Patents by Inventor John Van Der Oost

John Van Der Oost 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: 11976306
    Abstract: Thermostable Cas9 nucleases. The present invention relates to the field of genetic engineering and more particularly to nucleic acid editing and genome modification. The present invention provides an isolated Cas protein or polypeptide fragment thereof having an amino acid sequence of SEQ ID NO: 1 or a sequence of at least 77% identity therewith. The Cas protein or polypeptide is capable of binding, cleaving, marking or modifying a double stranded target polynucleotide at a temperature in the range 20° C. and 100° C. inclusive. The invention further provides isolated nucleic acid molecules encoding said Cas9 nucleases, expression vectors and host cells. The invention also provides PAM sequences recognized by the Cas protein or polypeptide, The Cas9 nucleases disclosed herein provide novel tools for genetic engineering in general, in particular at elevated temperatures.
    Type: Grant
    Filed: August 16, 2017
    Date of Patent: May 7, 2024
    Assignees: Stichting Voor De Technische Wetenschappen, WAGENINGEN UNIVERSITEIT
    Inventors: John Van Der Oost, Richard Van Kranenburg, Elleke Fenna Bosma, Ioannis Mougiakos, Prarthana Mohanraju
  • Publication number: 20240110163
    Abstract: The invention relates to methods for clustered regularly interspaced short palindromic repeat (CRISPR)-mediated A to G and/or C to T editing of the guide-complementary strand of a double stranded target DNA. The invention further relates to a nucleotide molecule encoding said CRISPR-mediated base editing system, to an expression vector comprising the nucleotide molecule, and to a cell comprising the expression vector. The invention further relates to an isolated Cas nuclease that allows A to G and/or C to T editing of the complementary strand of a double stranded target nucleic acid.
    Type: Application
    Filed: January 28, 2022
    Publication date: April 4, 2024
    Inventors: John VAN DER OOST, Wen Ying WU, Ricardo VILLEGAS WARREN
  • Publication number: 20240101989
    Abstract: The invention related to the field of genetic engineering tools, methods and techniques for gene or genome editing. Specifically, the invention concerns isolated polypeptides having nuclease activity, host cells and expression vectors comprising nucleic acids encoding said polypeptides as well as methods of cleaving and editing target nucleic acids in a sequence-specific matter. The poly peptides, nucleic acids, expression vectors, host cells and methods of the present invention have application in many fields of biotechnology, including, for example, synthetic biology and gene therapy.
    Type: Application
    Filed: September 6, 2023
    Publication date: March 28, 2024
    Applicant: Wageningen Universiteit
    Inventor: John VAN DER OOST
  • Patent number: 11939605
    Abstract: Thermostable Cas9 nucleases. The present invention relates to the field of genetic engineering and more particularly to nucleic acid editing and genome modification. The present invention provides an isolated Cas protein or polypeptide fragment thereof having an amino acid sequence of SEQ ID NO: 1 or a sequence of at least 77% identity therewith. The Cas protein or polypeptide is capable of binding, cleaving, marking or modifying a double stranded target polynucleotide at a temperature in the range 20° C. and 100° C. inclusive. The invention further provides isolated nucleic acid molecules encoding the Cas9 nucleases, expression vectors and host cells. The invention also provides PAM sequences recognized by the Cas protein or polypeptide, The Cas9 nucleases disclosed herein provide novel tools for genetic engineering in general, in particular at elevated temperatures and are of particular value in the genetic manipulation of thermophilic organisms; particularly microorganisms.
    Type: Grant
    Filed: January 14, 2022
    Date of Patent: March 26, 2024
    Assignees: Wageningen Universiteit, Stichting Voor De Technische Wetenschappen
    Inventors: John Van Der Oost, Richard Van Kranenburg, Elleke Fenna Bosma, Ioannis Mougiakos, Prarthana Mohanraju
  • Patent number: 11939604
    Abstract: A clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for adaptive antiviral defence (Cascade); the Cascade protein complex comprising at least CRISPR-associated protein subunits Cas7, Cas5 and Cash which includes at least one subunit with an additional amino acid sequence possessing nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing activity. The Cascade complex with additional activity is combined with an RNA molecule to produce a ribonucleoprotein complex. The RNA molecule is selected to have substantial complementarity to a target sequence. Targeted ribonucleoproteins can be used as genetic engineering tools for precise cutting of nucleic acids in homologous recombination, non-homologous end joining, gene modification, gene integration, mutation repair or for their visualisation, transcriptional activation or repression.
