CA2533579A1 - Determining the sequence of a polynucleotide - Google Patents
Determining the sequence of a polynucleotide Download PDFInfo
- Publication number
- CA2533579A1 CA2533579A1 CA002533579A CA2533579A CA2533579A1 CA 2533579 A1 CA2533579 A1 CA 2533579A1 CA 002533579 A CA002533579 A CA 002533579A CA 2533579 A CA2533579 A CA 2533579A CA 2533579 A1 CA2533579 A1 CA 2533579A1
- Authority
- CA
- Canada
- Prior art keywords
- target polynucleotide
- polymerase
- carried out
- measuring
- 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.)
- Granted
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
- C12Q1/6844—Nucleic acid amplification reactions
- C12Q1/6858—Allele-specific amplification
-
- 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
- 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
- C12Q2521/101—DNA polymerase
-
- 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
- C12Q2527/00—Reactions demanding special reaction conditions
- C12Q2527/113—Time
-
- 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
- C12Q2565/50—Detection characterised by immobilisation to a surface
- C12Q2565/501—Detection characterised by immobilisation to a surface being an array of oligonucleotides
Landscapes
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Organic Chemistry (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Health & Medical Sciences (AREA)
- Wood Science & Technology (AREA)
- Zoology (AREA)
- Engineering & Computer Science (AREA)
- Immunology (AREA)
- Biochemistry (AREA)
- Microbiology (AREA)
- Molecular Biology (AREA)
- Physics & Mathematics (AREA)
- Biotechnology (AREA)
- Analytical Chemistry (AREA)
- Biophysics (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
- General Health & Medical Sciences (AREA)
- Genetics & Genomics (AREA)
- Chemical Kinetics & Catalysis (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Investigating, Analyzing Materials By Fluorescence Or Luminescence (AREA)
- Investigating Or Analysing Materials By Optical Means (AREA)
Abstract
The sequence of a target polynucleotide can be determined by: (i) contacting the target polynucleotide with a polymerase enzyme and one of the nuncleotides A, T(U), G and C under conditions suitable for the polymerase reaction to proceed; (ii) measuring the time taken for the polymerase to bind to and subsequently dissociate from the target polynucleotide, to thereby determine whether the polymerase has incorporated the nucleotide onto the target polynucleotide; (iii) optionally repeating steps (i) and (ii) with additional nucleotides, to thereby identify the sequence of the target polynucleotide.
Claims (13)
1. A method for identifying the sequence of a target polynucleotide, comprising:
(i) contacting the target polynucleotide with a polymerase enzyme and one of the nucleotides A, T (U), G and C under conditions suitable for the polymerase reaction to proceed;
(ii) measuring the time taken for the polymerase to bind to and subsequently dissociate from the target polynucleotide, to thereby determine whether the polymerase has incorporated the nucleotide onto the target polynucleotide;
(iii) optionally repeating steps (i) and (ii) with additional nucleotides, to thereby identify the sequence of the target polynucleotide.
(i) contacting the target polynucleotide with a polymerase enzyme and one of the nucleotides A, T (U), G and C under conditions suitable for the polymerase reaction to proceed;
(ii) measuring the time taken for the polymerase to bind to and subsequently dissociate from the target polynucleotide, to thereby determine whether the polymerase has incorporated the nucleotide onto the target polynucleotide;
(iii) optionally repeating steps (i) and (ii) with additional nucleotides, to thereby identify the sequence of the target polynucleotide.
2. A method for the identification of a mutation in a target polynucleotide, comprising the steps:
(i) contacting the target polynucleotide with a polymerase enzyme and one of the nucleotides A, T (U), G and C under conditions suitable for the polymerase reaction to proceed;
(ii) measuring the time taken for the polymerase to bind to and subsequently dissociate from the target polynucleotide, to thereby identify whether the polymerase has incorporated the nucleotide onto the target polynucleotide, and with reference to the native sequence of the target, determine whether a mutation exists.
(i) contacting the target polynucleotide with a polymerase enzyme and one of the nucleotides A, T (U), G and C under conditions suitable for the polymerase reaction to proceed;
(ii) measuring the time taken for the polymerase to bind to and subsequently dissociate from the target polynucleotide, to thereby identify whether the polymerase has incorporated the nucleotide onto the target polynucleotide, and with reference to the native sequence of the target, determine whether a mutation exists.
3. A method according to claim 1 or claim 2, wherein steps (i) - (ii) are carried out with each of the different nucleotides in turn, until incorporation is detected.
4. A method according to any preceding claim, wherein the target polynucleotide is immobilised on a support material.
5. A method according to any preceding claim, wherein a plurality of target polynucleotides are immobilised on a support material.
