CA3081451A1 - A method for assaying interactions between biological targets and binding agents - Google Patents

A method for assaying interactions between biological targets and binding agents Download PDF

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Publication number
CA3081451A1
CA3081451A1 CA3081451A CA3081451A CA3081451A1 CA 3081451 A1 CA3081451 A1 CA 3081451A1 CA 3081451 A CA3081451 A CA 3081451A CA 3081451 A CA3081451 A CA 3081451A CA 3081451 A1 CA3081451 A1 CA 3081451A1
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Canada
Prior art keywords
tag
recording
coding
immobilized
binding
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Pending
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CA3081451A
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English (en)
French (fr)
Inventor
Mark S. Chee
Kevin Gunderson
Michael Philip Weiner
Lei Shi
Norihito MURANAKA
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Encodia Inc
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Encodia Inc
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Application filed by Encodia Inc filed Critical Encodia Inc
Publication of CA3081451A1 publication Critical patent/CA3081451A1/en
Pending legal-status Critical Current

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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034Isolating an individual clone by screening libraries
    • C12N15/1065Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6804Nucleic acid analysis using immunogens
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2458/00Labels used in chemical analysis of biological material
    • G01N2458/10Oligonucleotides as tagging agents for labelling antibodies

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Zoology (AREA)
  • Immunology (AREA)
  • Wood Science & Technology (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biomedical Technology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Physics & Mathematics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Pathology (AREA)
  • Biophysics (AREA)
  • Hematology (AREA)
  • Urology & Nephrology (AREA)
  • Food Science & Technology (AREA)
  • General Physics & Mathematics (AREA)
  • Medicinal Chemistry (AREA)
  • Cell Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Plant Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Peptides Or Proteins (AREA)
CA3081451A 2017-10-31 2018-10-31 A method for assaying interactions between biological targets and binding agents Pending CA3081451A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201762579840P 2017-10-31 2017-10-31
US62/579,840 2017-10-31
US201762582916P 2017-11-07 2017-11-07
US62/582,916 2017-11-07
PCT/US2018/058583 WO2019089851A1 (en) 2017-10-31 2018-10-31 Methods and kits using nucleic acid encoding and/or label

Publications (1)

Publication Number Publication Date
CA3081451A1 true CA3081451A1 (en) 2019-05-09

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CA3081451A Pending CA3081451A1 (en) 2017-10-31 2018-10-31 A method for assaying interactions between biological targets and binding agents

Country Status (7)

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US (3) US20210355483A1 (enExample)
EP (1) EP3704246A4 (enExample)
JP (1) JP7253833B2 (enExample)
AU (1) AU2018358247A1 (enExample)
CA (1) CA3081451A1 (enExample)
SG (1) SG11202003923PA (enExample)
WO (1) WO2019089851A1 (enExample)