    Type: Grant
    Filed: February 18, 2021
    Date of Patent: March 26, 2024
    Assignee: Caribou Biosciences, Inc.
    Inventors: Stan Johan Jozef Brouns, John van der Oost
  • Publication number: 20240026383
    Abstract: Aspects described herein relate to methods for controlling expression of RNA and polypeptides of interest using a tuneable self-splicing intron. Specifically, there is provided modified 5? and 3? exons of the T4 td intron which function as a tuneable self-splicing intron that can be introduced to any gene of interest to multiple spots in the open reading frame therefore allowing the intron to be inserted without changing the amino acid sequence of the protein of interest. Methods and a system for inducer controlled modification of a target genomic locus in a cell are also provided herein. The invention further provides kits for expressing an RNA of interest or a polypeptide of interest, and wherein the expression is in transformed host cells under the control of an inducer molecule.
    Type: Application
    Filed: October 7, 2021
    Publication date: January 25, 2024
    Inventors: Constantinos PATINIOS, Sjoerd Constantijn Arnoud CREUTZBURG, John VAN DER OOST, Raymond Hubert Josephe STAALS
  • Publication number: 20230374480
    Abstract: The present invention relates to the field of gene genome editing. In particular, it relates to the provision of a Cas12a enzyme having nickase activity, as well as the means and methods for the modification of a genomic locus of interest with a Cas12a enzyme having nickase activity and uses thereof.
    Type: Application
    Filed: March 1, 2023
    Publication date: November 23, 2023
    Inventors: John VAN DER OOST, Ricardo Villegas WARREN, Maartje Janneke LUTEIJN, Raymond Hubert Josèphe STAALS, Wen Ying WU, David DE VLEESSCHAUWER, Katelijn D'HALLUIN, Frank MEULEWAETER
  • Patent number: 11802277
    Abstract: Thermostable Cas9 nucleases. The present invention relates to the field of genetic engineering and more particularly to nucleic acid editing and genome modification. The present invention provides in isolated Cas protein or polypeptide fragment thereof having an amino acid sequence of SEQ ID NO: 1 or a sequence of at least 77% identity therewith, wherein the Cas protein or polypeptide is capable of DNA cleavage at a temperature in the range 50° C. and 100° C. inclusive. The invention further provides isolated nucleic acid molecules encoding said Cas9 nucleases, expression vectors and host cells. The Cas9 nucleases disclosed herein provide novel tools for genetic engineering at elevated temperatures and are of particular value in the genetic manipulation of thermophilic organisms; particularly microorganisms.
    Type: Grant
    Filed: June 19, 2020
    Date of Patent: October 31, 2023
    Assignee: Wageningen Universiteit
    Inventors: John Van Der Oost, Martinus Johannes Arnoldus Daas, Servatius Wilhelmus Maria Kengen, Willem Meindert De Vos
  • Patent number: 11760985
    Abstract: The invention related to the field of genetic engineering tools, methods and techniques for gene or genome editing. Specifically, the invention concerns isolated polypeptides having nuclease activity, host cells and expression vectors comprising nucleic acids encoding said polypeptides as well as methods of cleaving and editing target nucleic acids in a sequence-specific matter. The poly peptides, nucleic acids, expression vectors, host cells and methods of the present invention have application in many fields of biotechnology, including, for example, synthetic biology and gene therapy.
    Type: Grant
    Filed: December 17, 2021
    Date of Patent: September 19, 2023
    Assignee: WAGENINGEN UNIVERSITEIT
    Inventor: John Van Der Oost
  • Publication number: 20220372455
    Abstract: The type V-U1 system from the bacterium Mycobacterium mucogenicum CCH10-A2 (Mmu) has a nuclease which binds dsDNA but it does not cleave it. Additionally, after dsDNA binding by the nuclease an RuvC-dependent interference of nascent transcript (mRNA) takes place and this mechanism has not been described before for any CRISPR system. CRISPR based gene manipulation can therefore use CRISPR endonucleases from the Type V-U1 system from Mycobacterium mucogenicum, including variant and modified endonucleases, so as to provide for methods of expression control and gene editing in cells of any living organism or of any nucleic acid in vitro.
