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WO2017151680A3 - Methods, compositions, and devices for information storage - Google Patents

Methods, compositions, and devices for information storage Download PDF

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Publication number
WO2017151680A3
WO2017151680A3 PCT/US2017/020044 US2017020044W WO2017151680A3 WO 2017151680 A3 WO2017151680 A3 WO 2017151680A3 US 2017020044 W US2017020044 W US 2017020044W WO 2017151680 A3 WO2017151680 A3 WO 2017151680A3
Authority
WO
WIPO (PCT)
Prior art keywords
devices
methods
novel
dna
compositions
Prior art date
Application number
PCT/US2017/020044
Other languages
French (fr)
Other versions
WO2017151680A2 (en
Inventor
Paul Predki
Maja CASSIDY
Original Assignee
Dodo Omnidata, 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
Priority to JP2018546548A priority Critical patent/JP7546345B2/en
Priority to MX2018010388A priority patent/MX2018010388A/en
Priority to KR1020257002997A priority patent/KR20250024857A/en
Priority to AU2017227608A priority patent/AU2017227608B2/en
Priority to EP17760661.3A priority patent/EP3423597A4/en
Priority to CA3016037A priority patent/CA3016037A1/en
Priority to KR1020187028197A priority patent/KR20180123062A/en
Priority to CN201780025380.6A priority patent/CN109415766A/en
Application filed by Dodo Omnidata, Inc. filed Critical Dodo Omnidata, Inc.
Priority to RU2018134197A priority patent/RU2765308C2/en
Priority to BR112018067903-8A priority patent/BR112018067903A2/en
Priority to SG11201807334SA priority patent/SG11201807334SA/en
Priority to US15/690,189 priority patent/US10438662B2/en
Publication of WO2017151680A2 publication Critical patent/WO2017151680A2/en
Publication of WO2017151680A3 publication Critical patent/WO2017151680A3/en
Priority to PCT/US2017/059100 priority patent/WO2018081745A1/en
Priority to JP2019523791A priority patent/JP7112394B2/en
Priority to KR1020197015597A priority patent/KR102464547B1/en
Priority to CA3079046A priority patent/CA3079046A1/en
Priority to CN201780080140.6A priority patent/CN110325653B/en
Priority to EP17865168.3A priority patent/EP3532639B1/en
Priority to US15/969,745 priority patent/US10640822B2/en
Priority to IL261424A priority patent/IL261424B/en
Priority to PH12018501843A priority patent/PH12018501843A1/en
Priority to US16/399,746 priority patent/US10859562B2/en
Priority to US17/052,519 priority patent/US11549140B2/en
Priority to US16/514,726 priority patent/US10714178B2/en
Priority to US16/836,689 priority patent/US10995373B2/en
Priority to US17/233,186 priority patent/US11505825B2/en
Priority to JP2022045490A priority patent/JP2022095695A/en
Priority to AU2022268325A priority patent/AU2022268325B2/en
Priority to US18/057,650 priority patent/US20230279485A1/en
Priority to US18/152,110 priority patent/US20230340584A1/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/04—Compounds 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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/90—Isomerases (5.)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P19/00—Preparation of compounds containing saccharide radicals
    • C12P19/26—Preparation of nitrogen-containing carbohydrates
    • C12P19/28—N-glycosides
    • C12P19/30—Nucleotides
    • C12P19/34—Polynucleotides, e.g. nucleic acids, oligoribonucleotides
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N27/00—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
    • G01N27/26—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variables; by using electrolysis or electrophoresis
    • G01N27/28—Electrolytic cell components
    • G01N27/30—Electrodes, e.g. test electrodes; Half-cells
    • G01N27/327—Biochemical electrodes, e.g. electrical or mechanical details for in vitro measurements
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/20—Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00497—Features relating to the solid phase supports
    • B01J2219/00511—Walls of reactor vessels
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00596—Solid-phase processes
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00718—Type of compounds synthesised
    • B01J2219/0072—Organic compounds
    • B01J2219/00722—Nucleotides
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/10—Nucleotidyl transfering
    • C12Q2521/131—Terminal transferase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/116—Nucleic acid detection characterized by the use of physical, structural and functional properties electrical properties of nucleic acids, e.g. impedance, conductivity or resistance
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/60—Detection means characterised by use of a special device
    • C12Q2565/631—Detection means characterised by use of a special device being a biochannel or pore
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y599/00—Other isomerases (5.99)
    • C12Y599/01—Other isomerases (5.99.1)
    • C12Y599/01002—DNA topoisomerase (5.99.1.2)
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/12—Computing arrangements based on biological models using genetic models
    • G06N3/123—DNA computing
    • G—PHYSICS
    • G11—INFORMATION STORAGE
    • G11C—STATIC STORES
    • G11C13/00—Digital stores characterised by the use of storage elements not covered by groups G11C11/00, G11C23/00, or G11C25/00
    • G11C13/0002—Digital stores characterised by the use of storage elements not covered by groups G11C11/00, G11C23/00, or G11C25/00 using resistive RAM [RRAM] elements
    • G11C13/0009—RRAM elements whose operation depends upon chemical change
    • G11C13/0014—RRAM elements whose operation depends upon chemical change comprising cells based on organic memory material
    • G—PHYSICS
    • G11—INFORMATION STORAGE
    • G11C—STATIC STORES
    • G11C13/00—Digital stores characterised by the use of storage elements not covered by groups G11C11/00, G11C23/00, or G11C25/00
    • G11C13/0002—Digital stores characterised by the use of storage elements not covered by groups G11C11/00, G11C23/00, or G11C25/00 using resistive RAM [RRAM] elements
    • G11C13/0009—RRAM elements whose operation depends upon chemical change
    • G11C13/0014—RRAM elements whose operation depends upon chemical change comprising cells based on organic memory material
    • G11C13/0019—RRAM elements whose operation depends upon chemical change comprising cells based on organic memory material comprising bio-molecules