6. A method according to any preceding claim, wherein step (ii) is carried out by measuring applied radiation.
7. A method according to any preceding claim, wherein step (ii) is carried out by measuring raman scattering.
8. A method according to any of claims 1 to 6, wherein step (ii) is carried out by applying a surface electromagnetic wave.
9. A method according to any claim 8, wherein the surface electromagnetic wave is a surface plasmon wave.
10. A method according to any of claims 1 to 8, wherein detection is carried out by measurement of a surface electromagnetic wave.
11. A method according to any preceding claim, wherein the polymerase comprises a detectable label attached thereto.
12. A method according to claim 11, wherein the label is a fluorophore.
13. A method according to claim 11 when pendent on any of claims 1 to 6, wherein the polymerase further comprises an energy donor label or an energy acceptor label, and wherein step (ii) is carried out by measuring energy transfer between the fluorophore and the energy donor or acceptor.
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CA2780958A CA2780958C (en) | 2003-07-24 | 2004-07-26 | Determining the sequence of a polynucleotide |
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| GB0317343.2 | 2003-07-24 | ||
| GBGB0317343.2A GB0317343D0 (en) | 2003-07-24 | 2003-07-24 | Polynucleotide sequencing |
| PCT/GB2004/003232 WO2005010210A2 (en) | 2003-07-24 | 2004-07-26 | Determining the sequence of a polynucleotide |
Related Child Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA2780958A Division CA2780958C (en) | 2003-07-24 | 2004-07-26 | Determining the sequence of a polynucleotide |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| CA2533579A1 true CA2533579A1 (en) | 2005-02-03 |
| CA2533579C CA2533579C (en) | 2012-09-11 |
Family
ID=27772590
Family Applications (2)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA2533579A Expired - Fee Related CA2533579C (en) | 2003-07-24 | 2004-07-26 | Determining the sequence of a polynucleotide |
| CA2780958A Expired - Fee Related CA2780958C (en) | 2003-07-24 | 2004-07-26 | Determining the sequence of a polynucleotide |
Family Applications After (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA2780958A Expired - Fee Related CA2780958C (en) | 2003-07-24 | 2004-07-26 | Determining the sequence of a polynucleotide |
Country Status (21)
| Country | Link |
|---|---|
| US (3) | US7604963B2 (en) |
| EP (1) | EP1649051B1 (en) |
| JP (1) | JP4394684B2 (en) |
| KR (1) | KR20060052863A (en) |
| CN (1) | CN1852991A (en) |
| AT (1) | ATE388243T1 (en) |
| AU (1) | AU2004259893A1 (en) |
| BR (1) | BRPI0412813A (en) |
| CA (2) | CA2533579C (en) |
| DE (1) | DE602004012273T2 (en) |
| DK (1) | DK1649051T3 (en) |
| ES (1) | ES2303083T3 (en) |
| GB (1) | GB0317343D0 (en) |
| IL (1) | IL173314A0 (en) |
| IS (1) | IS8314A (en) |
| MX (1) | MXPA06000962A (en) |
| PL (1) | PL1649051T3 (en) |
| PT (1) | PT1649051E (en) |
| RU (1) | RU2006105626A (en) |
| SI (1) | SI1649051T1 (en) |
| WO (1) | WO2005010210A2 (en) |
Families Citing this family (24)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| ATE225858T1 (en) * | 1997-07-28 | 2002-10-15 | Medical Biosystems Ltd | SEQUENCE ANALYSIS OF NUCLEIC ACIDS |
| GB9923644D0 (en) * | 1999-10-06 | 1999-12-08 | Medical Biosystems Ltd | DNA sequencing |
| GB0112238D0 (en) * | 2001-05-18 | 2001-07-11 | Medical Biosystems Ltd | Sequencing method |
| JP2004347621A (en) * | 2003-04-24 | 2004-12-09 | Dainippon Printing Co Ltd | Transmission type screen |
| JP4431549B2 (en) * | 2006-05-31 | 2010-03-17 | 株式会社日立ハイテクノロジーズ | Fluorescence analyzer |
