US Patent No: 6,117,635

Number of patents in Portfolio can not be more than 2000

Nucleic acid amplification oligonucleotides with molecular energy transfer labels and methods based thereon

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Abstract

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The present invention provides labeled nucleic acid amplification oligonucleotides, which can be linear or hairpin primers or blocking oligonucleotides. The oligonucleotides of the invention are labeled with donor and/or acceptor moieties of molecular energy transfer pairs. The moieties can be fluorophores, such that fluorescent energy emitted by the donor is absorbed by the acceptor. The acceptor may be a fluorophore that fluoresces at a wavelength different from the donor moiety, or it may be a quencher. The oligonucleotides of the invention are configured so that a donor moiety and an acceptor moiety are incorporated into the amplification product. The invention also provides methods and kits for directly detecting amplification products employing the nucleic acid amplification primers. When labeled linear primers are used, treatment with exonuclease or by using specific temperature eliminates the need for separation of unincorporated primers. This 'closed-tube' format greatly reduces the possibility of carryover contamination with amplification products, provides for high throughput of samples, and may be totally automated.

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First Claim

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Patent Owner(s)

Patent OwnerAddressTotal Patents
EMD MILLIPORE CORPORATIONBILLERICA, MA476

International Classification(s)

Inventor(s)

Inventor Name Address # of filed Patents Total Citations
Bhatnagar, Satish K Gaithersburg, MD 6 506
Hohman, Robert J Gaithersburg, MD 3 380
Nazarenko, Irina A Gaithersburg, MD 3 380
Winn-Deen, Emily S Potomac, MD 39 1460

Cited Art Landscape

Patent Info (Count) # Cites Year
 
BARCLAY, DOUGLAS C. (1)
* 5,866,336 Nucleic acid amplification oligonucleotides with molecular energy transfer labels and methods based thereon 249 1997
 
NANOGEN, INC. (1)
* 5,565,322 Hybridization of polynucleotides conjugated with chromophores and fluorophores to generate donor-to donor energy transfer system 191 1994
 
Beckman Instruments, Inc. (1)
* 5,593,840 Amplification of nucleic acid sequences 69 1995
 
UNIVERSITY OF MEDICINE AND DENTISTRY OF NEW JERSEY (1)
* 5,312,728 Assays and kits incorporating nucleic acid probes containing improved molecular switch 139 1992
 
PUBLIC HEALTH RESEARCH INSTITUTE (1)
* 5,118,801 Nucleic acid process containing improved molecular switch 197 1988
 
BIO MERIEUX B.V. (1)
* 5,409,818 Nucleic acid amplification process 288 1988
 
MAINE MEDICAL CENTER (1)
* 5,607,834 Fluorescent imperfect hairpin nucleic acid probes 91 1995
 
THE RESEARCH FOUNDATION OF STATE UNIVERSITY OF NEW YORK (1)
* 5,538,871 In situ polymerase chain reaction 39 1995
 
Biotronics Corporation (2)
* 5,348,853 Method for reducing non-specific priming in DNA amplification 83 1991
* 5,567,583 Methods for reducing non-specific priming in DNA detection 25 1994
 
Collaborative Research, Inc. (1)
* 5,391,480 Method for detecting a nucleotide at a specific location within a nucleic acid using exonuclease activity 74 1991
 
DORNIER MEDIZINTECHNIK GMBH (1)
* 5,119,801 Piezoelectric shock wave generator 27 1991
 
Syngene, Inc. (1)
* 4,996,143 Fluorescent stokes shift probes for polynucleotide hybridization 265 1990
 
Enterprise Partners II, L.P. (1)
* 5,532,129 Self-organizing molecular photonic structures based on chromophore- and fluorophore-containing polynucleotides and methods of their use 111 1994
 
BECTON, DICKINSON AND COMPANY (1)
* 5,691,145 Detection of nucleic acids using G-quartets 87 1996
 
