WO2018071849A2 - Engineered meganucleases specific for recognition sequences in the hepatitis b virus genome - Google Patents

Engineered meganucleases specific for recognition sequences in the hepatitis b virus genome Download PDF

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Publication number
WO2018071849A2
WO2018071849A2 PCT/US2017/056638 US2017056638W WO2018071849A2 WO 2018071849 A2 WO2018071849 A2 WO 2018071849A2 US 2017056638 W US2017056638 W US 2017056638W WO 2018071849 A2 WO2018071849 A2 WO 2018071849A2
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Prior art keywords
seq
hbv
meganuclease
engineered meganuclease
engineered
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Ceased
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PCT/US2017/056638
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English (en)
French (fr)
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WO2018071849A3 (en
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Derek Jantz
James Jefferson Smith
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Precision Biosciences Inc
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Precision Biosciences Inc
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Priority to FIEP17804977.1T priority Critical patent/FI3526323T3/fi
Priority to DK17804977.1T priority patent/DK3526323T5/da
Priority to AU2017342536A priority patent/AU2017342536A1/en
Priority to EP17804977.1A priority patent/EP3526323B1/en
Priority to IL308894A priority patent/IL308894A/en
Priority to PE2019000817A priority patent/PE20191353A1/es
Priority to KR1020197013312A priority patent/KR102305215B1/ko
Priority to KR1020237000425A priority patent/KR20230010826A/ko
Priority to CN202311305067.1A priority patent/CN117402852A/zh
Priority to IL265921A priority patent/IL265921B2/en
Priority to MX2019004349A priority patent/MX2019004349A/es
Priority to EA201990792A priority patent/EA201990792A1/ru
Priority to KR1020217029958A priority patent/KR20210118240A/ko
Priority to SG11201903042VA priority patent/SG11201903042VA/en
Priority to JP2019520125A priority patent/JP6811857B2/ja
Priority to CN201780074346.8A priority patent/CN110023495A/zh
Priority to KR1020247026203A priority patent/KR20240123417A/ko
Priority to US16/342,169 priority patent/US10662416B2/en
Application filed by Precision Biosciences Inc filed Critical Precision Biosciences Inc
Priority to EP23164434.5A priority patent/EP4234691A3/en
Priority to CR20190181A priority patent/CR20190181A/es
Priority to IL317537A priority patent/IL317537A/en
Priority to BR112019007450-3A priority patent/BR112019007450A2/pt
Priority to CA3040143A priority patent/CA3040143A1/en
Publication of WO2018071849A2 publication Critical patent/WO2018071849A2/en
Publication of WO2018071849A3 publication Critical patent/WO2018071849A3/en
Priority to PH12019500788A priority patent/PH12019500788A1/en
Priority to CONC2019/0003675A priority patent/CO2019003675A2/es
Anticipated expiration legal-status Critical
Priority to US16/852,296 priority patent/US10851358B2/en
Priority to US17/083,171 priority patent/US11274285B2/en
Priority to US17/665,265 priority patent/US20220243187A1/en
Priority to AU2023263542A priority patent/AU2023263542A1/en
Priority to US18/424,277 priority patent/US20240271111A1/en
Priority to US19/029,948 priority patent/US20250154486A1/en
Ceased legal-status Critical Current

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/43—Enzymes; Proenzymes; Derivatives thereof
    • A61K38/46—Hydrolases (3)
    • A61K38/465—Hydrolases (3) acting on ester bonds (3.1), e.g. lipases, ribonucleases
    • 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)
    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/22—Ribonucleases [RNase]; Deoxyribonucleases [DNase]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/43—Enzymes; Proenzymes; Derivatives thereof
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • A61K48/005—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'active' part of the composition delivered, i.e. the nucleic acid delivered
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/48—Preparations in capsules, e.g. of gelatin, of chocolate
    • A61K9/50—Microcapsules having a gas, liquid or semi-solid filling; Solid microparticles or pellets surrounded by a distinct coating layer, e.g. coated microspheres, coated drug crystals
    • A61K9/51—Nanocapsules; Nanoparticles
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/16—Drugs for disorders of the alimentary tract or the digestive system for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/20—Antivirals for DNA viruses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
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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
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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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
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C12N15/86—Viral vectors
    • C—CHEMISTRY; METALLURGY
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    • C12Y—ENZYMES
    • C12Y301/00—Hydrolases acting on ester bonds (3.1)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • C—CHEMISTRY; METALLURGY
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    • C12N2730/00—Reverse transcribing DNA viruses
    • C12N2730/00011—Details
    • C12N2730/10011—Hepadnaviridae
    • C12N2730/10111—Orthohepadnavirus, e.g. hepatitis B virus
    • C12N2730/10122—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2750/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssDNA viruses
    • C12N2750/00011—Details
    • C12N2750/14011—Parvoviridae
    • C12N2750/14111—Dependovirus, e.g. adenoassociated viruses
    • C12N2750/14141—Use of virus, viral particle or viral elements as a vector
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2750/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssDNA viruses
    • C12N2750/00011—Details
    • C12N2750/14011—Parvoviridae
    • C12N2750/14111—Dependovirus, e.g. adenoassociated viruses
    • C12N2750/14141—Use of virus, viral particle or viral elements as a vector
    • C12N2750/14143—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2800/00—Nucleic acids vectors
    • C12N2800/10—Plasmid DNA
    • C12N2800/106—Plasmid DNA for vertebrates
    • C12N2800/107—Plasmid DNA for vertebrates for mammalian

Definitions

  • the viral DNA is found in the nucleus soon after infection of the cell.
  • the partially double-stranded DNA is rendered fully double-stranded by completion of the (+) sense strand and removal of a protein molecule from the (-) sense strand and a short sequence of RNA from the (+) sense strand.
  • Non-coding bases are removed from the ends of the (-) sense strand and the ends are rejoined.
  • the first subunit can comprise an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, or more, sequence identity to residues 7-153 of SEQ ID NO: 18 or 19 or residues 198-344 of SEQ ID NO: 20 or 21, and the second subunit can comprise an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, or more, sequence identity to residues 198-344 of SEQ ID NO: 18 or 19 or residues 7-153 of SEQ ID NO: 20 or 21.
  • the first subunit can comprise residues 7-153 of SEQ ID NO: 18 or 19 or residues 198-344 of SEQ ID NO: 20 or 21.
  • the second subunit can comprise residues 198-344 of SEQ ID NO: 18 or 19 or residues 7-153 of SEQ ID NO: 20 or 21.
  • the viral vector comprises two or more cassettes, wherein each cassette comprises a promoter and a nucleic acid sequence encoding an engineered meganuclease described herein, and wherein each engineered meganuclease has specificity for a different HBV recognition sequence disclosed herein.
  • the viral vector comprises one cassette comprising a promoter and a polycistronic nucleic acid sequence, wherein the promoter drives expression of the polycistronic nucleic acid sequence to generate a polycistronic mRNA described herein in a target cell.
  • the pharmaceutical composition can comprise two or more engineered meganuclease proteins described herein, wherein the engineered
  • the methods of treatment for HBV infection or HCC comprise administering to the subject any pharmaceutical composition of the invention described herein which comprises, at least, a pharmaceutically acceptable carrier and (a) a nucleic acid encoding an engineered meganuclease described herein, wherein the engineered meganuclease is expressed in a target cell in vivo; or (b) an engineered meganuclease protein described herein.
  • Figure 9 Evaluation of HBV meganucleases for their ability to recognize and cleave recognition sequences within episomal DNA plasmids in an E. coli reporter system.
  • Figure 9A shows plasmid pARCUS and plasmid pHBVa.
  • Figure 9B shows the number of colonies present on each selective plate, providing evidence of the ability of HBV
  • the cells were washed and 24 hours later (day 2 post-infection) were transduced with either a lentivirus encoding RFP, HBV 5-6x.33, HBV l l-12x.26, or a 1 : 1 mixture of the lentiviruses encoding the HBV meganucleases.
  • infected cells were treated with DMSO.
  • Cell supernatants were harvested and medium was replaced on days 4, 8, 11, and 13 post-transduction.
  • HBsAg and HBeAg was measured in the cell supernatants by ELISA. Extracellular DNA in the supernatant was also measured at day 13 post-infection.
  • SEQ ID NO: 25 sets forth the amino acid sequence of the HBV 5-6x.4 meganuclease.
  • SEQ ID NO: 51 sets forth the amino acid sequence of the HBV 5-6x.4 meganuclease HBV5-binding subunit.
  • SEQ ID NO: 85 sets forth the nucleic acid sequence of the recognition sequence present in HBV genotype F that corresponds to the HBV 5-6 recognition sequence in HBV genotype A with a G to C substitution at position -3 of the first half-site.
  • SEQ ID NO: 86 sets forth the nucleic acid sequence of the recognition sequence present in HBV genotype E that corresponds to the HBV 7-8 recognition sequence in HBV genotype A with a C to T substitution at position -1 of the first half-site.
  • DNA-binding affinity or "binding affinity” means the tendency of a meganuclease to non-covalently associate with a reference DNA molecule (e.g., a recognition sequence or an arbitrary sequence). Binding affinity is measured by a dissociation constant, Kd.
  • Kd dissociation constant
  • a nuclease has "altered” binding affinity if the Kd of the nuclease for a reference recognition sequence is increased or decreased by a statistically significant (p ⁇ 0.05) amount relative to a reference nuclease.