    Type: Application
    Filed: July 3, 2020
    Publication date: November 24, 2022
    Inventors: John Van Der Oost, Prarthana Mohanraju, Wen Ying Wu, Sjoerd Creutzburg
  • Patent number: 11479761
    Abstract: The invention relates to the field of genetic engineering tools, methods and techniques for gene or genome editing. Specifically, the invention concerns isolated polypeptides having nuclease activity, host cells and expression vectors comprising nucleic acids encoding said polypeptides as well as methods of cleaving and editing target nucleic acids in a sequence-specific manner. The polypeptides, nucleic acids, expression vectors, host cells and methods of the present invention have application in many fields of biotechnology, including, for example, synthetic biology and gene therapy.
    Type: Grant
    Filed: April 30, 2019
    Date of Patent: October 25, 2022
    Assignee: WAGENINGEN UNIVERSITEIT
    Inventor: John Van Der Oost
  • Publication number: 20220325328
    Abstract: The invention relates to a clustered regularly interspaced short palindromic repeats (CRISPR) based ribonucleic acid detection system. The invention further relates to a method for determining presence or absence of a target nucleic acid molecule in a sample with the aid of such system, and to a device comprising the ribonucleic acid detection system according to the invention.
    Type: Application
    Filed: June 19, 2020
    Publication date: October 13, 2022
    Inventors: Aiko Jurre Steens, Stijn Hendrikus Petrus Prinsen, John Van Der Oost, Raymond Hubert Josèphe Staals
  • Publication number: 20220213455
    Abstract: Thermostable Cas9 nucleases. The present invention relates to the field of genetic engineering and more particularly to nucleic acid editing and genome modification. The present invention provides an isolated Cas protein or polypeptide fragment thereof having an amino acid sequence of SEQ ID NO: 1 or a sequence of at least 77% identity therewith. The Cas protein or polypeptide is capable of binding, cleaving, marking or modifying a double stranded target polynucleotide at a temperature in the range 20° C. and 100° C. inclusive. The invention further provides isolated nucleic acid molecules encoding said Cas9 nucleases, expression vectors and host cells. The invention also provides PAM sequences recognized by the Cas protein or polypeptide, The Cas9 nucleases disclosed herein provide novel tools for genetic engineering in general, in particular at elevated temperatures and are of particular value in the genetic manipulation of thermophilic organisms; particularly microorganisms.
    Type: Application
    Filed: January 14, 2022
    Publication date: July 7, 2022
    Inventors: John Van Der Oost, Richard Van Kranenburg, Elleke Fenna Bosma, Ioannis Mougiakos, Prarthana Mohanraju
  • Publication number: 20220213454
    Abstract: The invention related to the field of genetic engineering tools, methods and techniques for gene or genome editing. Specifically, the invention concerns isolated polypeptides having nuclease activity, host cells and expression vectors comprising nucleic acids encoding said polypeptides as well as methods of cleaving and editing target nucleic acids in a sequence-specific matter. The poly peptides, nucleic acids, expression vectors, host cells and methods of the present invention have application in many fields of biotechnology, including, for example, synthetic biology and gene therapy.
    Type: Application
    Filed: December 17, 2021
    Publication date: July 7, 2022
    Applicant: Wageningen Universiteit
    Inventor: John VAN DER OOST
  • Patent number: 11326162
    Abstract: Thermostable Cas9 nucleases. The present invention relates to the field of genetic engineering and more particularly to nucleic acid editing and genome modification. The present invention provides an isolated Cas protein or polypeptide fragment thereof having an amino acid sequence of SEQ ID NO: 1 or a sequence of at least 77% identity therewith. The Cas protein or polypeptide is capable of binding, cleaving, marking or modifying a double stranded target polynucleotide at a temperature in the range 20° C. and 100° C. inclusive. The invention further provides isolated nucleic acid molecules encoding the Cas9 nucleases, expression vectors and host cells. The invention also provides PAM sequences recognized by the Cas protein or polypeptide, The Cas9 nucleases disclosed herein provide novel tools for genetic engineering in general, in particular at elevated temperatures and are of particular value in the genetic manipulation of thermophilic organisms; particularly microorganisms.
    Type: Grant
    Filed: August 16, 2017
    Date of Patent: May 10, 2022
    Assignees: Wageningen Universiteit, Stichting Voor De Technische Wetenschappen
    Inventors: John Van Der Oost, Richard Van Kranenburg, Elleke Fenna Bosma, Ioannis Mougiakos, Prarthana Mohanraju
  • Patent number: 11242513
    Abstract: The present invention relates to the field of genetic engineering and more particularly to nucleic acid editing and genome modification. The present invention provides an isolated Cas protein or polypeptide fragment thereof having an amino acid sequence of SEQ ID NO: 1 or a sequence of at least 77% identity therewith. The Cas protein or polypeptide is capable of binding, cleaving, marking or modifying a double stranded target polynucleotide at a temperature in the range 30° C. and 100° C. inclusive. The invention further provides isolated nucleic acid molecules encoding the Cas9 nucleases, expression vectors and host cells. The invention also provides PAM sequences recognized by the Cas protein or polypeptide, The Cas9 nucleases disclosed herein provide novel tools for genetic engineering at elevated temperatures and are of particular value in the genetic manipulation of thermophilic organisms; particularly microorganisms.
