WO1999045153A3 - An iterative and regenerative dna sequencing method - Google Patents

An iterative and regenerative dna sequencing method Download PDF

Info

Publication number
WO1999045153A3
WO1999045153A3 PCT/US1999/004883 US9904883W WO9945153A3 WO 1999045153 A3 WO1999045153 A3 WO 1999045153A3 US 9904883 W US9904883 W US 9904883W WO 9945153 A3 WO9945153 A3 WO 9945153A3
Authority
WO
WIPO (PCT)
Prior art keywords
dna
segments
iterative
automation
sequence
Prior art date
Application number
PCT/US1999/004883
Other languages
French (fr)
Other versions
WO1999045153A2 (en
Inventor
Douglas H Jones
Original Assignee
Univ Iowa Res Found
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 Univ Iowa Res Found filed Critical Univ Iowa Res Found
Priority to AU30695/99A priority Critical patent/AU3069599A/en
Publication of WO1999045153A2 publication Critical patent/WO1999045153A2/en
Publication of WO1999045153A3 publication Critical patent/WO1999045153A3/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
    • 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
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • C12Q1/683—Hybridisation assays for detection of mutation or polymorphism involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
    • 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
    • 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
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • C12Q1/6855—Ligating adaptors
    • 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
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation

Abstract

An iterative and regenerative method for sequencing DNA is described. This method sequences DNA in discrete intervals starting at one end of a double stranded DNA segment. This method overcomes problems inherent in other sequencing methods, including the need for gel resolution of DNA fragments and the generation of artifacts caused by single-stranded DNA secondary structures. A particular advantage of this invention is that it can create offset collections of DNA segments and sequence the segments in parallel to provide continuous sequence information over long intervals. This method is also suitable for automation and multiplex automation to sequence large sets of segments.
PCT/US1999/004883 1998-03-05 1999-03-04 An iterative and regenerative dna sequencing method WO1999045153A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU30695/99A AU3069599A (en) 1998-03-05 1999-03-04 An iterative and regenerative dna sequencing method

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US09/035,183 1998-03-05
US09/035,183 US6258533B1 (en) 1996-11-01 1998-03-05 Iterative and regenerative DNA sequencing method

Publications (2)

Publication Number Publication Date
WO1999045153A2 WO1999045153A2 (en) 1999-09-10
WO1999045153A3 true WO1999045153A3 (en) 1999-10-21

Family

ID=21881154

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US1999/004883 WO1999045153A2 (en) 1998-03-05 1999-03-04 An iterative and regenerative dna sequencing method

Country Status (3)

Country Link
US (3) US6258533B1 (en)
AU (1) AU3069599A (en)
WO (1) WO1999045153A2 (en)

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9012144B2 (en) 2003-11-12 2015-04-21 Fluidigm Corporation Short cycle methods for sequencing polynucleotides
US9540689B2 (en) 1998-05-01 2017-01-10 Life Technologies Corporation Method of determining the nucleotide sequence of oligonucleotides and DNA molecules