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Molecular Biology (AREA)
  • Physics & Mathematics (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Biotechnology (AREA)
  • Biochemistry (AREA)
  • Biophysics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • General Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Theoretical Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Analytical Chemistry (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Immunology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Medical Informatics (AREA)
  • General Chemical & Material Sciences (AREA)
  • Biomedical Technology (AREA)
  • General Physics & Mathematics (AREA)
  • Artificial Intelligence (AREA)
  • Pathology (AREA)
  • Data Mining & Analysis (AREA)
  • Evolutionary Computation (AREA)
  • Computing Systems (AREA)
  • Medicinal Chemistry (AREA)
  • Mathematical Physics (AREA)
  • Software Systems (AREA)
  • Electrochemistry (AREA)
  • Computational Linguistics (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

The disclosure provides a novel system of storing information using a charged polymer, e.g., DNA, the monomers of which correspond to a machine-readable code, e.g., a binary code, and which can be synthesized and/or read using a novel nanochip device comprising nanopores; novel methods and devices for synthesizing oligonucleotides in a nanochip format; novel methods for synthesizing DNA in the 3' to 5' direction using topoisomerase; novel methods and devices for reading the sequence of a charged polymer, e.g., DNA, by measuring capacitive variance as the polymer passes through the nanopore; and further provides compounds, compositions, methods and devices useful therein.
PCT/US2017/020044 2016-02-29 2017-02-28 Methods, compositions, and devices for information storage WO2017151680A2 (en)

Priority Applications (30)