Families Citing this family (46)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
DE112012002570B4 (de) 2011-06-23 2023-11-23 Board Of Regents, The University Of Texas System Identifizieren von Peptiden auf der Einzelmolekülebene
US11435358B2 (en) 2011-06-23 2022-09-06 Board Of Regents, The University Of Texas System Single molecule peptide sequencing
EP3543703A1 (en) 2014-09-15 2019-09-25 Board of Regents, The University of Texas System Improved single molecule peptide sequencing
KR102741603B1 (ko) 2016-05-02 2024-12-16 엔코디아, 인코포레이티드 암호화 핵산을 사용한 거대분자 분석
EP3548652B1 (en) 2016-12-01 2024-04-03 Nautilus Subsidiary, Inc. Methods of assaying proteins
SG11202003923PA (en) 2017-10-31 2020-05-28 Encodia Inc Methods and kits using nucleic acid encoding and/or label
KR102556494B1 (ko) 2017-10-31 2023-07-18 엔코디아, 인코포레이티드 핵산 암호화 및/또는 표지를 이용한 분석용 키트
CA3086915A1 (en) 2017-12-29 2019-07-04 Sujal M. Patel Decoding approaches for protein identification
WO2019195633A1 (en) 2018-04-04 2019-10-10 Ignite Biosciences, Inc. Methods of generating nanoarrays and microarrays
US20210239705A1 (en) * 2018-06-06 2021-08-05 Nautilus Biotechnology, Inc. Methods and applications of protein identification
WO2020014586A1 (en) 2018-07-12 2020-01-16 Board Of Regents, The University Of Texas System Molecular neighborhood detection by oligonucleotides
WO2020051162A1 (en) * 2018-09-04 2020-03-12 Encodia, Inc. Proximity interaction analysis
EP3884048A4 (en) 2018-11-20 2022-08-17 Nautilus Biotechnology, Inc. DESIGN AND SELECTION OF AFFINITY REAGENTS
EP3963091A4 (en) 2019-04-29 2023-07-19 Nautilus Biotechnology, Inc. METHODS AND SYSTEMS FOR ON-CHIP INTEGRATED SINGLE MOLECULE DETECTION
EP3963070A4 (en) 2019-04-30 2023-02-22 Encodia, Inc. METHODS OF PREPARATION OF ANALYTES AND RELATED KITS
US20220235405A1 (en) * 2019-05-20 2022-07-28 Encodia, Inc. Methods and related kits for spatial analysis
US12377635B2 (en) 2019-10-30 2025-08-05 Nautilus Subsidiary, Inc. Flow cell systems and methods
IL289295B2 (en) * 2019-12-23 2025-07-01 Illumina Cambridge Ltd A nanoparticle with a single site for attaching a polynucleotide template
EP4073263A4 (en) 2020-01-07 2023-11-08 Encodia, Inc. METHOD FOR STABLE COMPLEX FORMATION AND CORRESPONDING KITS
WO2021141924A1 (en) 2020-01-07 2021-07-15 Encodia, Inc. Methods for stable complex formation and related kits
WO2021141922A1 (en) * 2020-01-07 2021-07-15 Encodia, Inc. Methods for information transfer and related kits
WO2021163625A1 (en) * 2020-02-12 2021-08-19 Universal Sequencing Technology Corporation Methods for intracellular barcoding and spatial barcoding
US20230146476A1 (en) * 2020-02-29 2023-05-11 President And Fellows Of Harvard College Nanoswitch caliper trains for high-throughput, high-resolution structural analysis of biomolecules
JP2023538074A (ja) 2020-08-19 2023-09-06 エンコディア, インコーポレイテッド 連続エンコーディング方法及び関連キット
WO2022067019A1 (en) * 2020-09-26 2022-03-31 The Regents Of The University Of California Hybrid protocols and barcoding schemes for multiple sequencing technologies
US20230220589A1 (en) * 2020-09-30 2023-07-13 Encodia, Inc. Polypeptide terminal binders and uses thereof
KR20230118570A (ko) 2020-11-11 2023-08-11 노틸러스 서브시디어리, 인크. 강화된 결합 및 검출 특성을 갖는 친화성 시약
US12467081B2 (en) 2020-11-23 2025-11-11 Pleno, Inc. Encoded endonuclease assays
WO2022115608A1 (en) * 2020-11-25 2022-06-02 Alida Biosciences, Inc. Multiplexed profiling of rna and dna modifications
WO2022251457A2 (en) * 2021-05-26 2022-12-01 Board Of Regents, The University Of Texas System Compositions, methods, and utility of conjugated biomolecule barcodes
CN113908589B (zh) * 2021-10-08 2022-09-27 天津工业大学 一种表面印迹抗体的疏水电荷诱导模式膜层析介质及其制备方法
US12474346B2 (en) 2021-11-05 2025-11-18 Encodia, Inc. Methods and kits for multicycle encoding assay
EP4437135A4 (en) * 2021-11-23 2025-12-03 Pleno Inc CODED ENDONUCLEASE ASSAYS
EP4437125A1 (en) * 2021-11-24 2024-10-02 Alida Biosciences, Inc. Rna and dna analysis using engineered surfaces
US20250101496A1 (en) * 2021-12-21 2025-03-27 Encodia, Inc. Methods for balancing encoding signals of analytes
EP4206674B1 (en) 2021-12-28 2025-10-22 Encodia, Inc. High-throughput serotyping and antibody profiling assays
CN120092180A (zh) 2022-08-02 2025-06-03 格里菲克生物技术公司 通过可聚合分子偶联进行蛋白质测序
WO2024040236A2 (en) 2022-08-19 2024-02-22 Abrus Bio, Inc. Determination of protein information by recoding amino acid polymers into dna polymers
WO2024050553A1 (en) * 2022-09-01 2024-03-07 The Johns Hopkins University Methods for measuring telomere length
US20240200058A1 (en) * 2022-12-06 2024-06-20 Shifeng Li Methods and appratus for protein and peptide sequencing
CN115881218B (zh) * 2022-12-15 2023-06-09 哈尔滨星云医学检验所有限公司 用于全基因组关联分析的基因自动选择方法
EP4638786A1 (en) * 2022-12-23 2025-10-29 Illumina, Inc. Spatial mrna/protein co-assays using aptamers
US20240327902A1 (en) * 2023-03-31 2024-10-03 Shifeng Li Methods for detecting and analysis of proteins
WO2025085861A1 (en) * 2023-10-20 2025-04-24 Spectral Therapeutics, Inc. Composite particles for use in generating spectrally encoded libraries of chemical compounds, and methods of making and using the same
US20250154584A1 (en) * 2023-11-09 2025-05-15 Encodia, Inc. Methods for identifying polypeptides
WO2025144972A1 (en) * 2023-12-29 2025-07-03 Illumina, Inc. Materials and methods for preparation of a spatial transcriptomics library

