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PH12018501843A1 - Methods, compositions, and devices for information storage - Google Patents

Methods, compositions, and devices for information storage

Info

Publication number
PH12018501843A1
PH12018501843A1 PH12018501843A PH12018501843A PH12018501843A1 PH 12018501843 A1 PH12018501843 A1 PH 12018501843A1 PH 12018501843 A PH12018501843 A PH 12018501843A PH 12018501843 A PH12018501843 A PH 12018501843A PH 12018501843 A1 PH12018501843 A1 PH 12018501843A1
Authority
PH
Philippines
Prior art keywords
devices
methods
novel
dna
compositions
Prior art date
Application number
PH12018501843A
Inventor
Paul Predki
Maja Cassidy
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 PH12018501843A1 publication Critical patent/PH12018501843A1/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

Landscapes

  • 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.
PH12018501843A 2016-02-29 2018-08-29 Methods, compositions, and devices for information storage PH12018501843A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201662301538P 2016-02-29 2016-02-29
US201662415430P 2016-10-31 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
PH12018501843A1 true PH12018501843A1 (en) 2019-05-15

Family

ID=59743186

Family Applications (1)

Application Number Title Priority Date Filing Date
PH12018501843A PH12018501843A1 (en) 2016-02-29 2018-08-29 Methods, compositions, and devices for information storage

Country Status (13)

Country Link
EP (1) EP3423597A4 (en)
JP (2) JP7546345B2 (en)
KR (2) KR20250024857A (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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EP3408219B1 (en) 2016-01-28 2022-08-17 Roswell Biotechnologies, Inc Massively parallel dna sequencing apparatus
WO2017132586A1 (en) 2016-01-28 2017-08-03 Roswell Biotechnologies, Inc. Methods and apparatus for measuring analytes using large scale molecular electronics sensor arrays
JP6854532B2 (en) 2016-02-09 2021-04-07 ロズウェル バイオテクノロジーズ，インコーポレイテッド Electronic, label-free DNA and genome sequencing
US10597767B2 (en) 2016-02-22 2020-03-24 Roswell Biotechnologies, Inc. Nanoparticle fabrication
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US9829456B1 (en) 2016-07-26 2017-11-28 Roswell Biotechnologies, Inc. Method of making a multi-electrode structure usable in molecular sensing devices
KR102622275B1 (en) 2017-01-10 2024-01-05 로스웰 바이오테크놀로지스 인코포레이티드 Methods and systems for DNA data storage
WO2018136148A1 (en) 2017-01-19 2018-07-26 Roswell Biotechnologies, Inc. Solid state sequencing devices comprising two dimensional layer materials
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
KR102606670B1 (en) 2017-05-09 2023-11-24 로스웰 바이오테크놀로지스 인코포레이티드 Coupled probe circuits for molecular sensors
US11174512B2 (en) 2017-05-31 2021-11-16 Molecular Assemblies, Inc. Homopolymer encoded nucleic acid memory
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WO2019075100A1 (en) * 2017-10-10 2019-04-18 Roswell Biotechnologies, Inc. Methods, apparatus and systems for amplification-free dna data storage
JP7191448B2 (en) 2018-01-04 2022-12-19 ツイスト バイオサイエンス コーポレーション DNA-based digital information storage
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EP3547315B1 (en) * 2018-03-26 2021-01-27 IMEC vzw Method of storing data
CA3111930A1 (en) 2018-09-07 2020-03-12 Iridia, Inc. Improved systems and methods for writing and reading data stored in a polymer
JP7431454B2 (en) * 2019-03-29 2024-02-15 パロゲン，インコーポレイテッド Nanopore device and biosynthesis method using it
US11655465B1 (en) 2019-05-02 2023-05-23 Iridia, Inc. Enzymes and systems for synthesizing DNA
TWI860366B (en) * 2019-06-19 2024-11-01 美商伊路米納有限公司 Reagent exchange in an instrument
US11837302B1 (en) 2020-08-07 2023-12-05 Iridia, Inc. Systems and methods for writing and reading data stored in a polymer using nano-channels
CN114196661B (en) * 2021-11-04 2023-08-11 北京全式金生物技术股份有限公司 Recombinant topoisomerase and application thereof in construction of sequencing library
US20230176033A1 (en) * 2021-12-08 2023-06-08 Western Digital Technologies, Inc. Devices, systems, and methods of using smart fluids to control molecule speeds
CN117079689A (en) * 2022-05-10 2023-11-17 密码子（杭州）科技有限公司 Molecular module assembling device and molecular module assembling method

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Also Published As

Publication number Publication date
JP7546345B2 (en) 2024-09-06
EP3423597A2 (en) 2019-01-09
AU2022268325A1 (en) 2022-12-15
AU2017227608A1 (en) 2018-09-27
SG11201807334SA (en) 2018-09-27
IL261424B (en) 2021-08-31
RU2765308C2 (en) 2022-01-28
RU2018134197A (en) 2020-04-01
KR20250024857A (en) 2025-02-19
WO2017151680A2 (en) 2017-09-08
JP2022095695A (en) 2022-06-28
WO2017151680A3 (en) 2017-10-12
KR20180123062A (en) 2018-11-14
MX2022010682A (en) 2022-09-23
EP3423597A4 (en) 2020-03-04
BR112018067903A2 (en) 2019-04-16
AU2017227608B2 (en) 2023-06-01
AU2022268325B2 (en) 2024-09-19
CN109415766A (en) 2019-03-01
JP2019512480A (en) 2019-05-16
IL261424A (en) 2018-10-31
RU2018134197A3 (en) 2021-07-02
RU2022101599A (en) 2022-02-25
CA3016037A1 (en) 2017-09-08
MX2018010388A (en) 2019-03-06

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