Application Number Priority Date Filing Date Title
KR1020187028197A KR20180123062A (en) 2016-02-29 2017-02-28 Method, composition, and apparatus for information storage
KR1020257002997A KR20250024857A (en) 2016-02-29 2017-02-28 Methods, compositions, and devices for information storage
AU2017227608A AU2017227608B2 (en) 2016-02-29 2017-02-28 Methods, compositions, and devices for information storage
EP17760661.3A EP3423597A4 (en) 2016-02-29 2017-02-28 METHODS, COMPOSITIONS AND DEVICES FOR STORING INFORMATION
CA3016037A CA3016037A1 (en) 2016-02-29 2017-02-28 Methods, compositions, and devices for information storage
JP2018546548A JP7546345B2 (en) 2016-02-29 2017-02-28 Methods, compositions and devices for information storage - Patents.com
BR112018067903-8A BR112018067903A2 (en) 2016-02-29 2017-02-28 methods, compositions and devices for storing information
CN201780025380.6A CN109415766A (en) 2016-02-29 2017-02-28 Method, composition and device for information storage
RU2018134197A RU2765308C2 (en) 2016-02-29 2017-02-28 Methods, compositions and devices for storing information
MX2018010388A MX2018010388A (en) 2016-02-29 2017-02-28 METHODS, COMPOSITIONS AND DEVICES FOR INFORMATION STORAGE.
SG11201807334SA SG11201807334SA (en) 2016-02-29 2017-02-28 Methods, compositions, and devices for information storage
US15/690,189 US10438662B2 (en) 2016-02-29 2017-08-29 Methods, compositions, and devices for information storage
EP17865168.3A EP3532639B1 (en) 2016-10-31 2017-10-30 Methods and devices for information storage
JP2019523791A JP7112394B2 (en) 2016-10-31 2017-10-30 Methods, compositions, and devices for information storage
CN201780080140.6A CN110325653B (en) 2016-10-31 2017-10-30 Method, composition and device for information storage
PCT/US2017/059100 WO2018081745A1 (en) 2016-10-31 2017-10-30 Methods, compositions, and devices for information storage
KR1020197015597A KR102464547B1 (en) 2016-10-31 2017-10-30 Methods, compositions, and devices for storing information
CA3079046A CA3079046A1 (en) 2016-10-31 2017-10-30 Methods, compositions, and devices for information storage
US15/969,745 US10640822B2 (en) 2016-02-29 2018-05-02 Systems and methods for writing, reading, and controlling data stored in a polymer
IL261424A IL261424B (en) 2016-02-29 2018-08-28 Methods, preparations and devices for storing information
PH12018501843A PH12018501843A1 (en) 2016-02-29 2018-08-29 Methods, compositions, and devices for information storage
US16/399,746 US10859562B2 (en) 2016-02-29 2019-04-30 Methods, compositions, and devices for information storage
US17/052,519 US11549140B2 (en) 2016-02-29 2019-05-02 Systems and methods for writing, reading, and controlling data stored in a polymer
US16/514,726 US10714178B2 (en) 2016-02-29 2019-07-17 Methods, compositions, and devices for information storage
US16/836,689 US10995373B2 (en) 2016-02-29 2020-03-31 Systems and methods for writing, reading, and controlling data stored in a polymer
US17/233,186 US11505825B2 (en) 2016-02-29 2021-04-16 Methods of synthesizing DNA
JP2022045490A JP2022095695A (en) 2016-02-29 2022-03-22 Methods, compositions and devices for information storage
AU2022268325A AU2022268325B2 (en) 2016-02-29 2022-11-09 Methods, compositions, and devices for information storage
US18/057,650 US20230279485A1 (en) 2016-02-29 2022-11-21 Systems and methods for writing, reading, and controlling data stored in a polymer
US18/152,110 US20230340584A1 (en) 2016-02-29 2023-01-09 Systems and methods for writing, reading, and controlling data stored in a polymer

Applications Claiming Priority (4)

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

Related Parent Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2017/059100 Continuation-In-Part WO2018081745A1 (en) 2016-02-29 2017-10-30 Methods, compositions, and devices for information storage

Related Child Applications (1)

Application Number Title Priority Date Filing Date
US15/690,189 Continuation-In-Part US10438662B2 (en) 2016-02-29 2017-08-29 Methods, compositions, and devices for information storage

Publications (2)

Publication Number Publication Date
WO2017151680A2 WO2017151680A2 (en) 2017-09-08
WO2017151680A3 true WO2017151680A3 (en) 2017-10-12

Family

ID=59743186

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2017/020044 WO2017151680A2 (en) 2016-02-29 2017-02-28 Methods, compositions, and devices for information storage

Country Status (13)

Country Link
EP (1) EP3423597A4 (en)
JP (2) JP7546345B2 (en)
KR (2) KR20180123062A (en)
CN (1) CN109415766A (en)
AU (2) AU2017227608B2 (en)
BR (1) BR112018067903A2 (en)
CA (1) CA3016037A1 (en)
IL (1) IL261424B (en)
MX (2) MX2018010388A (en)
PH (1) PH12018501843A1 (en)
RU (2) RU2765308C2 (en)
SG (1) SG11201807334SA (en)
WO (1) WO2017151680A2 (en)

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