Families Citing this family (41)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2130562A1 (en) * 1992-02-19 1993-09-02 Alexander B. Chetverin Novel oligonucleotide arrays and their use for sorting, isolating, sequencing, and manipulating nucleic acids
US5710000A (en) * 1994-09-16 1998-01-20 Affymetrix, Inc. Capturing sequences adjacent to Type-IIs restriction sites for genomic library mapping
US6780591B2 (en) 1998-05-01 2004-08-24 Arizona Board Of Regents Method of determining the nucleotide sequence of oligonucleotides and DNA molecules
US7056661B2 (en) * 1999-05-19 2006-06-06 Cornell Research Foundation, Inc. Method for sequencing nucleic acid molecules
US7501245B2 (en) 1999-06-28 2009-03-10 Helicos Biosciences Corp. Methods and apparatuses for analyzing polynucleotide sequences
US20030044785A1 (en) * 2001-05-01 2003-03-06 American Type Culture Collection Method for identifying and genotyping microorganisms
DE10144132A1 (en) * 2001-09-07 2003-03-27 Axaron Bioscience Ag Generating and sequencing nucleic acid tags of uniform length, useful e.g. in expression analysis, by cutting double stranded DNA with restriction enzyme then concatamerization
US6902914B2 (en) * 2001-09-28 2005-06-07 Sigma-Aldrich, Co. Recombinant DNA processes using a dNTP mixture containing modified nucleotides
WO2003070977A2 (en) * 2002-02-21 2003-08-28 Nanogen Recognomics Gmbh Method for detecting single nucleotide polymorphisms
AU2003249681A1 (en) * 2002-05-31 2003-12-19 Diversa Corporation Multiplexed systems for nucleic acid sequencing
ES2617576T3 (en) * 2002-08-29 2017-06-19 Becton, Dickinson And Company Substance administration through a rotating microabrasive system
US7049073B2 (en) 2002-10-30 2006-05-23 The University Of Chicago Double stranded nucleic acid biochips
GB0308851D0 (en) * 2003-04-16 2003-05-21 Lingvitae As Method
EP1716254B1 (en) 2004-02-19 2010-04-07 Helicos Biosciences Corporation Methods for analyzing polynucleotide sequences
US7170050B2 (en) 2004-09-17 2007-01-30 Pacific Biosciences Of California, Inc. Apparatus and methods for optical analysis of molecules
EP1790202A4 (en) * 2004-09-17 2013-02-20 Pacific Biosciences California Apparatus and method for analysis of molecules
DE102004049532A1 (en) * 2004-10-09 2006-04-13 Fischer, Achim, Dr. Sequencing of Nucleic Acids via Beach Displacement
CA2593855A1 (en) * 2005-01-31 2006-08-10 Pacific Biosciences Of California, Inc. Use of reversible extension terminator in nucleic acid sequencing
GB0504182D0 (en) * 2005-03-01 2005-04-06 Lingvitae As Method
US7666593B2 (en) 2005-08-26 2010-02-23 Helicos Biosciences Corporation Single molecule sequencing of captured nucleic acids
WO2007149789A2 (en) * 2006-06-22 2007-12-27 Applera Corporation Conversion of target specific amplification to universal sequencing
WO2008045575A2 (en) * 2006-10-13 2008-04-17 J. Craig Venter Institute, Inc. Sequencing method
EP4230747A3 (en) 2008-03-28 2023-11-15 Pacific Biosciences Of California, Inc. Compositions and methods for nucleic acid sequencing
KR20110036638A (en) 2008-07-25 2011-04-07 리차드 더블유. 와그너 Protein screening methods
CA2769006A1 (en) * 2009-07-29 2011-02-03 Pyrobett Pte Ltd. Method and apparatus for conducting an assay
WO2011053987A1 (en) * 2009-11-02 2011-05-05 Nugen Technologies, Inc. Compositions and methods for targeted nucleic acid sequence selection and amplification
SG10201510189WA (en) 2011-10-19 2016-01-28 Nugen Technologies Inc Compositions And Methods For Directional Nucleic Acid Amplification And Sequencing
SG10201504490QA (en) 2012-01-26 2015-07-30 Nugen Technologies Inc Compositions And Methods For Targeted Nucleic Acid Sequence Enrichment And High Efficiency Library Generation
US8597882B2 (en) * 2012-02-03 2013-12-03 Pyrobett Pte. Ltd. Method and apparatus for conducting an assay
SG11201408478QA (en) 2012-06-18 2015-02-27 Nugen Technologies Inc Compositions and methods for negative selection of non-desired nucleic acid sequences
US20150011396A1 (en) 2012-07-09 2015-01-08 Benjamin G. Schroeder Methods for creating directional bisulfite-converted nucleic acid libraries for next generation sequencing
EP3388533A1 (en) * 2012-07-13 2018-10-17 Life Technologies Corporation Human identification using a panel of snps
WO2014144092A1 (en) 2013-03-15 2014-09-18 Nugen Technologies, Inc. Sequential sequencing
WO2015073711A1 (en) 2013-11-13 2015-05-21 Nugen Technologies, Inc. Compositions and methods for identification of a duplicate sequencing read
WO2015131107A1 (en) 2014-02-28 2015-09-03 Nugen Technologies, Inc. Reduced representation bisulfite sequencing with diversity adaptors
MA45491A (en) 2016-06-27 2019-05-01 Juno Therapeutics Inc CMH-E RESTRICTED EPITOPES, BINDING MOLECULES AND RELATED METHODS AND USES
US20200182884A1 (en) 2016-06-27 2020-06-11 Juno Therapeutics, Inc. Method of identifying peptide epitopes, molecules that bind such epitopes and related uses
US11099202B2 (en) 2017-10-20 2021-08-24 Tecan Genomics, Inc. Reagent delivery system
US11851679B2 (en) 2017-11-01 2023-12-26 Juno Therapeutics, Inc. Method of assessing activity of recombinant antigen receptors
EP4192858A1 (en) * 2020-08-10 2023-06-14 Integral Molecular, Inc. Methods and compositions for making antibody libraries and antibodies isolated from the same
US20220336052A1 (en) * 2021-04-19 2022-10-20 University Of Utah Research Foundation Systems and methods for facilitating rapid genome sequence analysis

