Patents by Inventor Derek L. Stemple

Derek L. Stemple 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).

  • Patent number: 8945845
    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: March 27, 2013
    Date of Patent: February 3, 2015
    Assignee: Alere San Diego Inc.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Publication number: 20140234846
    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 hundreds of megabases in length.
    Type: Application
    Filed: September 23, 2013
    Publication date: August 21, 2014
    Applicant: Alere San Diego, Inc.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Publication number: 20140141434
    Abstract: This disclosure describe three related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of the bacterial RecA and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods has the advantage of not requiring thermocycling or thermophilic enzymes. Further, the improved processivity of the disclosed methods allow amplification of DNA up to hundreds of megabases in length.
    Type: Application
    Filed: June 6, 2013
    Publication date: May 22, 2014
    Inventors: Niall A. Armes, Derek L. Stemple
  • Publication number: 20140099674
    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: March 27, 2013
    Publication date: April 10, 2014
    Applicant: Alere San Diego Inc.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Patent number: 8574846
    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: August 4, 2011
    Date of Patent: November 5, 2013
    Assignee: Alere San Diego, Inc.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Patent number: 8460875
    Abstract: This disclosure provides methods for Recombinase-Polymerase Amplification (RPA) of a target DNA. The methods exploit the properties of the bacterial RecA and related proteins to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The methods have the advantage of not requiring thermocycling or thermophilic enzymes. Further, the methods allow amplification of DNA up to hundreds of megabases in length.
    Type: Grant
    Filed: July 28, 2011
    Date of Patent: June 11, 2013
    Assignee: Alere San Diego, Inc.
    Inventors: Niall A. Armes, Derek L. Stemple
  • Patent number: 8426134
    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: August 18, 2011
    Date of Patent: April 23, 2013
    Assignee: Alere San Diego, Inc.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Patent number: 8299226
    Abstract: This disclosure provides novel reversibly terminated ribonucleotides which can be used as a reagent for DNA sequencing reactions. Methods of sequencing nucleic acids using the disclosed nucleotides are also provided.
    Type: Grant
    Filed: August 10, 2011
    Date of Patent: October 30, 2012
    Assignee: Alere San Diego, Inc.
    Inventors: Olaf Piepenburg, Derek L. Stemple, Niall A. Armes
  • Publication number: 20120082990
    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: August 4, 2011
    Publication date: April 5, 2012
    Applicant: ALERE SAN DIEGO, INC.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Publication number: 20120058517
    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: August 18, 2011
    Publication date: March 8, 2012
    Applicant: ALERE SAN DIEGO, INC.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Publication number: 20120040345
    Abstract: This disclosure provides novel reversibly terminated ribonucleotides which can be used as a reagent for DNA sequencing reactions. Methods of sequencing nucleic acids using the disclosed nucleotides are also provided.
    Type: Application
    Filed: August 10, 2011
    Publication date: February 16, 2012
    Applicant: ALERE SAN DIEGO, INC.
    Inventors: Olaf Piepenburg, Derek L. Stemple, Niall A. Armes
  • Publication number: 20120021462
    Abstract: This disclosure describe three related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of the bacterial RecA and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods has the advantage of not requiring thermocycling or thermophilic enzymes. Further, the improved processivity of the disclosed methods allow amplification of DNA up to hundreds of megabases in length.
    Type: Application
    Filed: July 28, 2011
    Publication date: January 26, 2012
    Inventors: Niall A. Armes, Derek L. Stemple
  • Patent number: 8030000
    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 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. Further described are novel properties and approaches for use of probes monitored by light in dynamic recombination environments.
    Type: Grant
    Filed: February 19, 2010
    Date of Patent: October 4, 2011
    Assignee: Alere San Diego, Inc.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Patent number: 8022194
    Abstract: This disclosure provides novel reversibly terminated ribonucleotides which can be used as a reagent for DNA sequencing reactions. Methods of sequencing nucleic acids using the disclosed nucleotides are also provided.
    Type: Grant
    Filed: June 21, 2010
    Date of Patent: September 20, 2011
    Assignee: Alere San Diego, Inc.
    Inventors: Olaf Piepenburg, Derek L. Stemple, Niall A. Armes
  • Patent number: 8017339
    Abstract: This disclosure describes three 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 hundreds of megabases in length.
    Type: Grant
    Filed: June 14, 2010
    Date of Patent: September 13, 2011
    Assignee: Alere San Diego, Inc.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Publication number: 20110065106
    Abstract: This disclosure describe three related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of the bacterial RecA and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods has the advantage of not requiring thermocycling or thermophilic enzymes. Further, the improved processivity of the disclosed methods allow amplification of DNA up to hundreds of megabases in length.
    Type: Application
    Filed: April 30, 2010
    Publication date: March 17, 2011
    Applicant: TwistDx, Inc.
    Inventors: Niall A. Armes, Derek L. Stemple
  • Publication number: 20110059506
    Abstract: This disclosure describe three 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 hundreds of megabases in length.
    Type: Application
    Filed: June 14, 2010
    Publication date: March 10, 2011
    Applicant: Alere San Diego, Inc.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Publication number: 20110053154
    Abstract: This disclosure provides novel reversibly terminated ribonucleotides which can be used as a reagent for DNA sequencing reactions. Methods of sequencing nucleic acids using the disclosed nucleotides are also provided.
    Type: Application
    Filed: June 21, 2010
    Publication date: March 3, 2011
    Applicant: TwistDx, Inc.
    Inventors: Olaf Piepenburg, Derek L. Stemple, Niall A. Armes
  • Publication number: 20100311127
    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 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. Further described are novel properties and approaches for use of probes monitored by light in dynamic recombination environments.
    Type: Application
    Filed: February 19, 2010
    Publication date: December 9, 2010
    Applicant: TwistDix, Inc.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Patent number: 7763427
    Abstract: This disclosure describe three 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 hundreds of megabases in length.
    Type: Grant
    Filed: May 7, 2008
    Date of Patent: July 27, 2010
    Assignee: TwistDx, Inc.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple