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1. 发明授权

US11326209B2 Cell-based genomic recorded accumulative memory 有权
公开(公告)号：US11326209B2
公开(公告)日：2022-05-10
申请号：US14536128
申请日：2014-11-07
申请人： Massachusetts Institute of Technology , Whitehead Institute for Biomedical Research
发明人： Joseph M. Jacobson , Noah Jakimo , Naama Kanarek , David Sabatini
IPC分类号： C12Q1/6874 , C12Q1/6897 , G06N3/12 , C12N15/70 , C12N15/10 , C12N15/63
摘要： The present invention relates to a cell based genomic Recorded Accumulative Memory (geRAM) system (also referred to herein as Genomically Encoded Memory (GEM)) for recoding data (i.e., changes in nucleic acid sequences in cellular DNA in response to physical and/or chemical signal(s)) from the cellular environment.

2. 发明申请

US20160244784A1 Population-Hastened Assembly Genetic Engineering 审中-公开
标题翻译：人口加速大会遗传工程
公开(公告)号：US20160244784A1
公开(公告)日：2016-08-25
申请号：US15045243
申请日：2016-02-16
申请人： Massachusetts Institute of Technology
发明人： Joseph M. Jacobson , Noah Jakimo , Lisa Nip
IPC分类号： C12N15/90
CPC分类号： C12N15/902 , C07K2319/80 , C07K2319/85 , C12N9/16
摘要： Population-Hastened Assembly Genetic Engineering is a method for continuous genome recoding using a mixed population of cells. Nucleic acid donors are distributed amongst a population of cells that continuously transfer nucleic acids to achieve asynchronous recoding of genetic information within a subpopulation of the cells. Recombination is achieved with biochemical systems compatible with virtually any organism. An engineered directed endonuclease comprises a nucleic acid recognition domain, a nucleic acid endonuclease domain, and a linker fusing or causing interaction between the nucleic acid recognition domain and the nucleic acid endonuclease domain. The method includes causing at least one engineered directed endonuclease to create a nick in a nucleic acid strand, the nick being offset from the recognition sequence of the nucleic acid recognition domain; causing homologous recombination of the strand with a donor nucleotide to create a modified genome; and replicating the modified genome.
摘要翻译：人口加速组装遗传工程是使用混合细胞群进行连续基因组重编的方法。核酸供体分布在连续转移核酸的细胞群中，以实现细胞亚群内遗传信息的异步重新编码。使用与几乎任何生物相容的生化系统实现重组。工程引导的内切核酸酶包含核酸识别结构域，核酸内切核酸酶结构域和融合或引起核酸识别结构域与核酸内切核酸酶结构域之间相互作用的连接体。该方法包括使至少一个工程化的定向内切核酸酶在核酸链中产生切口，所述切口与核酸识别结构域的识别序列相抵消; 引起该链与供体核苷酸的同源重组以产生修饰的基因组; 并复制修饰的基因组。

3. 发明申请

US20180282722A1 Chimeric DNA:RNA Guide for High Accuracy Cas9 Genome Editing 审中-公开
公开(公告)号：US20180282722A1
公开(公告)日：2018-10-04
申请号：US15820425
申请日：2017-11-21
申请人： Massachusetts Institute of Technology
发明人： Noah Jakimo , Pranam Chatterjee , Joseph M. Jacobson
IPC分类号： C12N15/11 , C12N9/22 , C12N9/96 , C12N15/90
摘要： A chimeric DNA:RNA guide for very high accuracy Cas9 genome editing employs nucleotide-type substitutions in nucleic acid-guided endonucleases for enhanced specificity. The CRISPR-Cas9 gene editing system is manipulated to generate chimeric DNA:RNA guide strands to minimize the off-target cleavage events of the S. pyogenes Cas9 endonuclease. A DNA:RNA chimeric guide strand is sufficient to guide Cas9 to a specified target sequence for indel formation and minimize off-target cleavage events due to the specificity conferred by DNA-DNA interactions. Use of chimeric mismatch-evading lowered-thermostability guides (“melt-guides”) demonstrate that nucleotide-type substitutions in the spacer can reduce cleavage of sequences mismatched by as few as a single base pair. The chimeric mismatch-evading lowered-thermostability guides replace most gRNA spacer positions with DNA bases to suppress mismatched targets under Cas9's catalytic threshold.

4. 发明申请

US20230043848A1 Programmable Modification of DNA 有权
公开(公告)号：US20230043848A1
公开(公告)日：2023-02-09
申请号：US17865375
申请日：2022-07-14
申请人： Massachusetts Institute of Technology
发明人： Noah Jakimo , Peter A. Carr , Joseph M. Jacobson
IPC分类号： C12N15/63 , C12N15/10
摘要： A self-reconfiguring genome uses a cassette having operons or DNA sequences that code for guide RNA, reverse transcriptase, donor RNA, and a CRISPR cleavage enzyme. A self-reconfiguring genome may be based on lambda recombineering of in situ generated oligonucleotides. A method for programmable self-modification of a cellular genome includes transcribing guide RNA from a self-reconfiguring cassette, associating the transcribed guideRNA with the CRISPR enzyme, intercalating a region of complimentary sequence within an integration site of the genome, cutting upstream of a PAM site within the integration site; transcribing the donorRNA, translating donorRNA to double-stranded DNA, and recombining the double-stranded DNA via homologous recombination at the cut site of the integration site. A set of cascadable and multiplexable genetic logic gates with a universal RNA input/output based on single-strand annealing or non-homologous end joining, comprises transcription promoters or terminators, homologous regions, DNA sequences, RNA, and enzymes from the CRISPR system.

