US Patent No: 5,302,509

Number of patents in Portfolio can not be more than 2000

Method for sequencing polynucleotides

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Abstract

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A method is provided for determining the sequence of nucleotides on a single strand DNA molecule. The single strand DNA molecule is attached to a leader oligonucleotide and its complementary strand to a solid state support. Fluorescently-labeled 3'-blocked nucleotide triphosphates, with each of the bases A, G, C, T having a different fluorescent label, are mixed with the bound DNA molecule in the presence of DNA polymerase. The DNA polymerase causes selective addition of only the complementary labeled NTP, thus identifying the next unpaired base in the unknown DNA strand. The 3'-blocking group is then removed, setting the system up for the next NTP addition and so on. The sequence is repeated until no more fluorescently-labeled NTPs can be detected as being added by the polymerase.

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Patent Owner(s)

Patent OwnerAddressTotal Patents
BECKMAN INSTRUMENTS, INC.FULLERTON, CA103

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Inventor(s)

Inventor Name Address # of filed Patents Total Citations
Cheeseman, Peter C Palo Alto, CA 1 381

Cited Art Landscape

Patent Info (Count) # Cites Year
 
The Regents of the University of California (1)
* 5,001,051 Dose critical in-vivo detection of anti-cancer drug levels in blood 41 1986
* Cited By Examiner

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Patent Info (Count) # Cites Year
 
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The Trustees of Columbia University in the City of New York (29)
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NANOFLUIDICS, INC. (2)
7,170,050 Apparatus and methods for optical analysis of molecules 102 2004
* 2006/0060,766 Apparatus and methods for optical analysis of molecules 16 2004
 
Whitehead Institute for Biomedical Research (1)
6,203,993 Methods for the detection of nucleic acids 112 2000
 
FOCUS TECHNOLOGIES, INC. (4)
6,867,004 Methods of using oxidized fungal antigens in antibody testing 1 2001
* 2003/0124,630 Oxidized fungal antigens and methods of making and using thereof 0 2001
7,205,114 Oxidized fungal antigens and methods of making and using thereof 0 2004
* 2005/0112,708 Oxidized fungal antigens and methods of making and using thereof 0 2004
 
BECEEM COMMUNICATIONS, INC. (9)
* 5,837,860 Covalent attachment of nucleic acid molecules onto solid-phases via disulfide bonds 62 1997
6,322,968 De novo or "universal" sequencing array 26 1997
* 6,030,782 Covalent attachment of nucleic acid molecules onto solid-phases via disulfide bonds 41 1997
6,872,521 Polymerase signaling assay 2 1998
* 6,136,962 Covalent attachment of unmodified nucleic acids to silanized solid phase surfaces 27 1998
6,387,626 Covalent attachment of unmodified nucleic acids to silanized solid phase surfaces 17 2000
6,337,188 De novo or "universal" sequencing array 21 2000
6,946,249 De novo or "universal" sequencing array 7 2001
* 2005/0094,807 Accuracy array assay system and method 0 2003
 
THE GOVERNORS OF THE UNIVERSITY OF ALBERTA (2)
7,037,687 Method of determining the nucleotide sequence of oligonucleotides and DNA molecules 141 2002
* 2003/0138,809 Method of determining the nucleotide sequence of oligonucleotides and DNA molecules 60 2002
 
SPECTRAGEN, INC. (5)
* 5,695,934 Massively parallel sequencing of sorted polynucleotides 195 1994
* 5,604,097 Methods for sorting polynucleotides using oligonucleotide tags 271 1994
* 5,863,722 Method of sorting polynucleotides 142 1995
* 5,654,413 Compositions for sorting polynucleotides 89 1995
* 5,635,400 Minimally cross-hybridizing sets of oligonucleotide tags 115 1995
 
Orchid Bio Computer, Inc. (1)
* 5,919,626 Attachment of unmodified nucleic acids to silanized solid phase surfaces 65 1997
 
HOWARD HUGHES MEDICAL INSTITUTE (1)
6,326,489 Surface-bound, bimolecular, double-stranded DNA arrays 57 1997
 