Family Cites Families (51)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5573905A (en) * 1992-03-30 1996-11-12 The Scripps Research Institute Encoded combinatorial chemical libraries
US6875851B1 (en) 1999-03-05 2005-04-05 University Of Georgia Research Foundation, Inc. Prolyl tripeptidyl peptidases nucleic acid of Porphyromonas gingivalis
JP2003536048A (ja) 1999-03-23 2003-12-02 バイオヴェイション リミテッド タンパク質の単離および分析
US7306904B2 (en) 2000-02-18 2007-12-11 Olink Ab Methods and kits for proximity probing
US6511809B2 (en) 2000-06-13 2003-01-28 E. I. Du Pont De Nemours And Company Method for the detection of an analyte by means of a nucleic acid reporter
US6800453B2 (en) 2001-01-23 2004-10-05 President And Fellows Of Harvard College Nucleic-acid programmable protein arrays
EP1401850A1 (en) 2001-06-20 2004-03-31 Nuevolution A/S Nucleoside derivatives for library preparation
EP1451356A1 (en) 2001-11-23 2004-09-01 Simon Fredriksson Method and kit for proximity probing with multivalent proximity probes
EP1578935A2 (en) 2002-10-10 2005-09-28 Diversa Corporation Proteases, nucleic acids encoding them and methods for making and using them
WO2005015239A2 (en) 2003-08-07 2005-02-17 Cornell Research Foundation, Inc. Method for n-terminal labeling of proteins
US7198900B2 (en) 2003-08-29 2007-04-03 Applera Corporation Multiplex detection compositions, methods, and kits
ATE447626T1 (de) * 2003-09-18 2009-11-15 Nuevolution As Methode zur gewinnung struktureller informationen kodierter moleküle und zur selektion von verbindungen
EP1561755A2 (en) 2003-10-16 2005-08-10 Shimadzu Corporation Method for derivatizing protein or peptide to sulfonic acid derivative
JP5646127B2 (ja) 2003-12-17 2014-12-24 グラクソスミスクライン・リミテッド・ライアビリティ・カンパニーGlaxoSmithKline LLC コードされたライブラリーの合成のための方法
DE602005017370D1 (de) 2004-03-22 2009-12-10 Nuevolution As Ligationscodierung unter verwendung von oligonukleotidbausteinen
AU2005241003B2 (en) 2004-04-14 2011-05-19 President And Fellows Of Harvard College Nucleic-acid programmable protein arrays
US20060199279A1 (en) 2005-03-07 2006-09-07 Viorica Lopez-Avila Methods for identifying post-translationally modified polypeptides
US7883848B2 (en) 2005-07-08 2011-02-08 Olink Ab Regulation analysis by cis reactivity, RACR
LT3018206T (lt) 2005-12-01 2021-12-10 Nuevolution A/S Fermentiniai kodavimo būdai, skirti didelių bibliotekų efektyviai sintezei
WO2009050261A1 (en) 2007-10-19 2009-04-23 Pronota N.V. Preparation of samples for proteome analysis
WO2010065322A1 (en) 2008-12-01 2010-06-10 Research Triangle Institute Concurrent identification of multitudes of polypeptides
US9085798B2 (en) 2009-04-30 2015-07-21 Prognosys Biosciences, Inc. Nucleic acid constructs and methods of use
WO2011056185A2 (en) 2009-11-04 2011-05-12 President And Fellows Of Harvard College Reactivity-dependent and interaction-dependent pcr
AU2010328226A1 (en) 2009-12-07 2012-06-28 Prognosys Biosciences, Inc. Peptide display arrays
US20110245101A1 (en) 2010-04-05 2011-10-06 Prognosys Biosciences, Inc. Co-localization affinity assays
GB201101621D0 (en) 2011-01-31 2011-03-16 Olink Ab Method and product
EP3150750B1 (en) 2011-04-08 2018-12-26 Prognosys Biosciences, Inc. Peptide constructs and assay systems
US20130052665A1 (en) 2011-08-25 2013-02-28 Bruce Xuefeng Ling Methods for diagnosis of systemic juvenile idiopathic arthritis
