CA2390312A1 - Oligomer array with pna and/or dna oligomers on a surface - Google Patents

Oligomer array with pna and/or dna oligomers on a surface Download PDF

Info

Publication number
CA2390312A1
CA2390312A1 CA002390312A CA2390312A CA2390312A1 CA 2390312 A1 CA2390312 A1 CA 2390312A1 CA 002390312 A CA002390312 A CA 002390312A CA 2390312 A CA2390312 A CA 2390312A CA 2390312 A1 CA2390312 A1 CA 2390312A1
Authority
CA
Canada
Prior art keywords
general formula
oligomers
oligomer
array according
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
Application number
CA002390312A
Other languages
French (fr)
Other versions
CA2390312C (en
Inventor
Kurt Berlin
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.)
Epigenomics AG
Original Assignee
Epigenomics Ag
Kurt Berlin
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 Epigenomics Ag, Kurt Berlin filed Critical Epigenomics Ag
Publication of CA2390312A1 publication Critical patent/CA2390312A1/en
Application granted granted Critical
Publication of CA2390312C publication Critical patent/CA2390312C/en
Anticipated expiration legal-status Critical
Expired - Fee Related 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
    • C12Q1/68—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
    • 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
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips

Abstract

The invention relates to an oligomer array with PNA (Peptide Nucleic Acid) and/or DNA oligomers on a surface, said oligomers comprising oligomers of 6 to 20 monomers or nucleobases each. Said monomers or nucleobases comprise at least one sequence of the general formula DDCGDD or of the general formula DDTGDD or of the general formula HHCGHH or of the general formula HHCAHH, wherein H represents any of the bases adenine (A), cytosine (C) or thymine (T) and D represents any of the bases adenine (A), guanine (G) or thymine (T). The location of the oligomers on the surface is correlated with the sequence of the oligomers. The inventive oligomer arrays are used to detect cytosine methylations in genomic DNA.

Claims (11)

1. An oligomer array with PNA (peptide nucleic acids) and/or DNA oligomers on a surface, each comprising oligomers of between 6 and 20 monomers or nucleobases, whereby the latter each contain at least one sequence of the general formula DDCGDD or of the general formula DDTGDD or of the general formula HHCGHH or of the general formula HHCAHH, wherein H indicates one of the bases: adenine (A), cytosine (C), or thymine (T) and D represents one of the bases: adenine (A), guanine (G) or thymine (T), and wherein the site of the oligomers on the surface is correlated with the sequence of the oligomers, characterized in that at least 75% of the oligonudeotides contain a sequence of the general formula DDCGDD or of the general formula DDTGDD or of the general formula HHCGHH or of the general formula HHCAHH and that, fitted to each oligomer, which contains a CG sequence, an analogous oligomer is immobilized, which differs from said [first] oligomer only by the fact that it contains a TG
or a CA sequence instead of the CG sequence.
2. The oligomer array according to claim 1, further characterized in that the surface is planar and the oligomers are arranged thereon in a rectangular or hexagonal grid, which permits assignment to coordinates.
3. The oligomer array according to one of the preceding claims, comprising sequences of the general formula DDCGDD and of the general formula DDTGDD and of the general formula HHCGHH and of the general formula HHCAHH.
4. The oligomer array according to one of claims 1 to 2, comprising sequences of the general formula DDCGDD and of the general formula DDTGDD or sequences of the general formula HHCGHH and of the general formula HHCAHH.
5. The oligomer array according to one of the preceding claims, further characterized in that it comprises at least 100 different oligomers.
6. The oligomer array according to one of the preceding claims, further characterized in that the surface is [made] of glass.
7. The oligomer array according to one of claims 1 to 5, further characterized in that the surface is [made] of metal or another conductive material.
8. The oligomer array according to claim 7, further characterized in that the surface is the target of a MALDI mass spectrometer.
9. Use of an oligomer array according to claim 1 for the hybridization of DNA
fragments after prior amplification.
10. The use according to claim 9, further characterized in that the DNA is treated with a bisulfite solution (or hydrogen sulfite solution, disulfite solution) prior to the amplification.
11. The use of an oligomer array according to claim 1 for the detection of cytosine methylations in genomic DNA.
CA2390312A 1999-11-25 2000-11-24 Oligomer array with pna and/or dna oligomers on a surface Expired - Fee Related CA2390312C (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
DE19957827A DE19957827C2 (en) 1999-11-25 1999-11-25 Use of an oligomer array with PNA and / or DNA oligomers on a surface
DE19957827.3 1999-11-25
PCT/DE2000/004301 WO2001038565A2 (en) 1999-11-25 2000-11-24 Oligomer array with pna and/or dna oligomers on a surface

