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公开(公告)号：US11427814B2
公开(公告)日：2022-08-30
申请号：US17213169
申请日：2021-03-25
申请人： Encodia, Inc.
摘要： Provided herein are modified cleavases for removing amino acids from peptides, polypeptides, and proteins. Also provided are methods of using the modified cleavases for treating polypeptides, and kits comprising the modified cleavase. In some embodiments, the methods and the kits also include other components for macromolecule sequencing and/or analysis.
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公开(公告)号：US11788080B2
公开(公告)日：2023-10-17
申请号：US17850516
申请日：2022-06-27
申请人： Encodia, Inc.
摘要： Provided herein are modified cleavases for removing amino acids from peptides, polypeptides, and proteins. Also provided are methods of using the modified cleavases for treating polypeptides, and kits comprising the modified cleavase. In some embodiments, the methods and the kits also include other components for macromolecule sequencing and/or analysis.
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公开(公告)号：US12130291B2
公开(公告)日：2024-10-29
申请号：US17819263
申请日：2022-08-11
申请人： Encodia, Inc.
发明人： Mark S. Chee , John M. Beierle , Norihito Muranaka , Kevin L. Gunderson , Michael Phillip Weiner , Lei Shi , Robert C. James , Luca Monfregola
CPC分类号： G01N33/6842 , C40B40/10 , C40B70/00 , G01N33/6845
摘要： Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information. The kits may be used in high-throughput, multiplexed, and/or automated analysis, and are suitable for analysis of a proteome or subset thereof.
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公开(公告)号：US11782062B2
公开(公告)日：2023-10-10
申请号：US18166461
申请日：2023-02-08
申请人： Encodia, Inc.
发明人： Mark S. Chee , John M. Beierle , Norihito Muranaka , Kevin L. Gunderson , Michael Phillip Weiner , Lei Shi , Robert C. James , Luca Monfregola
CPC分类号： G01N33/6842 , C40B40/10 , C40B70/00 , G01N33/6845
摘要： Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information. The kits may be used in high-throughput, multiplexed, and/or automated analysis, and are suitable for analysis of a proteome or subset thereof.
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公开(公告)号：US11639366B2
公开(公告)日：2023-05-02
申请号：US17535516
申请日：2021-11-24
申请人： Encodia, Inc.
发明人： Robert C. James , Stephen Verespy, III , Eric Cunyu Zhou , Eric Okerberg , Kelsey Rose Schramma , Fei Huang
IPC分类号： C07C49/603 , C07K1/13 , G01N33/58 , G01N33/68 , C07K1/107 , C07D235/02
摘要： The present invention relates to methods to use cyclohexan-1,2-dione (CHD) groups to attach labels, linkers, and other molecules to a target compound comprising a CHD-reactive group such as a guanidine, amidine, urea, thiourea and the like. Methods of the invention include milder conditions than those previously known for promoting reaction of CHD with CHD-reactive groups, which makes the methods suitable for use with base-sensitive compounds and complex biomolecules. Methods of the invention are especially useful for attaching linking and labeling groups to a peptide that comprises at least one arginine residue, and can also be used to link such peptides to other target molecules such as nucleic acids. The invention also provides CHD-containing conjugation reagents and compositions comprising CHD-containing intermediates, and precursors useful for making CHD-containing compounds that can be used in the methods of the invention.
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公开(公告)号：US20230021091A1
公开(公告)日：2023-01-19
申请号：US17850516
申请日：2022-06-27
申请人： Encodia, Inc.
摘要： Provided herein are modified cleavases for removing amino acids from peptides, polypeptides, and proteins. Also provided are methods of using the modified cleavases for treating polypeptides, and kits comprising the modified cleavase. In some embodiments, the methods and the kits also include other components for macromolecule sequencing and/or analysis.
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公开(公告)号：US11513126B2
公开(公告)日：2022-11-29
申请号：US16760028
申请日：2018-10-31
申请人： Encodia, Inc.
发明人： Mark S. Chee , John M. Beierle , Norihito Muranaka , Kevin L. Gunderson , Michael Phillip Weiner , Lei Shi , Robert C. James , Luca Monfregola
IPC分类号： C12Q1/6804 , G01N33/68 , C40B40/10 , C40B70/00
摘要： Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information. The kits may be used in high-throughput, multiplexed, and/or automated analysis, and are suitable for analysis of a proteome or subset thereof.
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公开(公告)号：US20220144885A1
公开(公告)日：2022-05-12
申请号：US17535516
申请日：2021-11-24
申请人： Encodia, Inc.
发明人： Robert C. James , Stephen Verespy, III , Eric Cunyu Zhou , Eric Okerberg , Kelsey Rose Schramma , Fei HUANG
摘要： The present invention relates to methods to use cyclohexan-1,2-dione (CHD) groups to attach labels, linkers, and other molecules to a target compound comprising a CHD-reactive group such as a guanidine, amidine, urea, thiourea and the like. Methods of the invention include milder conditions than those previously known for promoting reaction of CHD with CHD-reactive groups, which makes the methods suitable for use with base-sensitive compounds and complex biomolecules. Methods of the invention are especially useful for attaching linking and labeling groups to a peptide that comprises at least one arginine residue, and can also be used to link such peptides to other target molecules such as nucleic acids. The invention also provides CHD-containing conjugation reagents and compositions comprising CHD-containing intermediates, and precursors useful for making CHD-containing compounds that can be used in the methods of the invention.
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