CN109517878A - 使用纳米管的核酸聚合酶构象变化的检测 - Google Patents

使用纳米管的核酸聚合酶构象变化的检测 Download PDF

Info

Publication number
CN109517878A
CN109517878A CN201811305798.5A CN201811305798A CN109517878A CN 109517878 A CN109517878 A CN 109517878A CN 201811305798 A CN201811305798 A CN 201811305798A CN 109517878 A CN109517878 A CN 109517878A
Authority
CN
China
Prior art keywords
thio
nucleic acid
nucleotide
dntp
substitution
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
CN201811305798.5A
Other languages
English (en)
Chinese (zh)
Inventor
P·G·柯林斯
G·A·韦斯
崔龙起
T·奥尔森
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.)
University of California San Diego UCSD
Original Assignee
University of California San Diego UCSD
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 University of California San Diego UCSD filed Critical University of California San Diego UCSD
Publication of CN109517878A publication Critical patent/CN109517878A/zh
Pending legal-status Critical Current

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
    • C12Q1/48—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving 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
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/48—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving transferase
    • C12Q1/485—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving transferase involving kinase
    • 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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y207/00—Transferases transferring phosphorus-containing groups (2.7)
    • C12Y207/07—Nucleotidyltransferases (2.7.7)
    • C12Y207/07007—DNA-directed DNA polymerase (2.7.7.7), i.e. DNA replicase
    • 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
    • G01N27/403—Cells and electrode assemblies
    • G01N27/414—Ion-sensitive or chemical field-effect transistors, i.e. ISFETS or CHEMFETS
    • G01N27/4146—Ion-sensitive or chemical field-effect transistors, i.e. ISFETS or CHEMFETS involving nanosized elements, e.g. nanotubes, nanowires
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/483—Physical analysis of biological material
    • G01N33/487—Physical analysis of biological material of liquid biological material
    • G01N33/48707—Physical analysis of biological material of liquid biological material by electrical means
    • G01N33/48721—Investigating individual macromolecules, e.g. by translocation through nanopores
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/90—Enzymes; Proenzymes
    • G01N2333/91—Transferases (2.)
    • G01N2333/912—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
    • G01N2333/91205—Phosphotransferases in general
    • G01N2333/91245—Nucleotidyltransferases (2.7.7)
    • G01N2333/9125—Nucleotidyltransferases (2.7.7) with a definite EC number (2.7.7.-)
    • G01N2333/9126—DNA-directed DNA polymerase (2.7.7.7)

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • General Health & Medical Sciences (AREA)
  • Biochemistry (AREA)
  • Molecular Biology (AREA)
  • Physics & Mathematics (AREA)
  • Immunology (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Biophysics (AREA)
  • Microbiology (AREA)
  • Biotechnology (AREA)
  • Nanotechnology (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Electrochemistry (AREA)
  • Microelectronics & Electronic Packaging (AREA)
  • Biomedical Technology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medicinal Chemistry (AREA)
  • Food Science & Technology (AREA)
  • Urology & Nephrology (AREA)
  • Hematology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
CN201811305798.5A 2014-12-18 2015-12-17 使用纳米管的核酸聚合酶构象变化的检测 Pending CN109517878A (zh)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201462093671P 2014-12-18 2014-12-18
US62/093,671 2014-12-18
CN201580072789.4A CN107109466A (zh) 2014-12-18 2015-12-17 使用纳米管的核酸聚合酶构象变化的检测

Related Parent Applications (1)

Application Number Title Priority Date Filing Date
CN201580072789.4A Division CN107109466A (zh) 2014-12-18 2015-12-17 使用纳米管的核酸聚合酶构象变化的检测

Publications (1)

Publication Number Publication Date
CN109517878A true CN109517878A (zh) 2019-03-26

Family

ID=56127582

Family Applications (2)

Application Number Title Priority Date Filing Date
CN201811305798.5A Pending CN109517878A (zh) 2014-12-18 2015-12-17 使用纳米管的核酸聚合酶构象变化的检测
CN201580072789.4A Pending CN107109466A (zh) 2014-12-18 2015-12-17 使用纳米管的核酸聚合酶构象变化的检测

Family Applications After (1)

Application Number Title Priority Date Filing Date
CN201580072789.4A Pending CN107109466A (zh) 2014-12-18 2015-12-17 使用纳米管的核酸聚合酶构象变化的检测