CALIFORNIA INSTITUTE OF TECHNOLOGY (10)
6,818,395 Methods and apparatus for analyzing polynucleotide sequences 167 2000
6,911,345 Methods and apparatus for analyzing polynucleotide sequences 143 2001
* 2002/0025,529 Methods and apparatus for analyzing polynucleotide sequences 28 2001
7,297,518 Methods and apparatus for analyzing polynucleotide sequences by asynchronous base extension 107 2002
* 2002/0164,629 Methods and apparatus for analyzing polynucleotide sequences by asynchronous base extension 45 2002
7,462,449 Methods and apparatuses for analyzing polynucleotide sequences 13 2004
* 2005/0147,992 Methods and apparatus for analyzing polynucleotide sequences 20 2004
* 2006/0172,408 Device for immobilizing chemical and biochemical species and methods of using same 73 2004
* 7,981,604 Methods and kits for analyzing polynucleotide sequences 5 2005
* 2006/0019,267 Methods and kits for analyzing polynucleotide sequences 22 2005
 
Intelligent Biosystems Inc. (5)
* 8,612,161 Methods and compositions for base calling nucleic acids 2 2009
8,481,259 Methods and devices for sequencing nucleic acids in smaller batches 5 2010
* 2010/0323,350 Methods And Devices For Sequencing Nucleic Acids In Smaller Batches 15 2010
9,017,973 Methods and compositions for incorporating nucleotides 0 2011
9,145,589 Methods and devices for sequencing nucleic acids in smaller batches 0 2014
 
INDUSTRIAL TECHNOLOGY RESEARCH INSTITUTE (3)
7,767,441 Bioassay system including optical detection apparatuses, and method for detecting biomolecules 15 2008
* 2009/0146,076 BIOASSAY SYSTEM INCLUDING OPTICAL DETECTION APPARATUSES, AND METHOD FOR DETECTING BIOMOLECULES 15 2008
7,811,810 Bioassay system including optical detection apparatuses, and method for detecting biomolecules 12 2009
 
HELICOS BIOSCIENCES CORPORATION (3)
* 2005/0239,085 Methods for nucleic acid sequence determination 19 2004
* 2005/0170,367 Fluorescently labeled nucleoside triphosphates and analogs thereof for sequencing nucleic acids 20 2004
* 2006/0118,754 Stabilizing a polyelectrolyte multilayer 1 2004
 
BP CORPORATION NORTH AMERICA INC. (2)
7,291,460 Multiplexed systems for nucleic acid sequencing 0 2003
* 2003/0224,439 Multiplexed systems for nucleic acid sequencing 4 2003
 
Arroyo Optics, Inc. (1)
* 2003/0092,051 Pyrophosphorolysis activated polymerization (PAP): application to allele-specific amplification and nucleic acid sequence determination 0 2002
 
Dynex Technologies (1)
9,244,069 Sample plate systems and methods 0 2012
 
MDS ANALYTICAL TECHNOLOGIES (US) INC (2)
6,297,018 Methods and apparatus for detecting nucleic acid polymorphisms 116 2000
* 2005/0227,294 Molecular modification assays involving lipids 1 2005
 
ALERE SAN DIEGO, INC. (1)
7,270,951 Method for direct nucleic acid sequencing 30 2000
 
Pacific Biosciences (1)
* 2009/0082,212 SYSTEM AND METHODS FOR NUCLEIC ACID SEQUENCING OF SINGLE MOLECULES BY POLYMERASE SYNTHESIS 3 2007
 
APPLIED BIOSYSTEMS, LLC (9)
* 5,945,284 Length determination of nucleic acid repeat sequences by discontinuous primer extension 41 1997
6,309,829 Length determination of nucleic acid repeat sequences by discontinuous primer extension 12 1998
6,773,887 Length determination of nucleic acid repeat sequences by discontinuous primer extension 2 2001
7,414,115 Length determination of nucleic acid repeat sequences by discontinuous primer extension 2 2007
* 2009/0062,129 REAGENTS, METHODS, AND LIBRARIES FOR GEL-FREE BEAD-BASED SEQUENCING 15 2007
8,431,691 Reagents, methods, and libraries for bead-based sequencing 1 2008
* 2009/0062,132 ALTERNATIVE NUCLEIC ACID SEQUENCING METHODS 85 2008
8,329,404 Reagents, methods, and libraries for bead-based sequencing 1 2012
9,217,177 Methods for bead-based sequencing 0 2013
 
Genway Biotech Inc. (2)
6,951,742 Methods and vectors for generating antibodies in avian species and uses therefor 1 2000
* 2005/0208,628 Methods and vectors for generating antibodies in avian species and uses therefor 0 2005
 
