AU2018358247A1 - Methods and kits using nucleic acid encoding and/or label - Google Patents

Methods and kits using nucleic acid encoding and/or label Download PDF

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Publication number
AU2018358247A1
AU2018358247A1 AU2018358247A AU2018358247A AU2018358247A1 AU 2018358247 A1 AU2018358247 A1 AU 2018358247A1 AU 2018358247 A AU2018358247 A AU 2018358247A AU 2018358247 A AU2018358247 A AU 2018358247A AU 2018358247 A1 AU2018358247 A1 AU 2018358247A1
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AU
Australia
Prior art keywords
tag
recording
coding
immobilized
binding
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Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Abandoned
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AU2018358247A
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English (en)
Inventor
Mark S. Chee
Kevin Gunderson
Norihito MURANAKA
Lei Shi
Michael Philip Weiner
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Encodia Inc
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Encodia Inc
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Filing date
Publication date
Application filed by Encodia Inc filed Critical Encodia Inc
Publication of AU2018358247A1 publication Critical patent/AU2018358247A1/en
Abandoned 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)
AU2018358247A 2017-10-31 2018-10-31 Methods and kits using nucleic acid encoding and/or label Abandoned AU2018358247A1 (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
AU2018358247A1 true AU2018358247A1 (en) 2020-05-21

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Application Number Title Priority Date Filing Date
AU2018358247A Abandoned AU2018358247A1 (en) 2017-10-31 2018-10-31 Methods and kits using nucleic acid encoding and/or label

Country Status (7)

Country Link
US (3) US20210355483A1 (https=)
EP (1) EP3704246A4 (https=)
JP (1) JP7253833B2 (https=)
AU (1) AU2018358247A1 (https=)
CA (1) CA3081451A1 (https=)
SG (1) SG11202003923PA (https=)
WO (1) WO2019089851A1 (https=)

Families Citing this family (51)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11435358B2 (en) 2011-06-23 2022-09-06 Board Of Regents, The University Of Texas System Single molecule peptide sequencing
CA2839702C (en) 2011-06-23 2021-04-20 Board Of Regents, The University Of Texas System Identifying peptides at the single molecule level
CA3208970A1 (en) 2014-09-15 2016-05-06 Board Of Regents, The University Of Texas System Improved single molecule peptide sequencing
EP3452591B1 (en) 2016-05-02 2023-08-16 Encodia, Inc. Macromolecule analysis employing nucleic acid encoding
EP3548652B1 (en) 2016-12-01 2024-04-03 Nautilus Subsidiary, Inc. Methods of assaying proteins
CN111566261B (zh) 2017-08-18 2025-03-25 诺迪勒思附属公司 选择结合试剂的方法
SG11202003923PA (en) 2017-10-31 2020-05-28 Encodia Inc Methods and kits using nucleic acid encoding and/or label
JP7390027B2 (ja) 2017-10-31 2023-12-01 エンコディア, インコーポレイテッド 核酸エンコーディングおよび/または標識を使用する解析のためのキット
KR20250152680A (ko) 2017-12-29 2025-10-23 노틸러스 서브시디어리, 인크. 단백질 식별을 위한 디코딩 접근법
EP3775196A4 (en) 2018-04-04 2021-12-22 Nautilus Biotechnology, Inc. METHOD FOR GENERATING NANOARRAYS AND MICROARRAYS
US20210239705A1 (en) * 2018-06-06 2021-08-05 Nautilus Biotechnology, Inc. Methods and applications of protein identification
CA3110800A1 (en) 2018-07-12 2020-01-16 Board Of Regents, The University Of Texas System Molecular neighborhood detection by oligonucleotides
EP3847253A4 (en) * 2018-09-04 2022-05-18 Encodia, Inc. Proximity interaction analysis
CA3117476A1 (en) 2018-10-05 2020-04-09 Board Of Regents, The University Of Texas System Solid-phase n-terminal peptide capture and release
US11993865B2 (en) 2018-11-20 2024-05-28 Nautilus Subsidiary, Inc. Selection of affinity reagents
CN114126476B (zh) 2019-04-23 2025-09-09 Encodia公司 用于蛋白质的空间分析的方法及相关试剂盒
CA3135206A1 (en) 2019-04-29 2020-11-05 Pierre Indermuhle Methods and systems for integrated on-chip single-molecule detection
CN114072499B (zh) 2019-04-30 2024-08-06 Encodia公司 用于制备分析物的方法和相关试剂盒
JP7578294B2 (ja) * 2019-05-20 2024-11-06 エンコディア, インコーポレイテッド 空間分析のための方法および関連キット
WO2021087402A1 (en) 2019-10-30 2021-05-06 Nautilus Biotechnology, Inc. Flow cell systems and methods
CA3144528A1 (en) * 2019-12-23 2021-07-01 Illumina, Inc. Nanoparticle with single site for template polynucleotide attachment
WO2021141922A1 (en) * 2020-01-07 2021-07-15 Encodia, Inc. Methods for information transfer and related kits
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
US20230081062A1 (en) * 2020-02-12 2023-03-16 Universal Sequencing Technology Corporation Methods for intracellular barcoding and spatial barcoding
WO2021174071A1 (en) * 2020-02-29 2021-09-02 President And Fellows Of Harvard College Nanoswitch caliper trains for high-throughput, high-resolution structural analysis of biomolecules
EP4196581B1 (en) 2020-08-19 2026-02-25 Encodia, Inc. Sequential encoding methods and related kits
US20230357834A1 (en) * 2020-09-26 2023-11-09 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
AU2021378290B2 (en) 2020-11-11 2025-10-30 Nautilus Subsidiary, Inc. Affinity reagents having enhanced binding and detection characteristics
WO2023096675A1 (en) * 2021-11-23 2023-06-01 Pleno, Inc. Encoded endonuclease assays
US12467081B2 (en) 2020-11-23 2025-11-11 Pleno, Inc. Encoded endonuclease assays
EP4251760A1 (en) * 2020-11-25 2023-10-04 Alida Biosciences, Inc. Multiplexed profiling of rna and dna modifications
CN117813506A (zh) * 2021-05-26 2024-04-02 德克萨斯大学系统董事会 缀合的生物分子条形码的组合物、方法和效用
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
AU2022397404A1 (en) 2021-11-24 2024-06-13 Alida Biosciences, Inc. Rna and dna analysis using engineered surfaces
AU2022402132A1 (en) 2021-11-30 2024-05-30 Nautilus Subsidiary, Inc. Particle-based isolation of proteins and other analytes
WO2023122698A1 (en) * 2021-12-21 2023-06-29 Encodia, Inc. Methods for balancing encoding signals of analytes
EP4453244A4 (en) * 2021-12-23 2025-12-24 Takara Bio Usa Inc METHODS AND COMPOSITIONS FOR THE PRODUCTION OF IDENTIFIABLE NUCLEIC ACID COLLECTIONS FROM CELLULAR SOURCES
US12043862B2 (en) * 2021-12-28 2024-07-23 Encodia, Inc. High-throughput serotyping and antibody profiling assays
EP4565882A1 (en) 2022-08-02 2025-06-11 Glyphic Biotechnologies, Inc. Protein sequencing via coupling of polymerizable molecules
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