ROCHE MOLECULAR SYSTEMS, INC. (6)
* 4,683,202 Process for amplifying nucleic acid sequences 3550 1985
* 4,683,195 Process for amplifying, detecting, and/or-cloning nucleic acid sequences 3073 1986
* 4,889,818 Purified thermostable enzyme 384 1987
* 5,079,352 Purified thermostable enzyme 163 1990
* 5,487,972 Nucleic acid detection by the 5'-3'exonuclease activity of polymerases acting on adjacently hybridized oligonucleotides 217 1993
* 5,573,906 Detection of nucleic acids using a hairpin forming oligonucleotide primer and an energy transfer detection system 163 1993
* Cited By Examiner

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Patent Info (Count) # Cites Year
 
Other [Check patent profile for assignment information] (5)
* 2003/0235,849 Unimolecular segment amplification and sequencing 10 2003
* 2007/0059,690 "Met/fret based method of target nucleic acid detection whereby the donor/acceptor moieties are on complementary strands" 4 2003
* 2006/0252,040 Strand specific detection and quantification 0 2003
* 2004/0265,897 Rolling circle replication reporter systems 15 2004
* 2010/0041,150 EXPANSION OF DEFINITIVE ENDODERM CELLS 2 2009
 
CALIPER LIFE SCIENCES, INC. (1)
6,977,163 Methods and systems for performing multiple reactions by interfacial mixing 38 2002
 
SECRETARY OF STATE FOR DEFENCE, THE (1)
* 7,015,018 Amplification method for detection of target nucleic acids involving-fluorescence energy transfer 2 2000
 
FORENSIC SCIENCE SERVICE LTD. (1)
* 2006/0099,614 Analysis of DNA 5 2005
 
BIOMERIEUX (4)
8,158,345 Labeled oligonucleotide 0 2007
8,663,923 Detection probe 0 2009
* 2011/0091,898 DETECTION PROBE 0 2009
* 2011/0104,762 Detection probe acting by molecular recognition 0 2010
 
ARKRAY, INC. (1)
7,501,239 Method of detecting β3 adrenaline receptor mutant gene and nucleic acid probe and kit therefor 0 2004
 
NIDEK CO., LTD. (1)
* 2006/0001,831 Perimeter 4 2005
 
QIAGEN GMBH (14)
7,205,129 Method for reducing artifacts in nucleic acid amplification 3 2000
* 6,498,023 Generation of single-strand circular DNA from linear self-annealing segments 28 2000
6,977,148 Multiple displacement amplification 94 2001
* 2004/0161,742 Nucleic acid amplification 11 2001
7,553,619 Detection method using dissociated rolling circle amplification 2 2002
7,074,600 Amplification of denatured and stabilized nucleic acids 12 2002
6,977,153 Rolling circle amplification of RNA 35 2002
* 2003/0175,788 Open circle probes with intramolecular stem structures 7 2003
7,297,485 Method for nucleic acid amplification that results in low amplification bias 20 2003
* 2004/0248,103 Proximity-mediated rolling circle amplification 12 2003
7,955,795 Method of whole genome amplification with reduced artifact production 1 2003
* 2004/0248,105 Method of whole genome amplification with reduced artifact production 6 2003
8,309,303 Reverse transcription and amplification of RNA with simultaneous degradation of DNA 0 2006
* 2008/0128,298 NUCLEIC ACID AMPLIFICATION 1 2007
 
Oxitec Limited (1)
9,284,607 Multiplex amplification and detection 0 2011
 
NATIONAL INSTITUTES OF HEALTH (NIH), U.S. DEPT. OF HEALTH AND HUMAN SERVICES (DHHS), U.S. GOVERNMENT (2)
* 2006/0188,902 Primer for nucleic acid detection 2 2006
7,709,626 Primer for nucleic acid detection 0 2008
 
CORNING INCORPORATED (1)
* 2003/0148,284 Solid phase detection of nucleic acid molecules 59 2001
 
GEN-PROBE CARDIFF, LTD. (1)
7,169,554 Monitoring oligonucleotide binding processes using chemiluminescence quenching 3 2000
 
UNIVERSITY OF UTAH (1)
8,557,532 Diagnosis and treatment of drug-resistant Ewing'S sarcoma 0 2010
 