CITY OF HOPE (13)
6,534,269 Pyrophosphorolysis activated polymerization (PAP): application to allele-specific amplification and nucleic acid sequence determination 14 2001
7,105,298 Serial coupling of restriction cleavage and extension for nucleic acid amplification 1 2002
7,033,763 Pyrophosphorolysis activated polymerization (PAP) 3 2003
* 2004/0009,515 Pyrophosphorolysis activated polymerization (PAP) 1 2003
7,238,480 Pyrophosphorolysis activated polymerization (PAP) 1 2004
* 2005/0095,608 Pyrophosphorolysis activated polymerization (PAP) 0 2004
7,504,221 Pyrophosphorolysis activated polymerization (PAP) 2 2007
* 2007/0298,428 PYROPHOSPHOROLYSIS ACTIVATED POLYMERIZATION (PAP) 0 2007
7,914,995 Reaction mixture for pyrophosphorolysis activated polymerization (PAP) 0 2009
7,919,253 Serial coupling of nucleic acid metabolism and extension for nucleic acid amplification 1 2009
* 2010/0129,871 PYROPHOSPHOROLYSIS ACTIVATED POLYMERIZATION (PAP) 1 2009
8,173,371 Serial coupling of nucleic acid metabolism and extension for nucleic acid amplification 0 2010
* 2011/0124,051 PYROPHOSPHOROLYSIS ACTIVATED POLYMERIZATION (PAP) 1 2010
 
454 LIFE SCIENCES CORPORATION (7)
6,274,320 Method of sequencing a nucleic acid 265 1999
7,244,559 Method of sequencing a nucleic acid 172 2001
7,335,762 Apparatus and method for sequencing a nucleic acid 121 2002
* 2007/0092,872 Apparatus and method for sequencing a nucleic acid 102 2002
7,264,929 Method of sequencing a nucleic acid 156 2002
7,211,390 Method of sequencing a nucleic acid 133 2004
* 2004/0248,161 Method of sequencing a nucleic acid 113 2004
 
EXACT LABORATORIES, INC. (1)
* 2010/0173,320 Methods for Detecting Nucleic Acids Indicative of Cancer 0 2010
 
ROCHE MOLECULAR SYSTEMS, INC. (1)
9,322,062 Process for biosensor well formation 0 2014
 
VERIZON PATENT AND LICENSING INC. (1)
* 2008/0235,019 AGE DETERMINATION USING SPEECH 2 2007
 
ESOTERIX GENETIC LABORATORIES, LLC (25)
* 5,928,870 Methods for the detection of loss of heterozygosity 103 1997
* 6,100,029 Methods for the detection of chromosomal aberrations 71 1997
* 6,146,828 Methods for detecting differences in RNA expression levels and uses therefor 60 1998
* 6,020,137 Methods for the detection of loss of heterozygosity 45 1998
6,280,947 Methods for detecting nucleotide insertion or deletion using primer extension 28 1999
6,919,174 Methods for disease detection 16 2000
6,300,077 Methods for the detection of nucleic acids 38 2000
6,849,403 Apparatus and method for drug screening 9 2000
6,503,718 Methods for detecting mutations using primer extension for detecting disease 18 2001
6,428,964 Method for alteration detection 25 2001
6,498,012 Methods for detecting mutations using primer extension for detecting disease 13 2001
6,475,738 Methods for detecting mutations using primer extension for detecting disease 62 2001
6,482,595 Methods for detecting mutations using primer extension 17 2001
6,750,020 Method for alteration detection 5 2001
7,776,524 Methods for analysis of molecular events 1 2003
* 2003/0203,382 Methods for analysis of molecular events 0 2003
7,981,607 Method for detecting recombinant event 1 2005
* 2009/0170,077 Method for detecting recombinant event 0 2005
9,109,256 Method for monitoring disease progression or recurrence 0 2005
* 2009/0325,153 ANALYSIS OF HETEROGENEOUS NUCLEIC ACID SAMPLES 0 2006
7,811,757 Methods for disease detection 2 2006
* 2007/0202,513 Methods for disease detection 6 2006
* 2008/0248,471 Methods for disease detection 0 2007
8,409,829 Methods for analysis of molecular events 0 2010
8,389,220 Method for detecting a recombinant event 0 2011
 
AFFYMETRIX, INC. (7)
7,329,496 Sequencing of surface immobilized polymers utilizing microflourescence detection 19 2006
* 2006/0172,327 Sequencing of surface immobilized polymers utilizing microflourescence detection 1 2006
* 7,459,275 Sequencing of surface immobilized polymers utilizing microfluorescence detection 20 2006
* 2007/0105,131 Sequencing of surface immobilized polymers utilizing microfluorescence detection 1 2006
8,796,186 System and method for processing large number of biological microarrays 1 2009
* 2010/0081,583 FLUDIC SYSTEM AND METHOD FOR PROCESSING BIOLOGICAL MICROARRAYS IN PERSONAL INSTRUMENTATION 1 2009
* 2011/0009,297 Consumable elements for use with fluid processing and detection systems 3 2010
 