US9335292B2 (en) 2011-10-13 2016-05-10 Auburn University Electrochemical proximity assay
US9435810B2 (en) 2013-03-15 2016-09-06 Washington University Molecules and methods for iterative polypeptide analysis and processing
WO2014176355A1 (en) 2013-04-23 2014-10-30 President And Fellows Of Harvard College In situ interaction determination
WO2015070037A2 (en) * 2013-11-08 2015-05-14 Prognosys Biosciences, Inc. Polynucleotide conjugates and methods for analyte detection
US9834814B2 (en) * 2013-11-22 2017-12-05 Agilent Technologies, Inc. Spatial molecular barcoding of in situ nucleic acids
WO2015148606A2 (en) 2014-03-25 2015-10-01 President And Fellows Of Harvard College Barcoded protein array for multiplex single-molecule interaction profiling
EP3143165A4 (en) 2014-05-15 2018-05-16 Two Pore Guys, Inc. Scaffold data storage and target detection in a sample using a nanopore
CN113249435B (zh) 2014-06-26 2024-09-03 10X基因组学有限公司 分析来自单个细胞或细胞群体的核酸的方法
WO2016011364A1 (en) 2014-07-18 2016-01-21 Cdi Laboratories, Inc. Methods and compositions to identify, quantify, and characterize target analytes and binding moieties
WO2016019360A1 (en) 2014-08-01 2016-02-04 Dovetail Genomics Llc Tagging nucleic acids for sequence assembly
EP3543703A1 (en) 2014-09-15 2019-09-25 Board of Regents, The University of Texas System Improved single molecule peptide sequencing
PL3650458T3 (pl) * 2015-02-24 2023-11-06 City Of Hope Platformy do analiz przesiewowych bibliotek kodowanych chemicznie i adresowanych przestrzennie
EP3262192B1 (en) 2015-02-27 2020-09-16 Becton, Dickinson and Company Spatially addressable molecular barcoding
US20180284125A1 (en) 2015-03-11 2018-10-04 The Broad Institute, Inc. Proteomic analysis with nucleic acid identifiers
KR102741603B1 (ko) * 2016-05-02 2024-12-16 엔코디아, 인코포레이티드 암호화 핵산을 사용한 거대분자 분석
WO2018005720A1 (en) 2016-06-30 2018-01-04 President And Fellows Of Harvard College Method of determining the molecular binding between libraries of molecules
CN109923216B (zh) 2016-08-31 2024-08-02 哈佛学院董事及会员团体 将生物分子的检测组合到使用荧光原位测序的单个试验的方法
EP4029939B1 (en) 2017-01-30 2023-06-28 10X Genomics, Inc. Methods and systems for droplet-based single cell barcoding
US20180251825A1 (en) 2017-02-02 2018-09-06 New York Genome Center Inc. Methods and compositions for identifying or quantifying targets in a biological sample
US20200348307A1 (en) 2017-10-31 2020-11-05 Encodia, Inc. Methods and compositions for polypeptide analysis
SG11202003923PA (en) 2017-10-31 2020-05-28 Encodia Inc Methods and kits using nucleic acid encoding and/or label
KR102556494B1 (ko) 2017-10-31 2023-07-18 엔코디아, 인코포레이티드 핵산 암호화 및/또는 표지를 이용한 분석용 키트
CA3086915A1 (en) 2017-12-29 2019-07-04 Sujal M. Patel Decoding approaches for protein identification

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JP2021501576A (ja) 2021-01-21
US20210355483A1 (en) 2021-11-18
WO2019089851A8 (en) 2020-05-28
EP3704246A1 (en) 2020-09-09
JP7253833B2 (ja) 2023-04-07
AU2018358247A1 (en) 2020-05-21
US12129463B2 (en) 2024-10-29
US20250051756A1 (en) 2025-02-13
EP3704246A4 (en) 2021-08-11
US12467049B2 (en) 2025-11-11
SG11202003923PA (en) 2020-05-28
WO2019089851A1 (en) 2019-05-09
US20230340458A1 (en) 2023-10-26

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