Publications (2)

Publication Number Publication Date
CA2390312A1 true CA2390312A1 (en) 2001-05-31
CA2390312C CA2390312C (en) 2011-05-31

Family

ID=7930999

Family Applications (1)

Application Number Title Priority Date Filing Date
CA2390312A Expired - Fee Related CA2390312C (en) 1999-11-25 2000-11-24 Oligomer array with pna and/or dna oligomers on a surface

Country Status (16)

Country Link
US (1) US6936419B1 (en)
EP (2) EP1232287B1 (en)
JP (2) JP2003514570A (en)
CN (1) CN1413263B (en)
AT (1) ATE362548T1 (en)
AU (1) AU784238B2 (en)
CA (1) CA2390312C (en)
DE (2) DE19957827C2 (en)
DK (1) DK1232287T3 (en)
ES (1) ES2287049T3 (en)
IL (1) IL149801A0 (en)
IS (1) IS2445B (en)
MX (1) MXPA02005221A (en)
NZ (1) NZ518548A (en)
PT (1) PT1232287E (en)
WO (1) WO2001038565A2 (en)

Families Citing this family (43)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2001247414A1 (en) 2000-03-14 2001-09-24 Active Motif Oligonucleotide analogues, methods of synthesis and methods of use
AUPR142500A0 (en) * 2000-11-13 2000-12-07 Human Genetic Signatures Pty Ltd A peptide nucleic acid-based assay for the detection of specific nucleic acid sequences
DE10142643A1 (en) * 2001-08-31 2003-04-24 Clondiag Chip Tech Gmbh Detection of interactions on probe arrays
DE10145226A1 (en) * 2001-09-13 2003-04-10 Lifebits Ag Manufacture of carrier-bound molecules
US20110151438A9 (en) 2001-11-19 2011-06-23 Affymetrix, Inc. Methods of Analysis of Methylation
US7238518B2 (en) * 2002-10-04 2007-07-03 Nisshinbo Industries, Inc. Oligonucleotide-immobilized substrate for detecting methylation
DE602004028478D1 (en) 2003-06-17 2010-09-16 Human Genetic Signatures Pty PROCESS FOR GENOMA PLIFICATION
EP1668148B1 (en) 2003-09-04 2008-12-31 Human Genetic Signatures PTY Ltd. Nucleic acid detection assay
US20050196792A1 (en) * 2004-02-13 2005-09-08 Affymetrix, Inc. Analysis of methylation status using nucleic acid arrays
US8168777B2 (en) 2004-04-29 2012-05-01 Human Genetic Signatures Pty. Ltd. Bisulphite reagent treatment of nucleic acid
DK1794173T3 (en) 2004-09-10 2010-10-25 Human Genetic Signatures Pty Amplification blocks containing intercalating nucleic acids (INA) containing intercalating pseudonucleotides (IPN)
EP1794319B1 (en) 2004-09-30 2014-08-13 Epigenomics AG Method for providing dna fragments derived from an archived sample
CN101111606B (en) 2004-12-03 2012-05-16 人类遗传标记控股有限公司 Methods for simplifying microbial nucleic acids by chemical modification of cytosines
EP1693468A1 (en) 2005-02-16 2006-08-23 Epigenomics AG Method for determining the methylation pattern of a polynucleic acid
EP1871912B1 (en) 2005-04-15 2012-02-29 Epigenomics AG Method for determining DNA methylation in blood or urine samples
CN101203618B (en) 2005-05-26 2013-03-13 人类遗传标记控股有限公司 Isothermal strand displacement amplification using primers containing a non-regular base
US8343738B2 (en) 2005-09-14 2013-01-01 Human Genetic Signatures Pty. Ltd. Assay for screening for potential cervical cancer
KR101211747B1 (en) 2005-09-22 2012-12-12 이데미쓰 고산 가부시키가이샤 Oxide material and sputtering target
EP1969139A1 (en) 2005-11-17 2008-09-17 Epigenomics AG Method for the determination of the dna methylation level of a cpg position in identical cells within a tissue sample
US7901882B2 (en) 2006-03-31 2011-03-08 Affymetrix, Inc. Analysis of methylation using nucleic acid arrays
JP5244103B2 (en) 2006-08-09 2013-07-24 ホームステッド クリニカル コーポレイション Organ-specific protein and method of use thereof
EP2479289B1 (en) 2007-06-08 2016-04-06 Epigenomics AG Method for methylation analysis
US8685675B2 (en) 2007-11-27 2014-04-01 Human Genetic Signatures Pty. Ltd. Enzymes for amplification and copying bisulphite modified nucleic acids