Country Status (10)

Country Link
US (1) US20180051316A1 (enExample)
EP (1) EP3234178A4 (enExample)
JP (1) JP2018500905A (enExample)
KR (1) KR20170091158A (enExample)
CN (2) CN109517878A (enExample)
AU (1) AU2015364602B2 (enExample)
CA (1) CA2971268A1 (enExample)
RU (1) RU2721965C2 (enExample)
SG (1) SG11201704862UA (enExample)
WO (2) WO2016100637A1 (enExample)

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN114555832A (zh) * 2019-05-27 2022-05-27 通用测序技术公司 鉴定核酸序列中组分的方法
CN117174183A (zh) * 2022-05-27 2023-12-05 中国科学院大连化学物理研究所 基于多尺度分子动力学模拟的rna结构预测方法

Families Citing this family (49)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2017132586A1 (en) 2016-01-28 2017-08-03 Roswell Biotechnologies, Inc. Methods and apparatus for measuring analytes using large scale molecular electronics sensor arrays
US10712334B2 (en) 2016-01-28 2020-07-14 Roswell Biotechnologies, Inc. Massively parallel DNA sequencing apparatus
EP3882616A1 (en) 2016-02-09 2021-09-22 Roswell Biotechnologies, Inc Electronic label-free dna and genome sequencing
US10597767B2 (en) 2016-02-22 2020-03-24 Roswell Biotechnologies, Inc. Nanoparticle fabrication
US9829456B1 (en) 2016-07-26 2017-11-28 Roswell Biotechnologies, Inc. Method of making a multi-electrode structure usable in molecular sensing devices
CN106244712B (zh) * 2016-08-31 2019-11-19 北京大学 Dna测序方法
WO2018098286A1 (en) * 2016-11-22 2018-05-31 Roswell Biotechnologies, Inc. Nucleic acid sequencing device containing graphene
CN110431148A (zh) 2017-01-10 2019-11-08 罗斯威尔生命技术公司 用于dna数据存储的方法和系统
CN110520517A (zh) * 2017-01-19 2019-11-29 罗斯威尔生命技术公司 包括二维层材料的固态测序装置
US10508296B2 (en) 2017-04-25 2019-12-17 Roswell Biotechnologies, Inc. Enzymatic circuits for molecular sensors
EP3615685B1 (en) 2017-04-25 2025-02-19 Roswell Biotechnologies, Inc Enzymatic circuits for molecular sensors
WO2018208505A1 (en) * 2017-05-09 2018-11-15 Roswell Biotechnologies, Inc. Binding probe circuits for molecular sensors
EP3676389A4 (en) 2017-08-30 2021-06-02 Roswell Biotechnologies, Inc PROCESSIVE ENZYMATIC MOLECULAR ELECTRONIC SENSORS FOR STORING DNA DATA
SG11201911977VA (en) 2017-09-15 2020-01-30 Illumina Inc Tuning and calibration features of a sequence-detection system
KR102620326B1 (ko) * 2017-09-15 2024-01-02 일루미나, 인코포레이티드 서열-검출 시스템
KR102717872B1 (ko) * 2017-10-10 2024-10-14 로스웰 엠이 아이엔씨. 무증폭 dna 데이터 저장을 위한 방법, 장치 및 시스템
CN111448319B (zh) 2017-10-13 2024-05-17 诺和诺德保健股份有限公司 用于抑制ldha表达的方法和组合物
JP7433300B2 (ja) 2018-05-17 2024-02-19 レコグニション アナリティクス インコーポレイテッド 酵素活性の直接電気測定用のデバイス、システムおよび方法
US20240011086A1 (en) 2018-11-15 2024-01-11 Omniome, Inc. Electronic detection of nucleic acid structure
WO2020117653A1 (en) 2018-12-04 2020-06-11 Omniome, Inc. Mixed-phase fluids for nucleic acid sequencing and other analytical assays
CN113874728B (zh) 2019-01-30 2024-09-17 代表亚利桑那大学的亚利桑那校董事会 生物电子电路、系统及其制备和使用方法
WO2020167574A1 (en) 2019-02-14 2020-08-20 Omniome, Inc. Mitigating adverse impacts of detection systems on nucleic acids and other biological analytes
US20220145377A1 (en) * 2019-03-01 2022-05-12 Universal Sequencing Technology Corporation Device and Method for Biopolymer Identification
US11180520B2 (en) 2019-09-10 2021-11-23 Omniome, Inc. Reversible modifications of nucleotides
DE202019106694U1 (de) 2019-12-02 2020-03-19 Omniome, Inc. System zur Sequenzierung von Nukleinsäuren in Fluidschaum