The Board of Trustees of the Leland Stanford Junior University (4)
7,622,281 Methods and compositions for clonal amplification of nucleic acid 4 2005
7,932,034 Heat and pH measurement for sequencing of DNA 99 2007
* 2008/0166,727 Heat and pH Measurement for Sequencing of DNA 90 2007
* 2011/0171,655 PH MEASUREMENT FOR SEQUENCING OF DNA 5 2011
 
MAYO FOUNDATION FOR MEDICAL EDUCATION AND RESEARCH (3)
7,368,233 Methods of screening for lung neoplasm based on stool samples containing a nucleic acid marker indicative of a neoplasm 24 2000
* 2004/0043,467 Supracolonic aerodigestive neoplasm detection 8 2003
7,981,612 Methods of screening for supracolonic neoplasms based on stool samples containing a nucleic acid marker indicative of a neoplasm 0 2008
 
MOLECULAR DEVICES, INC. (4)
6,982,431 Sample analysis systems 157 2002
7,745,142 Molecular modification assays 1 2003
* 2004/0249,586 Molecular modification assays 2 2003
7,632,651 Molecular modification assays 4 2005
 
APPLERA CORPORATION (2)
7,294,464 Length determination of nucleic acid repeat sequences by discontinuous primer extension 0 2004
* 2005/0112,619 Length determination of nucleic acid repeat sequences by discontinuous primer extension 0 2004
 
Pacific Biosciences of California, Inc. (21)
6,255,083 System and methods for nucleic acid sequencing of single molecules by polymerase synthesis 149 1999
6,762,048 System and apparatus for nucleic acid sequencing of single molecules by polymerase synthesis 61 2001
7,229,799 System and method for nucleic acid sequencing by polymerase synthesis 58 2003
* 2003/0194,740 System and method for nucleic acid sequencing by polymerase synthesis 73 2003
7,476,503 Apparatus and method for performing nucleic acid analysis 53 2005
7,315,019 Arrays of optical confinements and uses thereof 88 2005
7,302,146 Apparatus and method for analysis of molecules 52 2005
* 2006/0061,755 Apparatus and method for analysis of molecules 3 2005
* 2006/0063,264 Apparatus and method for performing nucleic acid analysis 29 2005
* 2006/0061,754 Arrays of optical confinements and uses thereof 17 2005
7,476,504 Use of reversible extension terminator in nucleic acid sequencing 43 2006
* 2006/0183,145 Use of reversible extension terminator in nucleic acid sequencing 76 2006
8,530,154 System and method for nucleic acid sequencing by polymerase synthesis 0 2006
7,313,308 Optical analysis of molecules 25 2007
* 2007/0206,189 Optical analysis of molecules 0 2007
* 2008/0241,833 SYSTEM AND METHOD FOR NUCLEIC ACID SEQUENCING BY POLYMERASE SYNTHESIS 6 2007
* 2008/0009,007 CONTROLLED INITIATION OF PRIMER EXTENSION 15 2007
8,980,584 System and methods for nucleic acid sequencing of single molecules by polymerase synthesis 0 2007
8,192,961 System and methods for nucleic acid sequencing of single molecules by polymerase synthesis 17 2007
8,709,725 Arrays of optical confinements and uses thereof 0 2007
7,906,284 Arrays of optical confinements and uses thereof 8 2007
 
TRUSTEES OF TUFTS COLLEGE (19)
6,200,737 Photodeposition method for fabricating a three-dimensional, patterned polymer microstructure 157 1995
6,406,845 Fiber optic biosensor for selectively detecting oligonucleotide species in a mixed fluid sample 50 1997
7,115,884 Self-encoding fiber optic sensor 204 1997
6,327,410 Target analyte sensors utilizing Microspheres 240 1998
6,482,593 Fiber optic biosensor for selectively detecting oligonucleotide species in a mixed fluid sample 82 1998
6,377,721 Biosensor array comprising cell populations confined to microcavities 147 1999
7,348,181 Self-encoding sensor with microspheres 28 1999
6,266,459 Fiber optic sensor with encoded microspheres 151 1999
6,667,159 Optical fiber biosensor array comprising cell populations confined to microcavities 69 2000
* 2003/0027,126 Methods for detecting target analytes and enzymatic reactions 35 2001
6,859,570 Target analyte sensors utilizing microspheres 158 2001
7,622,294 Methods for detecting target analytes and enzymatic reactions 37 2004
* 2005/0130,188 Methods for detecting target analytes and enzymatic reactions 86 2004
7,754,498 Self-encoding sensor with microspheres 5 2005
* 2009/0170,728 METHODS FOR DETECTING TARGET ANALYTES AND ENZYMATIC REACTIONS 100 2009
8,030,094 Self-encoding sensor with microspheres 3 2010
9,377,388 Methods for detecting target analytes and enzymatic reactions 0 2011
8,426,217 Self-encoding sensor with microspheres 1 2011
8,691,591 Self-encoding sensor with microspheres 0 2013
 