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1995027080A2 (en) * 1994-04-04 1995-10-12 Lynx Therapeutics Inc Dna sequencing by stepwise ligation and cleavage
US5858671A (en) * 1996-11-01 1999-01-12 The University Of Iowa Research Foundation Iterative and regenerative DNA sequencing method

Family Cites Families (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5102785A (en) 1987-09-28 1992-04-07 E. I. Du Pont De Nemours And Company Method of gene mapping
EP0489058B1 (en) 1989-08-22 2003-11-05 HSC Research Development Corporation Cystic fibrosis gene
CA2036946C (en) 1990-04-06 2001-10-16 Kenneth V. Deugau Indexing linkers
CA2105585A1 (en) 1991-03-06 1992-09-07 Pedro Santamaria Dna sequence-based hla typing method
GB9208733D0 (en) 1992-04-22 1992-06-10 Medical Res Council Dna sequencing method
US5403708A (en) 1992-07-06 1995-04-04 Brennan; Thomas M. Methods and compositions for determining the sequence of nucleic acids
US5500356A (en) * 1993-08-10 1996-03-19 Life Technologies, Inc. Method of nucleic acid sequence selection
US5714330A (en) * 1994-04-04 1998-02-03 Lynx Therapeutics, Inc. DNA sequencing by stepwise ligation and cleavage
US5695934A (en) * 1994-10-13 1997-12-09 Lynx Therapeutics, Inc. Massively parallel sequencing of sorted polynucleotides
US5604097A (en) * 1994-10-13 1997-02-18 Spectragen, Inc. Methods for sorting polynucleotides using oligonucleotide tags
US5763175A (en) * 1995-11-17 1998-06-09 Lynx Therapeutics, Inc. Simultaneous sequencing of tagged polynucleotides

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1995027080A2 (en) * 1994-04-04 1995-10-12 Lynx Therapeutics Inc Dna sequencing by stepwise ligation and cleavage
US5858671A (en) * 1996-11-01 1999-01-12 The University Of Iowa Research Foundation Iterative and regenerative DNA sequencing method