ES2742251T3 (en) 2009-03-16 2020-02-13 Pangu Biopharma Ltd Compositions and methods comprising variants of histidyl tarn synthetase splicing that have non-canonical biological activities
CA2757289A1 (en) 2009-03-31 2010-10-21 Atyr Pharma, Inc. Compositions and methods comprising aspartyl-trna synthetases having non-canonical biological activities
WO2011139714A2 (en) 2010-04-26 2011-11-10 Atyr Pharma, Inc. Innovative discovery of therapeutic, diagnostic, and antibody compositions related to protein fragments of cysteinyl-trna synthetase
CN103096911B (en) 2010-04-27 2018-05-29 Atyr 医药公司 Treatment relevant with the protein fragments of Isoleucyl-tRNA synthetase, diagnosis and the innovation of antibody compositions are found
WO2011139853A2 (en) 2010-04-28 2011-11-10 Atyr Pharma, Inc. Innovative discovery of therapeutic, diagnostic, and antibody compositions related to protein fragments of alanyl trna synthetases
WO2011150279A2 (en) 2010-05-27 2011-12-01 Atyr Pharma, Inc. Innovative discovery of therapeutic, diagnostic, and antibody compositions related to protein fragments of glutaminyl-trna synthetases
CN103097523B (en) 2010-04-29 2016-09-28 Atyr医药公司 The innovation for the treatment of, diagnosis and the antibody compositions relevant to the protein fragments of Asparaginyl-tRNA synthetase finds
AU2011248457B2 (en) 2010-04-29 2017-02-16 Pangu Biopharma Limited Innovative discovery of therapeutic, diagnostic, and antibody compositions related to protein fragments of valyl tRNA synthetases
US8981045B2 (en) 2010-05-03 2015-03-17 Atyr Pharma, Inc. Innovative discovery of therapeutic, diagnostic, and antibody compositions related to protein fragments of methionyl-tRNA synthetases
US8961961B2 (en) 2010-05-03 2015-02-24 a Tyr Pharma, Inc. Innovative discovery of therapeutic, diagnostic, and antibody compositions related protein fragments of arginyl-tRNA synthetases
CN105820252B (en) 2010-05-03 2020-07-21 Atyr 医药公司 Innovative discovery of therapeutic, diagnostic, and antibody compositions related to protein fragments of phenylalanyl- α -tRNA synthetases
CA2798139C (en) 2010-05-04 2019-09-24 Atyr Pharma, Inc. Innovative discovery of therapeutic, diagnostic, and antibody compositions related to protein fragments of p38 multi-trna synthetase complex
CN103200953B (en) 2010-05-14 2017-02-15 Atyr 医药公司 Innovative discovery of therapeutic, diagnostic, and antibody compositions related to protein fragments of phenylalanyl-beta-trna synthetases
AU2011256366C1 (en) 2010-05-17 2017-06-15 Pangu Biopharma Limited Innovative discovery of therapeutic, diagnostic, and antibody compositions related to protein fragments of leucyl-tRNA synthetases
EP2575857B1 (en) 2010-06-01 2018-01-24 aTyr Pharma, Inc. Innovative discovery of therapeutic, diagnostic, and antibody compositions related to protein fragments of lysyl-trna synthetases
AU2011289831C1 (en) 2010-07-12 2017-06-15 Pangu Biopharma Limited Innovative discovery of therapeutic, diagnostic, and antibody compositions related to protein fragments of glycyl-tRNA synthetases
CN103108650A (en) 2010-08-25 2013-05-15 Atyr医药公司 Innovative discovery of therapeutic, diagnostic, and antibody compositions related to protein fragments of tyrosyl-trna synthetases
MY167564A (en) 2011-09-07 2018-09-14 Human Genetic Signatures Pty Ltd Molecular detection assay
EP3311847A1 (en) 2012-02-16 2018-04-25 Atyr Pharma, Inc. Histidyl-trna synthetases for treating autoimmune and inflammatory diseases
MX367366B (en) 2012-11-27 2019-08-16 Univ Pontificia Catolica Chile Compositions and methods for diagnosing thyroid tumors.

