Patents by Inventor Niall Armes

Niall Armes 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).

  • Publication number: 20220145378
    Abstract: The invention relates to processes for performing biochemical reactions, such as in an aqueous in vitro reaction system. The processes involve macromolecules, particularly polypeptides, comprising one or more functional intrinsically disordered regions (IDRs). The invention also relates to IDR-macromolecules, including IDR-polypeptides, including macromolecules or polypeptides comprising a tagged amino acid sequence which comprises or consists of one or more functional IDRs. Such functional IDRs are capable of increasing the efficiency of the biochemical reaction. The invention relates to kits comprising any such macromolecules and polypeptides. The invention further relates to processes for stimulating or enhancing liquid-liquid demixing in a solution using any such macromolecules and polypeptides, including in combination with multivalent metal ions, thereby providing reagents capable of increasing the efficiency of a biochemical reaction.
    Type: Application
    Filed: November 19, 2021
    Publication date: May 12, 2022
    Inventors: Niall ARMES, Hannah WILLIAMS, Matthew FORREST, Matthew PARKER, Sidong LIU, Lauren PARKER
  • Publication number: 20220112547
    Abstract: The invention relates to processes for performing biochemical reactions, such as in an aqueous in vitro reaction system. The processes involve macromolecules, particularly polypeptides, comprising one or more functional intrinsically disordered regions (IDRs). The invention also relates to IDR-macromolecules, including IDR-polypeptides, including macromolecules or polypeptides comprising a tagged amino acid sequence which comprises or consists of one or more functional IDRs. Such functional IDRs are capable of increasing the efficiency of the biochemical reaction. The invention relates to kits comprising any such macromolecules and polypeptides. The invention further relates to processes for stimulating or enhancing liquid-liquid demixing in a solution using any such macromolecules and polypeptides, including in combination with multivalent metal ions, thereby providing reagents capable of increasing the efficiency of a biochemical reaction.
    Type: Application
    Filed: November 17, 2021
    Publication date: April 14, 2022
    Inventors: Niall ARMES, Hannah Williams, Matthew Forrest, Matthew Parker, Sidong Liu, Lauren Parker
  • Publication number: 20210180119
    Abstract: This disclosure describes related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of recombinase and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods have the advantage of not requiring thermocycling or thermophilic enzymes, thus offering easy and affordable implementation and portability relative to other amplification methods. Further disclosed are conditions to enable real-time monitoring of RPA reactions, methods to regulate RPA reactions using light and otherwise, methods to determine the nature of amplified species without a need for gel electrophoresis, methods to improve and optimize signal to noise ratios in RPA reactions, methods to optimize oligonucleotide primer function, methods to control carry-over contamination, and methods to employ sequence-specific third ‘specificity’ probes.
    Type: Application
    Filed: December 4, 2020
    Publication date: June 17, 2021
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Patent number: 10947584
    Abstract: This disclosure describes related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of recombinase and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods have the advantage of not requiring thermocycling or thermophilic enzymes, thus offering easy and affordable implementation and portability relative to other amplification methods. Further disclosed are conditions to enable real-time monitoring of RPA reactions, methods to regulate RPA reactions using light and otherwise, methods to determine the nature of amplified species without a need for gel electrophoresis, methods to improve and optimize signal to noise ratios in RPA reactions, methods to optimize oligonucleotide primer function, methods to control carry-over contamination, and methods to employ sequence-specific third ‘specificity’ probes.
    Type: Grant
    Filed: June 14, 2019
    Date of Patent: March 16, 2021
    Assignee: ABBOTT DIAGNOSTICS SCARBOROUGH, INC.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Publication number: 20200232050
    Abstract: A flu assay system including a sample module, a microfluidic nucleic acid amplification device, and an analyzer to facilitate fully automated nested recombinase polymerase amplification (RPA) on a sample delivered to the nucleic acid amplification device via the sample module. The assay includes providing a sample to a microfluidic device, and amplifying a target polynucleotide sequence in the sample. Amplifying the target polynucleotide sequence includes performing a first round of amplification on the sample to yield a first amplification product, and performing a second round of amplification on the first amplification product to yield a second amplification product. The second amplification product includes a smaller sequence completely contained within the first amplification product produced during the first round of amplification.