  • a variable which is described as having values between 0 and 2 can take the values 0, 1 or 2 if the variable is inherently discrete, and can take the values 0.0, 0.1, 0.01, 0.001, or any other real values ⁇ 0 and ⁇ 2 if the variable is inherently continuous.
  • HBV1 Subunit % and "HBV2 Subunit %" represent the amino acid sequence identity between the HBVl -binding and HBV2-binding subunit regions of each meganuclease and the HBVl -binding and HBV2-binding subunit regions, respectively, of the HBV l-2x.2 meganuclease.
  • HBV7 Subunit % and "HBV8 Subunit %" represent the amino acid sequence identity between the HBV7-binding and HBV8-binding subunit regions of each meganuclease and the HBV7-binding and HBV8-binding subunit regions, respectively, of the HBV 7-8x.2 meganuclease.
  • the recombinant DNA construct can comprise two cassettes, three cassettes, four cassettes, or more.
  • a cassette or combination of cassettes can encode any number or combination of an HBV 1-2 meganuclease, an HBV 5-6 meganuclease, an HBV 7-8 meganuclease, and an HBV 11-12 meganuclease.
  • a single cassette can encode an HBV 1-2 meganuclease, an HBV 5-6 meganuclease, an HBV 7-8 meganuclease, and an HBV 11-12 meganuclease.
  • a cassette or combination of cassettes can encode an HBV 5-6 meganuclease and an HBV 11-12 meganuclease.
  • meganucleases of the invention can be delivered as purified protein or as RNA or DNA encoding the meganuclease.
  • meganuclease proteins, or mRNA, or DNA vectors encoding endonucleases are supplied to target cells (e.g., cells in the liver) via injection directly to the target tissue.
  • endonuclease proteins or DNA/mRNA encoding endonucleases, are coupled covalently or, preferably, non-covalently to a nanoparticle or encapsulated within such a nanoparticle using methods known in the art (Sharma, et al.
  • a retroviral, pseudotype or adenoviral associated vector is constructed which encodes the engineered meganuclease and is administered to the subject.
  • the pharmaceutical composition can comprise one or more mRNAs described herein encapsulated within lipid nanoparticles, which are described elsewhere herein.
  • lipid nanoparticles can comprise two or more mRNAs described herein, each encoding an engineered meganuclease of the invention having specificity for a different HBV recognition sequence described herein.
  • lipid nanoparticles can comprise two, three, or four mRNAs described herein, each encoding an engineered meganuclease of the invention having specificity for a different HBV recognition sequence.
  • lipid nanoparticles can comprise two, three, or four mRNAs described herein, each encoding an engineered meganuclease of the invention having specificity for a different HBV recognition sequence.
  • lipid nanoparticles can comprise two, three, or four mRNAs described herein, each encoding an engineered meganuclease of the invention having specificity for a different HBV recognition sequence.
  • lipid nanoparticles
  • Cationic lipids can include, for example, one or more of the following:
  • palmitoyi-oleoyl-nor-arginine PONA
  • MPDACA GUADACA
  • MC3 heptatriaconta-6,9,28,31-tetraen-19-yl 4-(dimethylamino)butanoate)
  • MC3 LenMC3, CP- LenMC3, y-LenMC3, CP-y-LenMC3, MC3MC, MC2MC, MC3 Ether, MC4 Ether, MC3 Amide, Pan-MC3, Pan-MC4 and Pan MC5, l,2-dilinoleyloxy-N,N-dimethylaminopropane (DLinDMA), l,2-dilinolenyloxy-N,N-dimethylaminopropane (DLenDMA), 2,2-dilinoleyl-4- (2-dimethylaminoethyl)-[l,3]-diox
  • the endonuclease can be placed under the control of a tissue-specific promoter that is not active in the packaging cells.
  • a tissue-specific promoter that is not active in the packaging cells.
  • a muscle-specific promoter can be used.
  • muscle-specific promoters include C5-12 (Liu, et al. (2004) Hum Gene Ther. 15:783-92), the muscle-specific creatine kinase (MCK) promoter (Yuasa, et al. (2002) Gene Ther. 9: 1576-88), or the smooth muscle 22 (SM22) promoter (Haase, et al. (2013) BMC Biotechnol.
  • recombinant AAV particles are produced in a mammalian cell line that expresses a transcription repressor that prevents expression of the endonuclease.
  • Transcription repressors are known in the art and include the Tet-Repressor, the Lac-Repressor, the Cro repressor, and the Lambda-repressor.
  • Many nuclear hormone receptors such as the ecdysone receptor also act as transcription repressors in the absence of their cognate hormone ligand.