Family Cites Families (20)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5695926A (en) * 1990-06-11 1997-12-09 Bio Merieux Sandwich hybridization assays using very short capture probes noncovalently bound to a hydrophobic support
US5474796A (en) * 1991-09-04 1995-12-12 Protogene Laboratories, Inc. Method and apparatus for conducting an array of chemical reactions on a support surface
WO1993025563A1 (en) 1992-06-17 1993-12-23 City Of Hope A method of detecting and discriminating between nucleic acid sequences
US5824473A (en) * 1993-12-10 1998-10-20 California Institute Of Technology Nucleic acid mediated electron transfer
US5589330A (en) * 1994-07-28 1996-12-31 Genzyme Corporation High-throughput screening method for sequence or genetic alterations in nucleic acids using elution and sequencing of complementary oligonucleotides
US5514551A (en) * 1994-10-14 1996-05-07 Gen-Probe Incorporated Compositions for the detection of Chlamydia trachomatis
US6017704A (en) 1996-06-03 2000-01-25 The Johns Hopkins University School Of Medicine Method of detection of methylated nucleic acid using agents which modify unmethylated cytosine and distinguishing modified methylated and non-methylated nucleic acids
GB9620769D0 (en) * 1996-10-04 1996-11-20 Brax Genomics Ltd Nucleic acid sequencing
DK0937096T3 (en) * 1996-11-06 2004-06-14 Sequenom Inc Method of mass spectrometry analysis
GB9707980D0 (en) * 1997-04-21 1997-06-11 Brax Genomics Ltd Characterising DNA
AU742599B2 (en) * 1997-07-22 2002-01-10 Qiagen Genomics, Inc. Multiple functionalities within an array element and uses thereof
CN1265156A (en) * 1997-07-22 2000-08-30 拉普吉恩公司 Amplification and other enzymatic reactions preformed on nucleic acid arrays
DE19754482A1 (en) * 1997-11-27 1999-07-01 Epigenomics Gmbh Process for making complex DNA methylation fingerprints
DK1036202T3 (en) * 1997-12-05 2002-08-12 Max Planck Gesellschaft Method for Identifying Nucleic Acids by Matrix Assisted Laser Desorption / Ionization Mass Spectrometry
WO1999029897A1 (en) * 1997-12-05 1999-06-17 MAX-PLANCK-Gesellschaft zur Förderung der Wissenschaften e.V. Method for identifying nucleic acids by electro-spray mass spectrometry
DE69921982T2 (en) * 1998-04-30 2005-12-29 MAX-PLANCK-Gesellschaft zur Förderung der Wissenschaften e.V. NOVEL METHOD FOR IDENTIFYING CLONES WITH A DESIRED BIOLOGICAL PROPERTY, EXPRESSED FROM AN EXPRESSION BENCH
US6048695A (en) * 1998-05-04 2000-04-11 Baylor College Of Medicine Chemically modified nucleic acids and methods for coupling nucleic acids to solid support
US6664045B1 (en) * 1998-06-18 2003-12-16 Boston Probes, Inc. PNA probes, probe sets, methods and kits pertaining to the detection of microorganisms
US6605432B1 (en) * 1999-02-05 2003-08-12 Curators Of The University Of Missouri High-throughput methods for detecting DNA methylation
DE19951189C2 (en) * 1999-10-15 2003-11-06 Epigenomics Ag Method to distinguish 5-position methylation changes from cytosine bases and cytosine to thymine mutations and to detect single nucleotide polymorphisms (SNPs) or point mutations in genomic DNA

