond(s) is/are cleaved to yield an Xpandomer of a length longer than the plurality of the subunits of the daughter strand, the Xpandomer comprising the tethers and reporter elements for parsing genetic information in a sequence corresponding to the contiguous nucleotide sequence of all or a portion of the target nucleic acid. Reporter elements of the Xpandomer are then detected.Type: ApplicationFiled: November 30, 2012Publication date: July 4, 2013Applicant: STRATOS GENOMICS, INC.Inventor: Stratos Genomics, Inc.
-
Patent number: 8349565Abstract: Nucleic acid sequencing methods and related products are disclosed. Methods for sequencing a target nucleic acid comprise providing a daughter strand produced by a template-directed synthesis, the daughter strand comprising a plurality of subunits coupled in a sequence corresponding to a contiguous nucleotide sequence of all or a portion of the target nucleic acid, wherein the individual subunits comprise a tether, at least one probe or nucleobase residue, and at least one selectively cleavable bond. The selectively cleavable bond(s) is/are cleaved to yield an Xpandomer of a length longer than the plurality of the subunits of the daughter strand, the Xpandomer comprising the tethers and reporter elements for parsing genetic information in a sequence corresponding to the contiguous nucleotide sequence of all or a portion of the target nucleic acid. Reporter elements of the Xpandomer are then detected.Type: GrantFiled: March 30, 2011Date of Patent: January 8, 2013Assignee: Stratos Genomics, Inc.Inventors: Mark Stamatios Kokoris, Robert N. McRuer
-
Patent number: 8324360Abstract: Nucleic acid sequencing methods and related products are disclosed. Methods for sequencing a target nucleic acid comprise providing a daughter strand produced by a template-directed synthesis, the daughter strand comprising a plurality of subunits coupled in a sequence corresponding to a contiguous nucleotide sequence of all or a portion of the target nucleic acid, wherein the individual subunits comprise a tether, at least one probe or nucleobase residue, and at least one selectively cleavable bond. The selectively cleavable bond(s) is/are cleaved to yield an Xpandomer of a length longer than the plurality of the subunits of the daughter strand, the Xpandomer comprising the tethers and reporter elements for parsing genetic information in a sequence corresponding to the contiguous nucleotide sequence of all or a portion of the target nucleic acid. Reporter elements of the Xpandomer are then detected.Type: GrantFiled: March 30, 2011Date of Patent: December 4, 2012Assignee: Stratos Genomics, Inc.Inventors: Mark Stamatios Kokoris, Robert N. McRuer