GEN-PROBE INCORPORATED (15)
6,361,945 Molecular torches 80 1999
7,070,925 Method for determining the presence of an RNA analyte in a sample using a modified oligonucleotide probe 4 2000
7,399,852 Kits and reaction mixtures containing modified probe molecules 6 2001
6,534,274 Molecular torches 47 2001
6,849,412 Molecular torches 25 2003
6,835,542 Molecular torches 19 2003
6,946,254 Amplification of HIV-1 gag sequences for detection of sequences associated with drug-resistance mutations 5 2003
* 2005/0106,610 Kits containing modified amplification oligonucleotides 4 2004
7,252,947 Molecular torches and their use under denaturing conditions 0 2005
7,250,259 Molecular torches and their use under strand displacement conditions 0 2005
7,374,877 Amplification of HIV-1 gag sequences for detection of sequences associated with drug-resistance mutations 2 2005
7,563,579 Method for detecting a structured target 0 2007
7,495,093 Amplification and detection method 0 2007
7,572,588 Modified probe molecules having self-complementary regions 0 2007
7,741,027 Amplification of HIV-1 sequences for detection of sequences associated with drug-resistance mutations 1 2008
 
RESEARCH INSTITUTE OF INDUSTRIAL SCIENCE & TECHNOLOGY (1)
* 2007/0158,208 Apparatus and methods for treating ballast water by using electrolysis of natural seawater 3 2004
 
BANK OF AMERICA, N.A. (1)
* 2005/0042,666 Primers and methods for the detection and discrimination of nucleic acids 9 2004
 
TRANSNETTYX, INC. (2)
6,977,178 System and method for transgenic and targeted mutagenesis screening 4 2002
* 2003/0165,922 System, method and apparatus for transgenic and targeted mutagenesis screening 0 2002
 
APPLIED BIOSYSTEMS, LLC (10)
* 7,575,863 Methods, compositions, and kits comprising linker probes for quantifying polynucleotides 13 2004
* 2005/0266,418 Methods, compositions, and kits comprising linker probes for quantifying polynucleotides 45 2004
* 7,601,495 Methods, compositions, and kits comprising linker probes for quantifying polynucleotides 13 2005
* 2006/0078,906 Methods, compositions, and kits comprising linker probes for quantifying polynucleotides 9 2005
7,642,055 Two-color real-time/end-point quantitation of microRNAs (miRNAs) 1 2005
* 2006/0078,924 Two-color real-time/end-point quantitation of micrornas (miRNAs) 8 2005
* 2009/0087,858 Two-color Real-time/End-point Quantitation of MicroRNAs (miRNAs) 1 2008
* 9,068,222 Methods compositions, and kits comprising linker probes for quantifying polynucleotides 0 2009
8,187,815 Method to quantify siRNAs, miRNAs and polymorphic miRNAs 0 2011
8,710,208 Method to quantify siRNAs, miRNAs and polymorphic miRNAs 0 2012
 
VIRCO BVBA (2)
7,977,053 Circular probe amplification (CPA) using energy-transfer primers 0 2006
* 2007/0218,477 CIRCULAR PROBE AMPLIFICATION (CPA) USING ENERGY-TRANSFER PRIMERS 1 2006
 
LOVELACE RESPIRATORY RESEARCH INSTITUTE (2)
7,214,485 Nested methylation-specific polymerase chain reaction cancer detection method 8 2001
* 2004/0038,245 Nested methylation-specific polymerase chain reaction cancer detection method 0 2003
 
ROCHE MOLECULAR SYSTEMS, INC. (1)
7,741,467 Non-fluorescent energy transfer 0 2006
 
GOLDMAN SACHS BANK USA (1)
* 2005/0130,216 Molecular torches and their use under strand displacement conditions 21 2005
 
RIKEN (1)
* 2006/0160,084 Process for amplifying nucleic acid 4 2003
 
YALE UNIVERSITY (6)
6,686,157 Signal amplification with lollipop probes 5 2001
6,861,222 Nucleic acid detection using structured probes 5 2001
6,797,474 Rolling circle replication reporter systems 20 2002
* 2003/0032,024 Rolling circle replication reporter systems 1 2002
* 2004/0115,643 Thermodynamic equilibrium extension of primers 2 2002
7,618,776 Rolling circle replication reporter systems 5 2004
 
Kabushiki Kaisha Dnaform (1)
8,206,902 Method of amplifying nucleic acid and method of detecting mutated nucleic acid using the same 0 2004
 