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PCT/US2017/056638 2016-10-14 2017-10-13 Engineered meganucleases specific for recognition sequences in the hepatitis b virus genome Ceased WO2018071849A2 (en)

Priority Applications (31)

Application Number Priority Date Filing Date Title
DK17804977.1T DK3526323T5 (da) 2016-10-14 2017-10-13 Modificerede meganucleaser der er specifikke for en genkendelsessekvens i hepatitis b virusgenomet
AU2017342536A AU2017342536A1 (en) 2016-10-14 2017-10-13 Engineered meganucleases specific for recognition sequences in the Hepatitis B virus genome
EP17804977.1A EP3526323B1 (en) 2016-10-14 2017-10-13 Engineered meganucleases specific for recognition sequences in the hepatitis b virus genome
IL308894A IL308894A (en) 2016-10-14 2017-10-13 Engineered meganucleases specific for recognition sequences in the hepatitis b virus genome
PE2019000817A PE20191353A1 (es) 2016-10-14 2017-10-13 Meganucleasas disenadas especificamente para el reconocimiento de secuencias en el genoma del virus de la hepatitis b
KR1020197013312A KR102305215B1 (ko) 2016-10-14 2017-10-13 B형 간염 바이러스 게놈 내의 인식 서열에 대해 특이적인 조작된 메가뉴클레아제
KR1020237000425A KR20230010826A (ko) 2016-10-14 2017-10-13 B형 간염 바이러스 게놈 내의 인식 서열에 대해 특이적인 조작된 메가뉴클레아제
CN202311305067.1A CN117402852A (zh) 2016-10-14 2017-10-13 对乙肝病毒基因组中的识别序列特异性的工程化大范围核酸酶
IL265921A IL265921B2 (en) 2016-10-14 2017-10-13 Engineered meganucleases specific for recognition sequences in the hepatitis b virus genome
MX2019004349A MX2019004349A (es) 2016-10-14 2017-10-13 Meganucleasas manipuladas específicamente para el reconocimiento de secuencias en el genoma del virus de la hepatitis b.
EA201990792A EA201990792A1 (ru) 2017-06-30 2017-10-13 Сконструированные мегануклеазы, специфичные к последовательностям распознавания в геноме вируса гепатита b
KR1020217029958A KR20210118240A (ko) 2016-10-14 2017-10-13 B형 간염 바이러스 게놈 내의 인식 서열에 대해 특이적인 조작된 메가뉴클레아제
SG11201903042VA SG11201903042VA (en) 2016-10-14 2017-10-13 Engineered meganucleases specific for recognition sequences in the hepatitis b virus genome
JP2019520125A JP6811857B2 (ja) 2016-10-14 2017-10-13 Ｂ型肝炎ウイルスゲノムの認識配列に特異的な遺伝子操作メガヌクレアーゼ
CN201780074346.8A CN110023495A (zh) 2016-10-14 2017-10-13 对乙肝病毒基因组中的识别序列特异性的工程化大范围核酸酶
US16/342,169 US10662416B2 (en) 2016-10-14 2017-10-13 Engineered meganucleases specific for recognition sequences in the hepatitis B virus genome
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IL317537A IL317537A (en) 2016-10-14 2017-10-13 Engineered megacannolyases specific for recognition sequences in the hepatitis B virus genome
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CONC2019/0003675A CO2019003675A2 (es) 2016-10-14 2019-04-12 Meganucleasas diseñadas especificamente para el reconocimiento de secuencias en el genoma del virus de la hepatitis b.
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