CN115243792A (zh) 2020-02-04 2022-10-25 加利福尼亚太平洋生物科学股份有限公司 流通池及其制造和使用方法
US11913070B2 (en) * 2020-02-28 2024-02-27 Arizona Board Of Regents On Behalf Of Arizona State University Methods for sequencing biopolymers
US12298300B2 (en) 2020-04-17 2025-05-13 Arizona Board Of Regents On Behalf Of Arizona State University Single-molecule electronic sequence detector and methods of use
JP2023524079A (ja) 2020-04-30 2023-06-08 アリゾナ・ボード・オブ・リージェンツ・オン・ビハーフ・オブ・アリゾナ・ステイト・ユニバーシティー 生体高分子の配列決定のための方法
WO2021243113A1 (en) 2020-05-29 2021-12-02 Arizona Board Of Regents On Behalf Of Arizona State University Bioelectronic devices with programmable adaptors
EP4165549A1 (en) 2020-06-11 2023-04-19 Nautilus Biotechnology, Inc. Methods and systems for computational decoding of biological, chemical, and physical entities
EP4244382A1 (en) 2020-11-11 2023-09-20 Nautilus Subsidiary, Inc. Affinity reagents having enhanced binding and detection characteristics
WO2022159663A1 (en) 2021-01-21 2022-07-28 Nautilus Biotechnology, Inc. Systems and methods for biomolecule preparation
IL305336B2 (en) 2021-03-11 2025-09-01 Nautilus Subsidiary Inc Systems and methods for preserving biomolecules
EP4399528A1 (en) 2021-09-09 2024-07-17 Nautilus Subsidiary, Inc. Characterization and localization of protein modifications
US20230090454A1 (en) 2021-09-22 2023-03-23 Nautilus Biotechnology, Inc. Methods and systems for determining polypeptide interactions
US20230149883A1 (en) 2021-11-03 2023-05-18 Nautilus Biotechnology, Inc. Systems and methods for surface structuring
WO2023192917A1 (en) 2022-03-29 2023-10-05 Nautilus Subsidiary, Inc. Integrated arrays for single-analyte processes
EP4544077A1 (en) 2022-06-21 2025-04-30 Nautilus Subsidiary, Inc. Method for detecting analytes at sites of optically non-resolvable distances
WO2024073599A1 (en) 2022-09-29 2024-04-04 Nautilus Subsidiary, Inc. Preparation of array surfaces for single-analyte processes
EP4630816A1 (en) 2022-12-09 2025-10-15 Nautilus Subsidiary, Inc. A method comprising performing on a single-analyte array at least 50 cycles of a process
US20240201182A1 (en) 2022-12-15 2024-06-20 Nautilus Subsidiary, Inc. Inhibition of photon phenomena on single molecule arrays
WO2024206122A1 (en) 2023-03-24 2024-10-03 Nautilus Subsidiary, Inc. Improved transfer of nanoparticles to array surfaces
WO2024243237A1 (en) 2023-05-24 2024-11-28 Nautilus Subsidiary, Inc. Systems and methods for machine vision
US20250066841A1 (en) 2023-08-24 2025-02-27 Nautilus Subsidiary, Inc. Compositions and methods for detecting binding interactions under equilibrium or non-equilibrium conditions
US20250189519A1 (en) 2023-12-11 2025-06-12 Nautilus Subsidiary, Inc. Methods and compositions of particle-based arrays
WO2025137166A1 (en) 2023-12-20 2025-06-26 Nautilus Subsidiary, Inc. Fluidic devices for single-analyte assays
US20250298016A1 (en) 2024-03-22 2025-09-25 Nautilus Subsidiary, Inc. Plasmonic particle systems for single-analyte assays
WO2025212338A1 (en) 2024-04-01 2025-10-09 Nautilus Subsidiary, Inc. Nanostructures for modulation of analyte conformation

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20130078622A1 (en) * 2011-09-26 2013-03-28 The Regents Of The University Of California Electronic device for monitoring single molecule dynamics