PHYSICIANS CHOICE LABORATORY SERVICES, LLC (1)
* 2011/0177,512 METHOD FOR ASSURING AMPLIFICATION OF AN ABNORMAL NUCLEIC ACID IN A SAMPLE 0 2010
 
VIACYTE, INC. (13)
8,647,873 PDX1 expressing endoderm 0 2005
* 2009/0011,502 Pdx1 Expressing Endoderm 4 2005
7,985,585 Preprimitive streak and mesendoderm cells 2 2006
* 2007/0004,038 Preprimitive streak and mesendoderm cells 10 2006
7,989,204 Hepatocyte lineage cells 0 2007
8,633,024 PDX1 expressing endoderm 0 2008
8,623,645 Definitive endoderm 2 2009
8,216,836 Methods for identifying factors for differentiating definitive endoderm 2 2009
* 2009/0311,703 METHODS FOR IDENTIFYING FACTORS FOR DIFFERENTIATING DEFINITIVE ENDODERM 4 2009
8,658,151 Expansion of definitive endoderm cells 0 2009
7,993,916 Methods for increasing definitive endoderm production 4 2010
8,574,905 Hepatocyte lineage cells 0 2011
9,222,069 Methods for making anterior foregut endoderm 0 2014
 
Allelogic Biosciences Corporation (3)
7,667,024 Oligonucleotides labeled with a plurality of fluorophores 1 2004
* 2005/0272,053 Oligonucleotides labeled with a plurality of fluorophores 4 2004
* 2010/0240,103 OLIGONUCLEOTIDES LABELED WITH A PLURALITY OF FLUOROPHORES 0 2009
 
ONCOMETHYLOME SCIENCES SA (2)
* 9,050,280 Methylation detection of MGMT 0 2008
* 2011/0287,416 METHYLATION DETECTION 0 2008
 
QLAGEN GmbH (1)
6,921,642 Protein expression profiling 4 2003
 
TRANSNETYX, INC. (10)
7,011,943 Method for detecting a designated genetic sequence in murine genomic DNA 2 2001
* 2003/0082,605 Genomic DNA detection method and system thereof 6 2002
7,282,361 Systems and methods for transgenic and targeted mutagenesis screening 21 2005
* 2005/0170,423 Systems and methods for transgenic and targeted mutagenesis screening 0 2005
* 2005/0221,370 Systems and methods for ordering, performing, and reporting genetic screening 3 2005
* 2006/0014,186 Methods for genotype screening of a strain disposed on an adsorbent carrier 3 2005
* 2005/0272,085 Methods for forensic and congenic screening 2 2005
7,494,817 Methods for genotype screening using magnetic particles 0 2005
* 2006/0014,192 Methods for genotype screening using magnetic particles 3 2005
* 2005/0266,494 System and method for computer network ordering of biological testing 11 2005
 
INVITROGEN DYNAL AS (1)
* 2007/0299,249 Polymer Particles 8 2005
 
NEW YORK BLOOD CENTER, INC. (4)
7,348,164 Universal multi-variant detection system 10 2002
* 2004/0053,284 Universal multi-variant detection system 0 2003
8,192,939 Universal multi-variant detection system 1 2008
* 2011/0053,138 Universal multi-variant detection system 0 2008
 
Olink AB (2)
8,268,554 Method for analyte detection using proximity probes 0 2007
* 2010/0021,890 METHOD FOR ANALYTE DETECTION USING PROXIMITY PROBES 0 2007
 
UT-BATTELLE, LLC (2)
* 2005/0074,779 SERS molecular probe for diagnostics and therapy 4 2003
7,951,535 SERS molecular probe for diagnostics and therapy and methods of use thereof 0 2008
 
GENEOHM SCIENCES CANADA INC. (3)
7,449,289 Methods for detection and identification of methicillin-resistant Staphylococcus aureus 5 2002
* 2005/0019,893 Sequences for detection and identification of methicillin-resistant staphyloccocus 7 2002
* 2006/0252,078 Sequences for detection and identification of methicillin-resistant Staphylococcus aureus 10 2006
 
