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).
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Patent number: 11976306Abstract: 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: GrantFiled: August 16, 2017Date of Patent: May 7, 2024Assignees: Stichting Voor De Technische Wetenschappen, WAGENINGEN UNIVERSITEITInventors: John Van Der Oost, Richard Van Kranenburg, Elleke Fenna Bosma, Ioannis Mougiakos, Prarthana Mohanraju
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Publication number: 20240110163Abstract: 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: ApplicationFiled: January 28, 2022Publication date: April 4, 2024Inventors: John VAN DER OOST, Wen Ying WU, Ricardo VILLEGAS WARREN
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Publication number: 20240101989Abstract: 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: ApplicationFiled: September 6, 2023Publication date: March 28, 2024Applicant: Wageningen UniversiteitInventor: John VAN DER OOST
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Patent number: 11939605Abstract: 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: GrantFiled: January 14, 2022Date of Patent: March 26, 2024Assignees: Wageningen Universiteit, Stichting Voor De Technische WetenschappenInventors: John Van Der Oost, Richard Van Kranenburg, Elleke Fenna Bosma, Ioannis Mougiakos, Prarthana Mohanraju
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Patent number: 11939604Abstract: 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: GrantFiled: February 18, 2021Date of Patent: March 26, 2024Assignee: Caribou Biosciences, Inc.Inventors: Stan Johan Jozef Brouns, John van der Oost
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Publication number: 20240026383Abstract: 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: ApplicationFiled: October 7, 2021Publication date: January 25, 2024Inventors: Constantinos PATINIOS, Sjoerd Constantijn Arnoud CREUTZBURG, John VAN DER OOST, Raymond Hubert Josephe STAALS
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Publication number: 20230374480Abstract: 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: ApplicationFiled: March 1, 2023Publication date: November 23, 2023Inventors: 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
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Patent number: 11802277Abstract: 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: GrantFiled: June 19, 2020Date of Patent: October 31, 2023Assignee: Wageningen UniversiteitInventors: John Van Der Oost, Martinus Johannes Arnoldus Daas, Servatius Wilhelmus Maria Kengen, Willem Meindert De Vos
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Patent number: 11760985Abstract: 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: GrantFiled: December 17, 2021Date of Patent: September 19, 2023Assignee: WAGENINGEN UNIVERSITEITInventor: John Van Der Oost
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Publication number: 20220372455Abstract: 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: ApplicationFiled: July 3, 2020Publication date: November 24, 2022Inventors: John Van Der Oost, Prarthana Mohanraju, Wen Ying Wu, Sjoerd Creutzburg
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Patent number: 11479761Abstract: 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: GrantFiled: April 30, 2019Date of Patent: October 25, 2022Assignee: WAGENINGEN UNIVERSITEITInventor: John Van Der Oost
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Publication number: 20220325328Abstract: 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: ApplicationFiled: June 19, 2020Publication date: October 13, 2022Inventors: Aiko Jurre Steens, Stijn Hendrikus Petrus Prinsen, John Van Der Oost, Raymond Hubert Josèphe Staals
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Publication number: 20220213455Abstract: 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: ApplicationFiled: January 14, 2022Publication date: July 7, 2022Inventors: John Van Der Oost, Richard Van Kranenburg, Elleke Fenna Bosma, Ioannis Mougiakos, Prarthana Mohanraju
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Publication number: 20220213454Abstract: 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: ApplicationFiled: December 17, 2021Publication date: July 7, 2022Applicant: Wageningen UniversiteitInventor: John VAN DER OOST
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Patent number: 11326162Abstract: 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: GrantFiled: August 16, 2017Date of Patent: May 10, 2022Assignees: Wageningen Universiteit, Stichting Voor De Technische WetenschappenInventors: John Van Der Oost, Richard Van Kranenburg, Elleke Fenna Bosma, Ioannis Mougiakos, Prarthana Mohanraju
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Patent number: 11242513Abstract: 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: GrantFiled: December 14, 2016Date of Patent: February 8, 2022Assignees: Wageningen Universiteit, Stichting Voor De Technische WetenschappenInventors: John Van Der Oost, Richard Van Kranenburg, Elleke Fenna Bosma, Ioannis Mougiakos
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Publication number: 20210340532Abstract: 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: ApplicationFiled: August 16, 2017Publication date: November 4, 2021Inventors: John Van Der Oost, Richard Van Kranenburg, Elleke Fenna Bosma, Ioannis Mougiakos, Prarthana Mohanraju
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Patent number: 11053482Abstract: 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: GrantFiled: April 15, 2016Date of Patent: July 6, 2021Assignee: WAGENINGEN UNIVERSITEITInventor: John Van Der Oost
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Publication number: 20210171926Abstract: 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: ApplicationFiled: February 18, 2021Publication date: June 10, 2021Applicant: Caribou Biosciences, Inc.Inventors: Stan Johan Jozef Brouns, John van der Oost
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Patent number: 10954498Abstract: 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: GrantFiled: June 26, 2020Date of Patent: March 23, 2021Assignee: Caribou Biosciences, Inc.Inventors: Stan Johan Jozef Brouns, John van der Oost