US20250361504A1 (en) * 2022-12-23 2025-11-27 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
WO2000057183A1 (en) 1999-03-23 2000-09-28 Biovation Limited Protein isolation and analysis
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
JP2005509444A (ja) 2001-11-23 2005-04-14 シモン・フレデリックソン 多価近接プローブにより近接プロービングするための方法およびキット
MX282672B (es) 2002-10-10 2011-01-10 Diversa Corp Proteasas, acidos nucleicos que los codifican, y metodos de hacer y usar los mismos.
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
US11118215B2 (en) * 2003-09-18 2021-09-14 Nuevolution A/S Method for obtaining structural information concerning an encoded molecule and method for selecting compounds
US7579165B2 (en) 2003-10-16 2009-08-25 Shimadzu Corporation Methods for derivatizing protein or peptide with sulfonic acid groups
EP1694693A2 (en) 2003-12-17 2006-08-30 Praecis Pharmaceuticals Inc. Methods for synthesis of encoded libraries
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
PT3305900T (pt) * 2005-12-01 2021-10-27 Nuevolution As Métodos de codificação enzimática para síntese eficaz de bibliotecas grandes
US20100311114A1 (en) 2007-10-19 2010-12-09 Pronota N.V. Preparation of samples for proteome analysis
CA2745197A1 (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
WO2011071943A1 (en) 2009-12-07 2011-06-16 Prognosys Biosciences, Inc. Peptide display arrays
WO2011127006A1 (en) 2010-04-05 2011-10-13 Prognosys Biosciences, Inc. Co-localization affinity assays
GB201101621D0 (en) 2011-01-31 2011-03-16 Olink Ab Method and product
EP2694709B1 (en) 2011-04-08 2016-09-14 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
US10053725B2 (en) 2013-04-23 2018-08-21 President And Fellows Of Harvard College In situ interaction determination
US10288608B2 (en) * 2013-11-08 2019-05-14 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
US10858698B2 (en) 2014-03-25 2020-12-08 President And Fellows Of Harvard College Barcoded protein array for multiplex single-molecule interaction profiling
WO2015176034A1 (en) 2014-05-15 2015-11-19 Two Pore Guys, Inc. Scaffold data storage and target detection in a sample using a nanopore
WO2015200893A2 (en) 2014-06-26 2015-12-30 10X Genomics, Inc. Methods of analyzing nucleic acids from individual cells or cell populations
US20170212101A1 (en) 2014-07-18 2017-07-27 Cdi Laboratories, Inc. Methods and compositions to identify, quantify, and characterize target analytes and binding moieties
US10526641B2 (en) 2014-08-01 2020-01-07 Dovetail Genomics, Llc Tagging nucleic acids for sequence assembly
CA3208970A1 (en) 2014-09-15 2016-05-06 Board Of Regents, The University Of Texas System Improved single molecule peptide sequencing
ES2965764T3 (es) 2015-02-24 2024-04-16 Hope City Plataformas de cribado de bibliotecas abordadas espacialmente codificadas químicamente
WO2016138496A1 (en) 2015-02-27 2016-09-01 Cellular Research, Inc. Spatially addressable molecular barcoding
WO2016145416A2 (en) 2015-03-11 2016-09-15 The Broad Institute, Inc. Proteomic analysis with nucleic acid identifiers
EP3452591B1 (en) * 2016-05-02 2023-08-16 Encodia, Inc. Macromolecule analysis employing nucleic acid encoding
WO2018005720A1 (en) 2016-06-30 2018-01-04 President And Fellows Of Harvard College Method of determining the molecular binding between libraries of molecules
CN118853848A (zh) 2016-08-31 2024-10-29 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
CN117887804A (zh) 2017-02-02 2024-04-16 纽约基因组研究中心公司 用于识别或量化在生物样品中的靶标的方法和组合物
CA3081446A1 (en) 2017-10-31 2019-05-09 Encodia, Inc. Methods and compositions for polypeptide analysis
JP7390027B2 (ja) 2017-10-31 2023-12-01 エンコディア, インコーポレイテッド 核酸エンコーディングおよび/または標識を使用する解析のためのキット
SG11202003923PA (en) 2017-10-31 2020-05-28 Encodia Inc Methods and kits using nucleic acid encoding and/or label
KR20250152680A (ko) 2017-12-29 2025-10-23 노틸러스 서브시디어리, 인크. 단백질 식별을 위한 디코딩 접근법

Also Published As

Publication number Publication date
SG11202003923PA (en) 2020-05-28
WO2019089851A8 (en) 2020-05-28
US20210355483A1 (en) 2021-11-18
EP3704246A4 (en) 2021-08-11
WO2019089851A1 (en) 2019-05-09
JP2021501576A (ja) 2021-01-21
US12467049B2 (en) 2025-11-11
JP7253833B2 (ja) 2023-04-07
US12129463B2 (en) 2024-10-29
US20230340458A1 (en) 2023-10-26
US20250051756A1 (en) 2025-02-13
CA3081451A1 (en) 2019-05-09
EP3704246A1 (en) 2020-09-09

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