    Type: Grant
    Filed: December 14, 2016
    Date of Patent: February 8, 2022
    Assignees: Wageningen Universiteit, Stichting Voor De Technische Wetenschappen
    Inventors: John Van Der Oost, Richard Van Kranenburg, Elleke Fenna Bosma, Ioannis Mougiakos
  • Publication number: 20210340532
    Abstract: Thermostable Cas9 nucleases. The present invention relates to the field of genetic engineering and more particularly to nucleic acid editing and genome modification. The present invention provides an isolated Cas protein or polypeptide fragment thereof having an amino acid sequence of SEQ ID NO: 1 or a sequence of at least 77% identity therewith. The Cas protein or polypeptide is capable of binding, cleaving, marking or modifying a double stranded target polynucleotide at a temperature in the range 20° C. and 100° C. inclusive. The invention further provides isolated nucleic acid molecules encoding said Cas9 nucleases, expression vectors and host cells. The invention also provides PAM sequences recognized by the Cas protein or polypeptide, The Cas9 nucleases disclosed herein provide novel tools for genetic engineering in general, in particular at elevated temperatures and are of particular value in the genetic manipulation of thermophilic organisms; particularly microorganisms.
    Type: Application
    Filed: August 16, 2017
    Publication date: November 4, 2021
    Inventors: John Van Der Oost, Richard Van Kranenburg, Elleke Fenna Bosma, Ioannis Mougiakos, Prarthana Mohanraju
  • Patent number: 11053482
    Abstract: The invention relates to the field of genetic engineering tools, methods and techniques for gene or genome editing. Specifically, the invention concerns isolated polypeptides having nuclease activity, host cells and expression vectors comprising nucleic acids encoding said polypeptides as well as methods of cleaving and editing target nucleic acids in a sequence-specific manner. The polypeptides, nucleic acids, expression vectors, host cells and methods of the present invention have application in many fields of biotechnology, including, for example, synthetic biology and gene therapy.
    Type: Grant
    Filed: April 15, 2016
    Date of Patent: July 6, 2021
    Assignee: WAGENINGEN UNIVERSITEIT
    Inventor: John Van Der Oost
  • Publication number: 20210171926
    Abstract: A clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for adaptive antiviral defence (Cascade); the Cascade protein complex comprising at least CRISPR-associated protein subunits Cas7, Cas5 and Cash which includes at least one subunit with an additional amino acid sequence possessing nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing activity. The Cascade complex with additional activity is combined with an RNA molecule to produce a ribonucleoprotein complex. The RNA molecule is selected to have substantial complementarity to a target sequence. Targeted ribonucleoproteins can be used as genetic engineering tools for precise cutting of nucleic acids in homologous recombination, non-homologous end joining, gene modification, gene integration, mutation repair or for their visualisation, transcriptional activation or repression.
    Type: Application
    Filed: February 18, 2021
    Publication date: June 10, 2021
    Applicant: Caribou Biosciences, Inc.
    Inventors: Stan Johan Jozef Brouns, John van der Oost
  • Patent number: 10954498
    Abstract: A clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for adaptive antiviral defence (Cascade); the Cascade protein complex comprising at least CRISPR-associated protein subunits Cas7, Cas5 and Cas6 which includes at least one subunit with an additional amino acid sequence possessing nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing activity. The Cascade complex with additional activity is combined with an RNA molecule to produce a ribonucleoprotein complex. The RNA molecule is selected to have substantial complementarity to a target sequence. Targeted ribonucleoproteins can be used as genetic engineering tools for precise cutting of nucleic acids in homologous recombination, non-homologous end joining, gene modification, gene integration, mutation repair or for their visualisation, transcriptional activation or repression.
    Type: Grant
    Filed: June 26, 2020
    Date of Patent: March 23, 2021
    Assignee: Caribou Biosciences, Inc.
    Inventors: Stan Johan Jozef Brouns, John van der Oost