Exiqon A/S (3)
* 8,192,937 Methods for quantification of microRNAs and small interfering RNAs 2 2005
* 2005/0272,075 Novel methods for quantification of microRNAs and small interfering RNAs 21 2005
8,383,344 Methods for quantification of microRNAs and small interfering RNAs 0 2009
 
SEEGENE, INC. (2)
9,328,377 Detection of target nucleic acid using a target hybridization and detection primer 0 2009
* 2012/0258,447 REAL-TIME MULTIPLEXING DETECTION OF TARGET NUCLEIC ACID SEQUENCES WITH ELIMINATION OF FALSE SIGNALS 1 2010
 
GENEOHM SCIENCES, INC. (2)
7,838,221 (MRSA) 3 2005
8,518,646 0 2007
 
LIFE TECHNOLOGIES CORPORATION (16)
7,537,886 Primers and methods for the detection and discrimination of nucleic acids 25 2000
* 2003/0165,859 Primers and methods for the detection and discrimination of nucleic acids 21 2001
7,160,997 Methods of using FET labeled oligonucleotides that include a 3'.fwdarw.5' exonuclease resistant quencher domain and compositions for practicing the same 13 2002
* 2003/0165,920 Methods of using FET labeled oligonucleotides that include a 3'-5' exonuclease resistant quencher domain and compositions for practicing the same 11 2002
* 2006/0105,348 Compositions and methods for the detection and discrimination of nucleic acids 11 2004
8,304,189 Nucleic acid molecules containing recombination sites and methods of using the same 0 2004
8,030,066 Methods and compositions for synthesis of nucleic acid molecules using multiple recognition sites 2 2006
7,754,453 Methods of using FET labeled oligonucleotides that include a 3′-5′ exonuclease resistant quencher domain and compositions for practicing the same 2 2008
* 2009/0081,676 METHODS OF USING FET LABELED OLIGONUCLEOTIDES THAT INCLUDE A 3'-5' EXONUCLEASE RESISTANT QUENCHER DOMAIN AND COMPOSITIONS FOR PRACTICING THE SAME 2 2008
* 2010/0112,573 Methods, Compositions, and Kits Comprising Linker Probes for Quantifying Polynucleotides 1 2009
8,394,609 Primers and methods for the detection and discrimination of nucleic acids 0 2009
* 2010/0233,699 PRIMERS AND METHODS FOR THE DETECTION AND DISCRIMINATION OF NUCLEIC ACIDS 3 2009
8,088,583 Methods of using FET labeled oligonucleotides that include a 3′-5′ exonuclease resistant quencher domain and compositions for practicing the same 1 2010
8,822,673 Methods of using FET labeled oligonucleotides that include a 3′-5′ exonuclease resistant quencher domain and compositions for practicing the same 0 2010
8,945,884 Methods and compositions for synthesis of nucleic acid molecules using multiplerecognition sites 1 2013
9,309,520 Methods and compositions for synthesis of nucleic acid molecules using multiple recognition sites 0 2014
 
AGILIX CORPORATION (1)
8,043,834 Universal reagents for rolling circle amplification and methods of use 0 2003
 
CYNTHERA, INC. (1)
8,586,357 Markers of definitive endoderm 0 2006
 
THE OHIO STATE UNIVERSITY (2)
* 8,192,938 Methods for quantifying microRNA precursors 0 2006
* 2009/0123,917 METHODS FOR QUANTIFYING MICRORNA PRECURSORS 0 2006
 
GEORGIA TECH RESEARCH CORPORATION (6)
7,081,336 Dual resonance energy transfer nucleic acid probes 27 2002
* 2003/0129,611 Dual resonance energy transfer nucleic acid probes 6 2002
7,297,494 Activatable probes and methods for in vivo gene detection 2 2005
* 2005/0287,548 Activatable probes and methods for in vivo gene detection 3 2005
7,399,591 Dual resonance energy transfer nucleic acid probes 2 2006
* 2006/0127,940 Dual resonance energy transfer nucleic acid probes 2 2006
 
RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY (2)
* 6,277,607 High specificity primers, amplification methods and kits 43 1999
6,365,729 High specificity primers, amplification methods and kits 41 2001
* Cited By Examiner