    Type: Application
    Filed: March 3, 2017
    Publication date: July 23, 2020
    Inventors: Murray John Whyte, Niall A. Armes, Olaf Piepenburg, Catherine Jean Greenwood, Oliver Nentwich
  • Publication number: 20200095584
    Abstract: This disclosure provides for methods and reagents for rapid multiplex RPA reactions and improved methods for detection of multiplex RPA reaction products. In addition, the disclosure provides new methods for eliminating carryover contamination between RPA processes.
    Type: Application
    Filed: December 4, 2019
    Publication date: March 26, 2020
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes
  • Patent number: 10538760
    Abstract: This disclosure provides for methods and reagents for rapid multiplex RPA reactions and improved methods for detection of multiplex RPA reaction products. In addition, the disclosure provides new methods for eliminating carryover contamination between RPA processes.
    Type: Grant
    Filed: December 11, 2015
    Date of Patent: January 21, 2020
    Assignee: ALERE SAN DIEGO, INC.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes
  • Publication number: 20190360030
    Abstract: This disclosure describes related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of recombinase and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods have the advantage of not requiring thermocycling or thermophilic enzymes, thus offering easy and affordable implementation and portability relative to other amplification methods. Further disclosed are conditions to enable real-time monitoring of RPA reactions, methods to regulate RPA reactions using light and otherwise, methods to determine the nature of amplified species without a need for gel electrophoresis, methods to improve and optimize signal to noise ratios in RPA reactions, methods to optimize oligonucleotide primer function, methods to control carry-over contamination, and methods to employ sequence-specific third ‘specificity’ probes.
    Type: Application
    Filed: June 14, 2019
    Publication date: November 28, 2019
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Patent number: 10329602
    Abstract: This disclosure describes related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of recombinase and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods have the advantage of not requiring thermocycling or thermophilic enzymes. Further, the improved processivity of the disclosed methods may allow amplification of DNA up to hundres of megabases in length.
    Type: Grant
    Filed: December 30, 2016
    Date of Patent: June 25, 2019
    Assignee: Alere San Diego, Inc.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Patent number: 10329603
    Abstract: This disclosure describes related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of recombinase and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods have the advantage of not requiring thermocycling or thermophilic enzymes, thus offering easy and affordable implementation and portability relative to other amplification methods. Further disclosed are conditions to enable real-time monitoring of RPA reactions, methods to regulate RPA reactions using light and otherwise, methods to determine the nature of amplified species without a need for gel electrophoresis, methods to improve and optimize signal to noise ratios in RPA reactions, methods to optimize oligonucleotide primer function, methods to control carry-over contamination, and methods to employ sequence-specific third ‘specificity’ probes.
    Type: Grant
    Filed: April 25, 2017
    Date of Patent: June 25, 2019
    Assignee: ALERE SAN DIEGO INC.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Publication number: 20190136300
    Abstract: This invention relates to sequence specific electrochemically-labeled oligonucleotide probes for the detection of nucleic acids and methods associated therewith.
    Type: Application
    Filed: February 24, 2017
    Publication date: May 9, 2019
    Inventors: Frank Ray Bowler, Grzegorz Artur Orlowski, Hazel Lucy Greetham, Cheng Zhou, Niall A. Armes, Olaf Piepenburg
  • Publication number: 20190093088
    Abstract: The present invention features novel, diverse, hybrid and engineered recombinase enzymes, and the utility of such proteins with associated recombination factors for carrying out DNA amplification assays. The present invention also features different recombinase ‘systems’ having distinct biochemical activities in DNA amplification assays, and differing requirements for loading factors, single-stranded DNA binding proteins (SSBs), and the quantity of crowding agent employed.
    Type: Application
    Filed: October 9, 2018
    Publication date: March 28, 2019
    Inventors: Olaf Piepenburg, Niall A. Armes, Matthew James David Parker
  • Publication number: 20190078147
    Abstract: This disclosure relates to methods and compositions for detecting a target nucleic acid sequence using a dual-hapten probe. More specifically, the present disclosure relates to using recombinase polymerase amplification (RPA) and a dual-hapten probe to detect a target nucleic acid sequence. In some cases, the detection is on lateral flow strips.