Also Published As

Publication number Publication date
WO2001038565A3 (en) 2001-11-15
CN1413263B (en) 2012-07-04
AU2827001A (en) 2001-06-04
IL149801A0 (en) 2002-11-10
DE19957827A1 (en) 2001-06-21
ES2287049T3 (en) 2007-12-16
IS2445B (en) 2008-11-15
EP1816216A2 (en) 2007-08-08
ATE362548T1 (en) 2007-06-15
PT1232287E (en) 2007-08-21
DK1232287T3 (en) 2007-09-24
EP1232287B1 (en) 2007-05-16
NZ518548A (en) 2004-12-24
WO2001038565A2 (en) 2001-05-31
DE50014333D1 (en) 2007-06-28
JP2003514570A (en) 2003-04-22
EP1232287A2 (en) 2002-08-21
DE19957827C2 (en) 2003-06-12
IS6364A (en) 2002-04-26
AU784238B2 (en) 2006-02-23
EP1816216A3 (en) 2009-06-03
CN1413263A (en) 2003-04-23
JP2007175051A (en) 2007-07-12
CA2390312C (en) 2011-05-31
US6936419B1 (en) 2005-08-30
MXPA02005221A (en) 2004-08-23

Similar Documents

Publication Publication Date Title
CA2390312A1 (en) Oligomer array with pna and/or dna oligomers on a surface
US8758995B2 (en) Solid phase sequencing of biopolymers
US7144699B2 (en) Iterative resequencing
IS6705A (en) A method for determining the level of methylation of targeted cytosines in the DNA genome in the sequence 5'-CPG-3 '
AU5544696A (en) Solid phase sequencing of biopolymers
WO1999014375A3 (en) Dna typing by mass spectrometry with polymorphic dna repeat markers
WO2001073119A3 (en) Methods for genotyping by hybridization analysis
HK1015416A1 (en) Expression monitoring by hybridization to high density oligonucleotide arrays
WO2003052134A3 (en) Oligonucleotides comprising intercalator pseudonucleotide(s) for detection of nucleic acids and mutants hereof
IL102765A (en) Reagents and methods to detect and determine mycobacterium nucleic acids
US7008770B1 (en) Method for the controlled implementation of complex PCR amplifications
EP1312685A3 (en) Oligonucleotide array for detecting the methylation state
CA2413427A1 (en) Multiplex sequencing method
US20050202420A1 (en) Oligonucleotides or pna oligomers and a method for detecting the methylation state of genomic dna in a parallel manner
Fu et al. A DNA sequencing strategy that requires only five bases of known terminal sequence for priming.
CA2442438A1 (en) Oligonucleotide-immobilized substrate for detecting methylation
Corona et al. High throughput screening of genetic polymorphisms by matrix-assisted laser desorption ionization time-of-flight mass spectrometry
US20060063193A1 (en) Solid phase sequencing of double-stranded nucleic acids
AU4251800A (en) Solid phase sequencing of biopolymers
Bray et al. Genotyping by mass spectrometry
DE20121966U1 (en) Designing primers and probes for analyzing diseases associated with cytosine methylation state e.g. arthritis, cancer, aging, arteriosclerosis comprising fragments of chemically modified genes associated with cell cycle
US20040248176A1 (en) Iterative resequencing
EP1398389A3 (en) Variant of HNF-1alpha gene having a single nucleotide polymorphism and variant of protein encoded by the same

Legal Events

Date Code Title Description
EEER Examination request
MKLA Lapsed

Effective date: 20131126