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CA3016037A1 - Methods, compositions, and devices for information storage - Google Patents

Methods, compositions, and devices for information storage Download PDF

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Publication number
CA3016037A1
CA3016037A1 CA3016037A CA3016037A CA3016037A1 CA 3016037 A1 CA3016037 A1 CA 3016037A1 CA 3016037 A CA3016037 A CA 3016037A CA 3016037 A CA3016037 A CA 3016037A CA 3016037 A1 CA3016037 A1 CA 3016037A1
Authority
CA
Canada
Prior art keywords
dna
nanopore
polymer
nanochip
sequence
Prior art date
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.)
Pending
Application number
CA3016037A
Other languages
English (en)
French (fr)
Inventor
Paul Predki
Maja CASSIDY
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Iridia Inc
Original Assignee
Iridia Inc
Priority date (The priority date 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 date listed.)
Filing date
Publication date
Application filed by Iridia Inc filed Critical Iridia Inc
Publication of CA3016037A1 publication Critical patent/CA3016037A1/en
Pending legal-status Critical Current

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Classifications

    • 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
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07HSUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/04Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
    • 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
    • C12N9/00Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/90Isomerases (5.)
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12PFERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P19/00Preparation of compounds containing saccharide radicals
    • C12P19/26Preparation of nitrogen-containing carbohydrates
    • C12P19/28N-glycosides
    • C12P19/30Nucleotides
    • C12P19/34Polynucleotides, e.g. nucleic acids, oligoribonucleotides
    • 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
    • C12Q1/6844Nucleic acid amplification reactions
    • 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
    • C12Q1/6869Methods for sequencing
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N27/00Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
    • G01N27/26Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variables; by using electrolysis or electrophoresis
    • G01N27/28Electrolytic cell components
    • G01N27/30Electrodes, e.g. test electrodes; Half-cells
    • G01N27/327Biochemical electrodes, e.g. electrical or mechanical details for in vitro measurements
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/20Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277Apparatus
    • B01J2219/00497Features relating to the solid phase supports
    • B01J2219/00511Walls of reactor vessels
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583Features relative to the processes being carried out
    • B01J2219/00596Solid-phase processes
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00718Type of compounds synthesised
    • B01J2219/0072Organic compounds
    • B01J2219/00722Nucleotides
    • 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
    • C12Q2521/00Reaction characterised by the enzymatic activity
    • C12Q2521/10Nucleotidyl transfering
    • C12Q2521/131Terminal transferase
    • 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
    • C12Q2563/00Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/116Nucleic acid detection characterized by the use of physical, structural and functional properties electrical properties of nucleic acids, e.g. impedance, conductivity or resistance
    • 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
    • C12Q2565/00Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/60Detection means characterised by use of a special device
    • C12Q2565/631Detection means characterised by use of a special device being a biochannel or pore
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12YENZYMES
    • C12Y599/00Other isomerases (5.99)
    • C12Y599/01Other isomerases (5.99.1)
    • C12Y599/01002DNA topoisomerase (5.99.1.2)
    • GPHYSICS
    • G06COMPUTING OR CALCULATING; COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00Computing arrangements based on biological models
    • G06N3/12Computing arrangements based on biological models using genetic models
    • G06N3/123DNA computing
    • GPHYSICS
    • G11INFORMATION STORAGE
    • G11CSTATIC STORES
    • G11C13/00Digital stores characterised by the use of storage elements not covered by groups G11C11/00, G11C23/00, or G11C25/00
    • G11C13/0002Digital stores characterised by the use of storage elements not covered by groups G11C11/00, G11C23/00, or G11C25/00 using resistive RAM [RRAM] elements
    • G11C13/0009RRAM elements whose operation depends upon chemical change
    • G11C13/0014RRAM elements whose operation depends upon chemical change comprising cells based on organic memory material
    • GPHYSICS
    • G11INFORMATION STORAGE
    • G11CSTATIC STORES
    • G11C13/00Digital stores characterised by the use of storage elements not covered by groups G11C11/00, G11C23/00, or G11C25/00
    • G11C13/0002Digital stores characterised by the use of storage elements not covered by groups G11C11/00, G11C23/00, or G11C25/00 using resistive RAM [RRAM] elements
    • G11C13/0009RRAM elements whose operation depends upon chemical change
    • G11C13/0014RRAM elements whose operation depends upon chemical change comprising cells based on organic memory material
    • G11C13/0019RRAM elements whose operation depends upon chemical change comprising cells based on organic memory material comprising bio-molecules