    Type: Application
    Filed: September 14, 2018
    Publication date: March 14, 2019
    Inventors: Michael L. Powell, Frank Ray Bowler, Catherine Jean Greenwood, Olaf Piepenburg, Niall A. Armes
  • Publication number: 20180320228
    Abstract: This invention relates to methods and compositions for detecting a polymorphism in a target nucleic acid sequence using isothermal nucleic acid amplification. More specifically, the present invention relates to using recombinase polymerase amplification (RPA) or Nicking and Extension Amplification Reaction (NEAR) to detect single nucleotide polymorphisms in a target nucleic acid sequence.
    Type: Application
    Filed: October 7, 2016
    Publication date: November 8, 2018
    Inventors: Matthew Simon Forrest, Niall A. Armes
  • Patent number: 10093908
    Abstract: The present invention features novel, diverse, hybrid and engineered recombinase enzymes, and the utility of such proteins with associated recombination factors for carrying out DNA amplification assays. The present invention also features different recombinase ‘systems’ having distinct biochemical activities in DNA amplification assays, and differing requirements for loading factors, single-stranded DNA binding proteins (SSBs), and the quantity of crowding agent employed.
    Type: Grant
    Filed: December 19, 2013
    Date of Patent: October 9, 2018
    Assignee: Alere San Diego, Inc.
    Inventors: Olaf Piepenburg, Niall A. Armes, Mathew James David Parker
  • Publication number: 20180243739
    Abstract: A microfluidic device includes an inlet port configured to receive a sample, a first reaction chamber fluidically coupled to the inlet port, a first pump fluidically coupled to the inlet port, a second pump fluidically coupled to a mixing chamber, a metering channel fluidically coupled to the first reaction chamber and to the mixing chamber, and one or more second reaction chambers fluidically coupled to the mixing chamber. The first pump is configured to move fluid from the inlet port to the first reaction chamber and from the first pump to the inlet port. The second pump is configured to move fluid from the second pump to the mixing chamber, from the first reaction chamber to the mixing chamber, and from the mixing chamber to the one or more second reaction chambers.
    Type: Application
    Filed: February 27, 2018
    Publication date: August 30, 2018
    Inventors: Alexander Schenk zu Schweinsberg, Austin Matthew Derfus, Justin Davidson, Karthikeyan Kumaravadivelu, Maulik Vinod Patel, Niall A. Armes, Olaf Piepenburg, Catherine Jean Greenwood, Oliver Nentwich
  • Patent number: 10036057
    Abstract: This disclosure describes related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of recombinase and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods have the advantage of not requiring thermocycling or thermophilic enzymes, thus offering easy and affordable implementation and portability relative to other amplification methods. Further disclosed are conditions to enable real-time monitoring of RPA reactions, methods to regulate RPA reactions using light and otherwise, methods to determine the nature of amplified species without a need for gel electrophoresis, methods to improve and optimize signal to noise ratios in RPA reactions, methods to optimize oligonucleotide primer function, methods to control carry-over contamination, and methods to employ sequence-specific third ‘specificity’ probes.
    Type: Grant
    Filed: September 25, 2015
    Date of Patent: July 31, 2018
    Assignee: ALERE SAN DIEGO, INC.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Patent number: 9932577
    Abstract: This disclosure provides for methods and reagents for rapid multiplex RPA reactions and improved methods for detection of multiplex RPA reaction products. In addition, the disclosure provides new methods for eliminating carryover contamination between RPA processes.
    Type: Grant
    Filed: October 29, 2013
    Date of Patent: April 3, 2018
    Assignee: ALERE SAN DIEGO, INC.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes
  • Patent number: 9896719
    Abstract: A new class of nucleic acid substrates for AP endonucleases and members of the glycosylase/lyase family of enzymes is described. Representatives of each family, the enzymes Nfo and fpg, respectively, cleave nucleic acid backbones at positions in which a base has been replaced by a linker to which a variety of label moieties may be attached. The use of these synthetic substrates embedded within oligonucleotides is of utility in a number of applications.
    Type: Grant
    Filed: October 3, 2016
    Date of Patent: February 20, 2018
    Assignee: Alere San Diego Inc.
    Inventors: Olaf Piepenburg, Niall A. Armes
  • Publication number: 20170342473
    Abstract: This disclosure describes related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of recombinase and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods have the advantage of not requiring thermocycling or thermophilic enzymes. Further, the improved processivity of the disclosed methods may allow amplification of DNA up to hundres of megabases in length.
    Type: Application
    Filed: December 30, 2016
    Publication date: November 30, 2017
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple