CA3222560A1 - Deaminase-based rna sensors - Google Patents

Deaminase-based rna sensors Download PDF

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Publication number
CA3222560A1
CA3222560A1 CA3222560A CA3222560A CA3222560A1 CA 3222560 A1 CA3222560 A1 CA 3222560A1 CA 3222560 A CA3222560 A CA 3222560A CA 3222560 A CA3222560 A CA 3222560A CA 3222560 A1 CA3222560 A1 CA 3222560A1
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CA
Canada
Prior art keywords
rna
sensor
adar
sensor system
ssrna
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Pending
Application number
CA3222560A
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English (en)
French (fr)
Inventor
Kaiyi JIANG
Rohan Neil Krajeski
Omar Osama Abudayyeh
Jonathan S. Gootenberg
Yifan Zhang
Fei Chen
Xi Chen
Jeremy G. Koob
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Massachusetts Institute of Technology
Broad Institute Inc
Harvard University
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Massachusetts Institute of Technology
Broad Institute Inc
Harvard University
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Publication of CA3222560A1 publication Critical patent/CA3222560A1/en
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/6825—Nucleic acid detection involving sensors
    • C—CHEMISTRY; METALLURGY
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1055—Protein x Protein interaction, e.g. two hybrid selection
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/635—Externally inducible repressor mediated regulation of gene expression, e.g. tetR inducible by tetracyline
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    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/48—Hydrolases (3) acting on peptide bonds (3.4)
    • C12N9/50—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/78—Hydrolases (3) acting on carbon to nitrogen bonds other than peptide bonds (3.5)
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6897—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids involving reporter genes operably linked to promoters
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    • C12Y—ENZYMES
    • C12Y305/00—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5)
    • C12Y305/04—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5) in cyclic amidines (3.5.4)
    • C12Y305/04004—Adenosine deaminase (3.5.4.4)
    • C—CHEMISTRY; METALLURGY
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/14—Type of nucleic acid interfering nucleic acids [NA]
    • C—CHEMISTRY; METALLURGY
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    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/30—Phosphoric diester hydrolysing, i.e. nuclease
    • C12Q2521/301—Endonuclease
    • C—CHEMISTRY; METALLURGY
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    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/30—Phosphoric diester hydrolysing, i.e. nuclease
    • C12Q2521/327—RNAse, e.g. RNAseH
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/107—Nucleic acid detection characterized by the use of physical, structural and functional properties fluorescence
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/131—Nucleic acid detection characterized by the use of physical, structural and functional properties the label being a member of a cognate binding pair, i.e. extends to antibodies, haptens, avidin
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/20—Detection means characterised by being a gene reporter based analysis
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/60—Detection means characterised by use of a special device
    • C12Q2565/607—Detection means characterised by use of a special device being a sensor, e.g. electrode
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/12—Computing arrangements based on biological models using genetic models
    • G06N3/123—DNA computing

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  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
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  • Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • Molecular Biology (AREA)
  • Biomedical Technology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Plant Pathology (AREA)
  • Medicinal Chemistry (AREA)
  • Immunology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
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  • Evolutionary Computation (AREA)
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  • Computational Linguistics (AREA)
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  • General Physics & Mathematics (AREA)
  • Mathematical Physics (AREA)
  • Software Systems (AREA)
  • Artificial Intelligence (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Enzymes And Modification Thereof (AREA)
CA3222560A 2021-06-15 2022-06-14 Deaminase-based rna sensors Pending CA3222560A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US202163210829P 2021-06-15 2021-06-15
US63/210,829 2021-06-15
US202263267177P 2022-01-26 2022-01-26
US63/267,177 2022-01-26
PCT/US2022/033459 WO2022266117A2 (en) 2021-06-15 2022-06-14 Deaminase-based rna sensors

Publications (1)

Publication Number Publication Date
CA3222560A1 true CA3222560A1 (en) 2022-12-22

Family

ID=84527393

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3222560A Pending CA3222560A1 (en) 2021-06-15 2022-06-14 Deaminase-based rna sensors