| GB0721340D0 (en) * | 2007-10-30 | 2007-12-12 | Isis Innovation | Polymerase-based single-molecule DNA sequencing |
| JP4982523B2 (en) * | 2009-05-11 | 2012-07-25 | 株式会社日立ハイテクノロジーズ | Fluorescence analysis method, fluorescence analysis apparatus and image detection method |
| WO2011159942A1 (en) | 2010-06-18 | 2011-12-22 | Illumina, Inc. | Conformational probes and methods for sequencing nucleic acids |
| WO2013096692A1 (en) | 2011-12-21 | 2013-06-27 | Illumina, Inc. | Apparatus and methods for kinetic analysis and determination of nucleic acid sequences |
| US9593371B2 (en) * | 2013-12-27 | 2017-03-14 | Intel Corporation | Integrated photonic electronic sensor arrays for nucleic acid sequencing |
| US9146248B2 (en) | 2013-03-14 | 2015-09-29 | Intelligent Bio-Systems, Inc. | Apparatus and methods for purging flow cells in nucleic acid sequencing instruments |
| US9591268B2 (en) | 2013-03-15 | 2017-03-07 | Qiagen Waltham, Inc. | Flow cell alignment methods and systems |
| US10077470B2 (en) | 2015-07-21 | 2018-09-18 | Omniome, Inc. | Nucleic acid sequencing methods and systems |
| EP3458082A4 (en) * | 2016-04-04 | 2020-07-29 | The Trustees of Columbia University in the City of New York | Dna sequencing by synthesis with nucleotide analogues and raman detection |
| AU2017258619B2 (en) | 2016-04-29 | 2020-05-14 | Pacific Biosciences Of California, Inc. | Sequencing method employing ternary complex destabilization to identify cognate nucleotides |
| JP6828140B2 (en) | 2016-08-15 | 2021-02-10 | オムニオム インコーポレイテッドＯｍｎｉｏｍｅ， Ｉｎｃ． | Methods and systems for sequencing nucleic acids |
| WO2018034780A1 (en) | 2016-08-15 | 2018-02-22 | Omniome, Inc. | Sequencing method for rapid identification and processing of cognate nucleotide pairs |
| WO2018125759A1 (en) | 2016-12-30 | 2018-07-05 | Omniome, Inc. | Method and system employing distinguishable polymerases for detecting ternary complexes and identifying cognate nucleotides |
| US9932631B1 (en) | 2017-09-11 | 2018-04-03 | Omniome, Inc. | Genotyping by polymerase binding |
| CA3050695C (en) | 2017-01-20 | 2024-02-20 | Omniome, Inc. | Process for cognate nucleotide detection in a nucleic acid sequencing workflow |
| SG11201906567YA (en) | 2017-01-20 | 2019-08-27 | Omniome Inc | Allele-specific capture of nucleic acids |
| US10161003B2 (en) | 2017-04-25 | 2018-12-25 | Omniome, Inc. | Methods and apparatus that increase sequencing-by-binding efficiency |
| US9951385B1 (en) | 2017-04-25 | 2018-04-24 | Omniome, Inc. | Methods and apparatus that increase sequencing-by-binding efficiency |
| CA3079411C (en) | 2017-10-19 | 2023-12-05 | Omniome, Inc. | Simultaneous background reduction and complex stabilization in binding assay workflows |
Family Cites Families (12)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US6416952B1 (en) * | 1989-06-07 | 2002-07-09 | Affymetrix, Inc. | Photolithographic and other means for manufacturing arrays |
| ATE428801T1 (en) * | 1996-06-04 | 2009-05-15 | Univ Utah Res Found | MONITORING HYBRIDIZATION DURING PCR |
| ATE225858T1 (en) | 1997-07-28 | 2002-10-15 | Medical Biosystems Ltd | SEQUENCE ANALYSIS OF NUCLEIC ACIDS |
| CN1245218A (en) | 1998-08-19 | 2000-02-23 | 中国人民解放军军事医学科学院放射医学研究所 | Solid-phase one-by-one base nucleic acid analysis method and its instrument |
| ES2310514T3 (en) | 1999-03-10 | 2009-01-16 | Asm Scientific, Inc. | A METHOD FOR DIRECT SEQUENCING OF NUCLEIC ACID. |
| US7056661B2 (en) * | 1999-05-19 | 2006-06-06 | Cornell Research Foundation, Inc. | Method for sequencing nucleic acid molecules |
| WO2001016375A2 (en) | 1999-08-30 | 2001-03-08 | The Government Of The United States Of America, As Represented By The Secretary, Department Of Health And Human Services | High speed parallel molecular nucleic acid sequencing |