5. 发明申请

US20210324382A1 Chimeric DNA:RNA Guide for High Accuracy Cas9 Genome Editing 有权
公开(公告)号：US20210324382A1
公开(公告)日：2021-10-21
申请号：US17156492
申请日：2021-01-22
申请人： Massachusetts Institute of Technology
发明人： Noah Jakimo , Pranam Chatterjee , Joseph M. Jacobson
IPC分类号： C12N15/11 , C12N9/22 , C12N15/90 , C12N9/96
摘要： A chimeric DNA:RNA guide for very high accuracy Cas9 genome editing employs nucleotide-type substitutions in nucleic acid-guided endonucleases for enhanced specificity. The CRISPR-Cas9 gene editing system is manipulated to generate chimeric DNA:RNA guide strands to minimize the off-target cleavage events of the S. pyogenes Cas9 endonuclease. A DNA:RNA chimeric guide strand is sufficient to guide Cas9 to a specified target sequence for indel formation and minimize off-target cleavage events due to the specificity conferred by DNA-DNA interactions. Use of chimeric mismatch-evading lowered-thermostability guides (“melt-guides”) demonstrate that nucleotide-type substitutions in the spacer can reduce cleavage of sequences mismatched by as few as a single base pair. The chimeric mismatch-evading lowered-thermostability guides replace most gRNA spacer positions with DNA bases to suppress mismatched targets under Cas9's catalytic threshold.

6. 发明申请

US20200048658A1 Population-Hastened Assembly Genetic Engineering 审中-公开
公开(公告)号：US20200048658A1
公开(公告)日：2020-02-13
申请号：US16443841
申请日：2019-06-17
申请人： Massachusetts Institute of Technology
发明人： Joseph M. Jacobson , Noah Jakimo , Lisa Nip
IPC分类号： C12N15/90 , C12N9/16
摘要： Population-Hastened Assembly Genetic Engineering is a method for continuous genome recoding using a mixed population of cells. Nucleic acid donors are distributed amongst a population of cells that continuously transfer nucleic acids to achieve asynchronous recoding of genetic information within a subpopulation of the cells. Recombination is achieved with biochemical systems compatible with virtually any organism. An engineered directed endonuclease comprises a nucleic acid recognition domain, a nucleic acid endonuclease domain, and a linker fusing or causing interaction between the nucleic acid recognition domain and the nucleic acid endonuclease domain. The method includes causing at least one engineered directed endonuclease to create a nick in a nucleic acid strand, the nick being offset from the recognition sequence of the nucleic acid recognition domain; causing homologous recombination of the strand with a donor nucleotide to create a modified genome; and replicating the modified genome.

7. 发明申请

US20180298391A1 Programmable Modification of DNA 审中-公开
公开(公告)号：US20180298391A1
公开(公告)日：2018-10-18
申请号：US15905817
申请日：2018-02-26
申请人： Massachusetts Institute of Technology
发明人： Noah Jakimo , Peter A. Carr , Joseph M. Jacobson
IPC分类号： C12N15/63 , C12N15/10
摘要： A self-reconfiguring genome uses a cassette having operons or DNA sequences that code for guide RNA, reverse transcriptase, donor RNA, and a CRISPR cleavage enzyme. A self-reconfiguring genome may be based on lambda recombineering of in situ generated oligonucleotides. A method for programmable self-modification of a cellular genome includes transcribing guide RNA from a self-reconfiguring cassette, associating the transcribed guideRNA with the CRISPR enzyme, intercalcating a region of complimentary sequence within an integration site of the genome, cutting upstream of a PAM site within the integration site; transcribing the donorRNA, translating donorRNA to double-stranded DNA, and recombining the double-stranded DNA via homologous recombination at the cut site of the integration site. A set of cascadable and multiplexable genetic logic gates with a universal RNA input/output based on single-strand annealing or non-homologous end joining, comprises transcription promoters or terminators, homologous regions, DNA sequences, RNA, and enzymes from the CRISPR system.

8. 发明申请

US20150133315A1 CELL-BASED GENOMIC RECORDED ACCUMULATIVE MEMORY 审中-公开
标题翻译：基于细胞的基因记录记忆累积记忆
公开(公告)号：US20150133315A1
公开(公告)日：2015-05-14
申请号：US14536128
申请日：2014-11-07
申请人： Massachusetts Institute of Technology
发明人： Joseph M. Jacobson , Noah Jakimo , Naama Kanarek , David Sabatini
IPC分类号： C12Q1/68 , C12N15/70
CPC分类号： C12Q1/6874 , C12N15/102 , C12N15/63 , C12N15/70 , C12Q1/6897 , G06N3/123
摘要： The present invention relates to a cell based genomic Recorded Accumulative Memory (geRAM) system (also referred to herein as Genomically Encoded Memory (GEM)) for recoding data (i.e., changes in nucleic acid sequences in cellular DNA in response to physical and/or chemical signal(s)) from the cellular environment.
摘要翻译：本发明涉及用于重新编码数据的基于细胞的基因组记录累积存储器（geRAM）系统（本文中也称为基因编码存储器（GEM）））（即，响应于物理和/或数据的细胞DNA中的核酸序列的变化）化学信号）。

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