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
JONES D.H.: "An iterative and regenerative method for DNA sequencing", BIOTECHNIQUES (ISSN: 0736-6205), vol. 22, no. 5, May 1997 (1997-05-01), US, pages 938 - 946, XP002111621 *
K.A.PADGETT ET AL.: "Creating seamless junctions independent of restriction sites in PCR cloning", GENE, vol. 168, 1996, nl, pages 31 - 35, XP002111954 *
R.A. GUILFOYLE ET AL.: "Ligation-mediated PCR amplification of specific fragments from a class-II restriction endonuclease total digest", NUCLEIC ACIDS RESEARCH, vol. 25, no. 9, 1997, GB, pages 1854 - 1858, XP002076198 *

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9540689B2 (en) 1998-05-01 2017-01-10 Life Technologies Corporation Method of determining the nucleotide sequence of oligonucleotides and DNA molecules
US9012144B2 (en) 2003-11-12 2015-04-21 Fluidigm Corporation Short cycle methods for sequencing polynucleotides

Also Published As

Publication number Publication date
AU3069599A (en) 1999-09-20
US20030044784A1 (en) 2003-03-06
US20030175780A1 (en) 2003-09-18
WO1999045153A2 (en) 1999-09-10
US6258533B1 (en) 2001-07-10

Similar Documents

Publication Publication Date Title
WO1999045153A3 (en) An iterative and regenerative dna sequencing method
EP0703991A1 (en) Dna sequencing by stepwise ligation and cleavage
PL322611A1 (en) Methods of obtaining l-amini acid by fermentation, dna as well as micro-organism
DE69809263T2 (en) METHODS AND SYSTEM FOR SELECTING DATA SETS
AU3471697A (en) An improved method for the capillary electrophoresis of nucleic acids, proteins and low molecular charged compounds
DK0910633T3 (en) Hybrid polyketide synthase I gene
AU4468696A (en) Conserved yeast nucleic acid sequences
AU2496900A (en) Enhanced sequencing by hybridization using pools of probes
AU3890795A (en) Improved method for nucleotide sequence amplification
AU2002225888A1 (en) Double transposition methods for manipulating nucleic acids
ATE396561T1 (en) METHOD FOR EFFICIENT SYNCHRONIZATION IN A MESSAGE TRANSMISSION SYSTEM
AU4355899A (en) Method for sequencing nucleic acids with reduced errors
DK0691980T3 (en) 7-deazapurine-modifying oligonucleotides
DE69901937T2 (en) METHOD FOR PRODUCING ELECTRODES
AU7086800A (en) High speed parallel molecular nucleic acid sequencing
EP1163359A4 (en) Method for generating transcriptionally active dna fragments
AU2699497A (en) Nucleic acid vaccination for parvoviral infections
AU2816897A (en) Method for sequencing of nucleic acid polymers
WO2000029623A3 (en) Nucleic acids containing single nucleotide polymorphisms and methods of use thereof
EP1131107A4 (en) Antisense modulation of inhibitor-kappa b kinase-alpha expression
AU6372099A (en) Method for the generation of dna fingerprints
WO2001068804A8 (en) Nucleic acid sequences associated with aging, particularly skin aging
AU2540297A (en) Methods for enriching target nucleic acid sequences
WO2001061036A8 (en) A method of mapping restriction endonuclease cleavage sites
WO1996039501A3 (en) Oligonucleotides specific for human papillomavirus

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AL AM AT AU AZ BA BB BG BR BY CA CH CN CU CZ DE DK EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MD MG MK MN MW MX NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT UA UG UZ VN YU ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): GH GM KE LS MW SD SL SZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

AK Designated states

Kind code of ref document: A3

Designated state(s): AL AM AT AU AZ BA BB BG BR BY CA CH CN CU CZ DE DK EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MD MG MK MN MW MX NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT UA UG UZ VN YU ZW

AL Designated countries for regional patents

Kind code of ref document: A3

Designated state(s): GH GM KE LS MW SD SL SZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
NENP Non-entry into the national phase

Ref country code: KR

REG Reference to national code

Ref country code: DE

Ref legal event code: 8642

122 Ep: pct application non-entry in european phase