| GB9923644D0 (en) * | 1999-10-06 | 1999-12-08 | Medical Biosystems Ltd | DNA sequencing |
| US6908736B1 (en) | 1999-10-06 | 2005-06-21 | Medical Biosystems, Ltd. | DNA sequencing method |
| GB0112238D0 (en) | 2001-05-18 | 2001-07-11 | Medical Biosystems Ltd | Sequencing method |
| US6982165B2 (en) * | 2001-09-24 | 2006-01-03 | Intel Corporation | Nucleic acid sequencing by raman monitoring of molecular deconstruction |
| GB0413082D0 (en) | 2004-06-11 | 2004-07-14 | Medical Biosystems Ltd | Method |
-
2003
- 2003-07-24 GB GBGB0317343.2A patent/GB0317343D0/en not_active Ceased
-
2004
- 2004-07-26 US US10/565,750 patent/US7604963B2/en active Active
- 2004-07-26 CN CNA2004800269313A patent/CN1852991A/en active Pending
- 2004-07-26 CA CA2533579A patent/CA2533579C/en not_active Expired - Fee Related
- 2004-07-26 MX MXPA06000962A patent/MXPA06000962A/en active IP Right Grant
- 2004-07-26 AU AU2004259893A patent/AU2004259893A1/en not_active Abandoned
- 2004-07-26 EP EP04743561A patent/EP1649051B1/en not_active Not-in-force
- 2004-07-26 DE DE602004012273T patent/DE602004012273T2/en active Active
- 2004-07-26 JP JP2006520906A patent/JP4394684B2/en not_active Expired - Fee Related
- 2004-07-26 AT AT04743561T patent/ATE388243T1/en not_active IP Right Cessation
- 2004-07-26 PL PL04743561T patent/PL1649051T3/en unknown
- 2004-07-26 ES ES04743561T patent/ES2303083T3/en active Active
- 2004-07-26 DK DK04743561T patent/DK1649051T3/en active
- 2004-07-26 PT PT04743561T patent/PT1649051E/en unknown
- 2004-07-26 WO PCT/GB2004/003232 patent/WO2005010210A2/en active IP Right Grant
- 2004-07-26 KR KR1020067001539A patent/KR20060052863A/en not_active Application Discontinuation
- 2004-07-26 SI SI200430736T patent/SI1649051T1/en unknown
- 2004-07-26 BR BRPI0412813-3A patent/BRPI0412813A/en not_active IP Right Cessation
- 2004-07-26 CA CA2780958A patent/CA2780958C/en not_active Expired - Fee Related
- 2004-07-26 RU RU2006105626/13A patent/RU2006105626A/en not_active Application Discontinuation
-
2006
- 2006-01-23 IL IL173314A patent/IL173314A0/en unknown
- 2006-02-20 IS IS8314A patent/IS8314A/en unknown
-
2009
- 2009-10-16 US US12/580,596 patent/US7888073B2/en active Active
-
2011
- 2011-01-05 US US12/984,822 patent/US8592183B2/en active Active
Also Published As
| Publication number | Publication date |
|---|---|
| BRPI0412813A (en) | 2006-09-26 |
| DK1649051T3 (en) | 2008-07-07 |
| CA2780958A1 (en) | 2005-02-03 |
| JP4394684B2 (en) | 2010-01-06 |
| US20080070236A1 (en) | 2008-03-20 |
| WO2005010210A2 (en) | 2005-02-03 |
| AU2004259893A1 (en) | 2005-02-03 |
| SI1649051T1 (en) | 2008-10-31 |
| DE602004012273T2 (en) | 2009-04-30 |
| US20110097729A1 (en) | 2011-04-28 |
| CA2780958C (en) | 2016-10-25 |
| US8592183B2 (en) | 2013-11-26 |
| KR20060052863A (en) | 2006-05-19 |
| US7888073B2 (en) | 2011-02-15 |
| RU2006105626A (en) | 2006-08-10 |
| CN1852991A (en) | 2006-10-25 |
| CA2533579C (en) | 2012-09-11 |
| EP1649051B1 (en) | 2008-03-05 |
| PL1649051T3 (en) | 2008-12-31 |
| WO2005010210A3 (en) | 2005-03-24 |
| PT1649051E (en) | 2008-05-26 |
| GB0317343D0 (en) | 2003-08-27 |
| US20100279288A1 (en) | 2010-11-04 |
| JP2006528485A (en) | 2006-12-21 |
| ES2303083T3 (en) | 2008-08-01 |
| MXPA06000962A (en) | 2006-03-30 |
| IL173314A0 (en) | 2006-06-11 |
| EP1649051A2 (en) | 2006-04-26 |
| DE602004012273D1 (en) | 2008-04-17 |
| US7604963B2 (en) | 2009-10-20 |
| ATE388243T1 (en) | 2008-03-15 |
| IS8314A (en) | 2006-02-20 |
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Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| EEER | Examination request | ||
| MKLA | Lapsed |
Effective date: 20220301 |
|
| MKLA | Lapsed |
Effective date: 20200831 |