Family Cites Families (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8911972B2 (en) * 2009-12-16 2014-12-16 Pacific Biosciences Of California, Inc. Sequencing methods using enzyme conformation
US20110287432A1 (en) * 2010-05-21 2011-11-24 454 Life Science Corporation System and method for tailoring nucleotide concentration to enzymatic efficiencies in dna sequencing technologies
CN102939261B (zh) * 2010-06-03 2015-09-23 六号元素有限公司 金刚石工具
CN103620403B (zh) * 2011-01-11 2016-08-10 纽约市哥伦比亚大学理事会 使用纳米管监测单分子的系统和方法
US9279154B2 (en) * 2011-12-21 2016-03-08 Illumina, Inc. Apparatus and methods for kinetic analysis and determination of nucleic acid sequences
IN2015DN01765A (enExample) * 2012-08-20 2015-05-29 Univ California

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20130078622A1 (en) * 2011-09-26 2013-03-28 The Regents Of The University Of California Electronic device for monitoring single molecule dynamics

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
DONGLIANG FU等: "Label-free electrical detection of DNA hybridization using carbon nanotubes and graphene", 《NANO REVIEWS》 *
KAITLIN M. PUGLIESE等: "Processive Incorporation of Deoxynucleoside Triphosphate Analogs by Single-Molecule DNA Polymerase I (Klenow Fragment) Nanocircuits", 《J AM CHEM SOC.》 *

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN114555832A (zh) * 2019-05-27 2022-05-27 通用测序技术公司 鉴定核酸序列中组分的方法
US20220251638A1 (en) * 2019-05-27 2022-08-11 Universal Sequencing Technology Corporation Methods to Identify Components in Nucleic Acid Sequences
CN117174183A (zh) * 2022-05-27 2023-12-05 中国科学院大连化学物理研究所 基于多尺度分子动力学模拟的rna结构预测方法
CN117174183B (zh) * 2022-05-27 2025-11-25 中国科学院大连化学物理研究所 基于多尺度分子动力学模拟的rna结构预测方法

Also Published As

Publication number Publication date
EP3234178A1 (en) 2017-10-25
JP2018500905A (ja) 2018-01-18
WO2016100637A1 (en) 2016-06-23
WO2016100635A1 (en) 2016-06-23
KR20170091158A (ko) 2017-08-08
EP3234178A4 (en) 2018-07-11
CN107109466A (zh) 2017-08-29
AU2015364602A1 (en) 2017-07-06
AU2015364602B2 (en) 2021-12-09
RU2721965C2 (ru) 2020-05-25
SG11201704862UA (en) 2017-07-28
RU2017125417A3 (enExample) 2019-05-27
US20180051316A1 (en) 2018-02-22
CA2971268A1 (en) 2016-06-23
RU2017125417A (ru) 2019-01-23

Similar Documents

Publication Publication Date Title
CN109517878A (zh) 使用纳米管的核酸聚合酶构象变化的检测
US20250251359A1 (en) Active-electrode integrated biosensor array and methods for use thereof
US12139749B2 (en) Charge perturbation detection system for DNA and other molecules
AU2014354726B2 (en) Compositions and methods for polynucleotide sequencing
JP6818995B2 (ja) 電極及び化学物質の分析のための方法
CN104359946B (zh) 一种基于纳米对电极的单分子核酸测序器件
CN104312914B (zh) 一种基于纳米孔结构的蛋白质分子电子器件
Ban et al. Direct DNA methylation profiling with an electric biosensor
US20200002758A1 (en) Sensor and sensing system
TWI310406B (en) Method for determining nucleic acid analytes
US20240011086A1 (en) Electronic detection of nucleic acid structure
HK40005350A (en) Detection of nucleic acid polymerase conformational changes using a nanotube
US20200216890A1 (en) Method for Sequencing a Polynucleotide
Choi et al. Single molecule sensing with carbon nanotube devices
NZ760030A (en) Sensor And Sensing System
Ling The potential and challenges of nanopore sequencing
Collins Single Molecule Sensing with Carbon Nanotube Devices

Legal Events

Date Code Title Description
PB01 Publication
PB01 Publication
SE01 Entry into force of request for substantive examination
SE01 Entry into force of request for substantive examination
REG Reference to a national code

Ref country code: HK

Ref legal event code: DE

Ref document number: 40005350

Country of ref document: HK

WD01 Invention patent application deemed withdrawn after publication
WD01 Invention patent application deemed withdrawn after publication

Application publication date: 20190326