Country Status (9)

Country Link
US (2) US12195734B2 (https=)
EP (1) EP4355906A2 (https=)
JP (1) JP7795747B2 (https=)
KR (1) KR20240021893A (https=)
AU (1) AU2022291759A1 (https=)
CA (1) CA3222560A1 (https=)
IL (1) IL309025B1 (https=)
MX (1) MX2023014550A (https=)
WO (1) WO2022266117A2 (https=)

Families Citing this family (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
MX2024004934A (es) * 2021-10-29 2024-09-10 Duke Univeristy Composiciones y sistemas para la edicion de celulas programables por arn y metodos para elaborar y usar los mismos.
KR20240155250A (ko) * 2022-02-24 2024-10-28 더 보드 오브 트러스티스 오브 더 리랜드 스탠포드 쥬니어 유니버시티 감각 반응 응용을 위해 adar 편집을 이용하는 살아있는 세포의 rna 센서
JPWO2024071424A1 (https=) 2022-09-29 2024-04-04
JP7847274B2 (ja) * 2022-10-27 2026-04-16 アリゾナ ボード オブ リージェンツ オン ビハーフ オブ アリゾナ ステート ユニバーシティ 核酸センサーに関連する組成物および方法
WO2025054355A1 (en) * 2023-09-06 2025-03-13 Radar Therapeutics Inc. Methods, systems, and compositions for exogenous control of protein expression
WO2025151800A1 (en) 2024-01-10 2025-07-17 Autonomous Therapeutics, Inc. Programmable, rna editor-controlled nucleic acid dose amplifiers and their methods of use
CN119505015B (zh) * 2024-11-15 2025-10-17 北京大学 一种融合蛋白及其应用方法
CN121344095B (zh) * 2025-12-16 2026-04-28 北京肿瘤医院(北京大学肿瘤医院) 一种细胞内mRNA传感器开关的DNA文库筛选方法及应用

Family Cites Families (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2015120197A1 (en) * 2014-02-05 2015-08-13 Regents Of The University Of California Rna editing biomarkers for diagnosis, pharmacological screening and prognostication in cancer
CN110612353A (zh) * 2017-03-03 2019-12-24 加利福尼亚大学董事会 经由抑制性tRNAs和脱氨酶对突变进行RNA靶向
US11359247B2 (en) * 2017-07-31 2022-06-14 Massachusetts Institute Of Technology High performance multi-input microRNA sensors and uses thereof
WO2019071048A1 (en) * 2017-10-04 2019-04-11 The Broad Institute, Inc. SYSTEMS, METHODS AND COMPOSITIONS FOR TARGETED NUCLEIC ACID EDITION
EP3864152B1 (en) * 2018-10-12 2023-08-16 Peking University Methods and compositions for editing rnas
WO2022003684A1 (en) * 2020-06-29 2022-01-06 Bar-Ilan University Composition and methods for identifying antisense guide rna for rna editing
MX2024004934A (es) * 2021-10-29 2024-09-10 Duke Univeristy Composiciones y sistemas para la edicion de celulas programables por arn y metodos para elaborar y usar los mismos.
KR20240155250A (ko) * 2022-02-24 2024-10-28 더 보드 오브 트러스티스 오브 더 리랜드 스탠포드 쥬니어 유니버시티 감각 반응 응용을 위해 adar 편집을 이용하는 살아있는 세포의 rna 센서

Also Published As

Publication number Publication date
IL309025B1 (en) 2026-03-01
US20250101426A1 (en) 2025-03-27
IL309025A (en) 2024-02-01
JP7795747B2 (ja) 2026-01-08
US20230123513A1 (en) 2023-04-20
KR20240021893A (ko) 2024-02-19
MX2023014550A (es) 2024-02-28
AU2022291759A1 (en) 2023-12-21
WO2022266117A3 (en) 2023-03-02
US12195734B2 (en) 2025-01-14
WO2022266117A2 (en) 2022-12-22
JP2024523877A (ja) 2024-07-02
EP4355906A2 (en) 2024-04-24

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