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Molecular Biology (AREA)
  • Physics & Mathematics (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Genetics & Genomics (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Biochemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biophysics (AREA)
  • General Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • General Chemical & Material Sciences (AREA)
  • General Physics & Mathematics (AREA)
  • Biomedical Technology (AREA)
  • Medicinal Chemistry (AREA)
  • Pathology (AREA)
  • Data Mining & Analysis (AREA)
  • Evolutionary Computation (AREA)
  • Computing Systems (AREA)
  • Artificial Intelligence (AREA)
  • Mathematical Physics (AREA)
  • Software Systems (AREA)
  • Electrochemistry (AREA)
  • Computational Linguistics (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
CA3016037A 2016-02-29 2017-02-28 Methods, compositions, and devices for information storage Pending CA3016037A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201662301538P 2016-02-29 2016-02-29
US62/301,538 2016-02-29
US201662415430P 2016-10-31 2016-10-31
US62/415,430 2016-10-31
PCT/US2017/020044 WO2017151680A2 (en) 2016-02-29 2017-02-28 Methods, compositions, and devices for information storage

Publications (1)

Publication Number Publication Date
CA3016037A1 true CA3016037A1 (en) 2017-09-08

Family

ID=59743186

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3016037A Pending CA3016037A1 (en) 2016-02-29 2017-02-28 Methods, compositions, and devices for information storage

Country Status (13)

Country Link
EP (1) EP3423597A4 (ru)
JP (2) JP7546345B2 (ru)
KR (2) KR20180123062A (ru)
CN (1) CN109415766A (ru)
AU (2) AU2017227608B2 (ru)
BR (1) BR112018067903A2 (ru)
CA (1) CA3016037A1 (ru)
IL (1) IL261424B (ru)
MX (2) MX2018010388A (ru)
PH (1) PH12018501843A1 (ru)
RU (2) RU2022101599A (ru)
SG (1) SG11201807334SA (ru)
WO (1) WO2017151680A2 (ru)

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KR102601324B1 (ko) 2017-01-19 2023-11-10 로스웰 바이오테크놀로지스 인코포레이티드 2차원 레이어 재료를 포함하는 솔리드 스테이트 시퀀싱 디바이스들
WO2018200687A1 (en) 2017-04-25 2018-11-01 Roswell Biotechnologies, Inc. Enzymatic circuits for molecular sensors
US10508296B2 (en) 2017-04-25 2019-12-17 Roswell Biotechnologies, Inc. Enzymatic circuits for molecular sensors
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KR102583062B1 (ko) 2017-05-31 2023-09-25 몰레큘러 어셈블리즈, 인크. 동종중합체 인코딩된 핵산 메모리
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EP3676389A4 (en) 2017-08-30 2021-06-02 Roswell Biotechnologies, Inc PROCESSIVE ENZYMATIC MOLECULAR ELECTRONIC SENSORS FOR STORING DNA DATA
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KR102804057B1 (ko) * 2018-01-04 2025-05-07 트위스트 바이오사이언스 코포레이션 Dna 기반 디지털 정보 저장
GB201801768D0 (en) 2018-02-02 2018-03-21 Oxford Nanopore Tech Ltd Synthesis method
EP3547315B1 (en) * 2018-03-26 2021-01-27 IMEC vzw Method of storing data
CN113302700B (zh) * 2018-09-07 2024-10-08 艾瑞迪亚公司 用于写入和读取存储在聚合物中的数据的改进的系统和方法
KR102653412B1 (ko) * 2019-03-29 2024-04-02 팔로젠 인코포레이티드 나노포어 디바이스 및 이를 사용한 바이오 합성 방법들
US11655465B1 (en) 2019-05-02 2023-05-23 Iridia, Inc. Enzymes and systems for synthesizing DNA
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Also Published As

Publication number Publication date
SG11201807334SA (en) 2018-09-27
RU2018134197A (ru) 2020-04-01
AU2022268325B2 (en) 2024-09-19
AU2017227608A1 (en) 2018-09-27
RU2022101599A (ru) 2022-02-25
EP3423597A2 (en) 2019-01-09
KR20250024857A (ko) 2025-02-19
PH12018501843A1 (en) 2019-05-15
RU2765308C2 (ru) 2022-01-28
CN109415766A (zh) 2019-03-01
EP3423597A4 (en) 2020-03-04
JP7546345B2 (ja) 2024-09-06
WO2017151680A3 (en) 2017-10-12
JP2019512480A (ja) 2019-05-16
WO2017151680A2 (en) 2017-09-08
MX2022010682A (es) 2022-09-23
AU2017227608B2 (en) 2023-06-01
RU2018134197A3 (ru) 2021-07-02
AU2022268325A1 (en) 2022-12-15
BR112018067903A2 (pt) 2019-04-16
MX2018010388A (es) 2019-03-06
JP2022095695A (ja) 2022-06-28
KR20180123062A (ko) 2018-11-14
IL261424B (en) 2021-08-31
IL261424A (en) 2018-10-31

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