MOLECULAR DEVICES, LLC (1)
7,070,921 Molecular modification assays 6 2001
 
GENIA TECHNOLOGIES, INC. (9)
* 2011/0193,249 Systems and methods for forming a nanopore in a lipid bilayer 10 2010
* 2011/0192,723 Systems and methods for manipulating a molecule in a nanopore 10 2010
8,962,242 System for detecting electrical properties of a molecular complex 2 2011
9,110,478 Temperature regulation of measurement arrays 1 2011
9,121,059 Nanopore-based single molecule characterization 0 2011
8,845,880 Nanopore-based single DNA molecule characterization, identification and isolation using speed bumps 0 2011
8,986,629 Sensor circuit for controlling, detecting, and measuring a molecular complex 0 2013
9,041,420 Systems and methods for characterizing a molecule 0 2013
9,377,437 Systems and methods for characterizing a molecule 0 2014
 
SMITH, BRUCE F. (1)
* 6,060,288 Method for performing amplification of nucleic acid on supports 89 1997
 
FLUIDIGM CORPORATION (22)
6,255,475 Chain terminators, the use thereof for nucleic acid sequencing and synthesis and a method of their preparation 65 1997
7,169,560 Short cycle methods for sequencing polynucleotides 156 2004
7,220,549 Stabilizing a nucleic acid for nucleic acid sequencing 61 2004
7,482,120 Methods and compositions for improving fidelity in a nucleic acid synthesis reaction 11 2005
* 2006/0046,258 Applications of single molecule sequencing 50 2005
* 2006/0263,790 Methods for improving fidelity in a nucleic acid synthesis reaction 4 2005
7,635,562 Methods and devices for nucleic acid sequence determination 27 2005
7,666,593 Single molecule sequencing of captured nucleic acids 34 2005
* 2007/0048,744 Single molecule sequencing of captured nucleic acids 5 2005
* 2007/0117,103 Nucleotide analogs 3 2005
* 2007/0117,102 Nucleotide analogs 6 2005
* 2007/0117,104 Nucleotide analogs 10 2005
7,476,734 Nucleotide analogs 13 2005
* 2007/0128,614 Nucleotide analogs 2 2005
* 2007/0196,832 Methods for mutation detection 1 2006
7,397,546 Systems and methods for reducing detected intensity non-uniformity in a laser beam 2 2006
* 2007/0211,467 Systems and methods for reducing detected intensity non-uniformity in a laser beam 0 2006
7,491,498 Short cycle methods for sequencing polynucleotides 11 2006
* 2009/0305,248 METHODS FOR INCREASING ACCURACY OF NUCLEIC ACID SEQUENCING 20 2006
7,897,345 Short cycle methods for sequencing polynucleotides 2 2009
9,012,144 Short cycle methods for sequencing polynucleotides 0 2011
* 2011/0152,114 SHORT CYCLE METHODS FOR SEQUENCING POLYNUCLEOTIDES 0 2011
 
TRUSTEES OF BOSTON UNIVERSITY (2)
8,288,098 Bioreactive agents 0 2011
8,742,084 Bioreactive agents 0 2012
 
LINGVITAE AS (1)
* 2009/0239,213 Identifying a target polynucleotide 0 2005
 
Genaissance Pharmaceuticals, Inc. (2)
6,355,433 Determination of nucleotide sequence variations through limited primer extension 13 2000
6,458,544 Methods for determining single nucleotide variations and genotyping 21 2000
 
Europaisches Laboratorium fur Molekularbiologie (EMBL) (1)
* 5,976,802 Simultaneous sequencing of nucleic acids 77 1997
 
MANTEIA SA (1)
8,143,008 Method of nucleic acid amplification 8 2010
 
AGILENT TECHNOLOGIES, INC. (11)
6,613,508 Methods and compositions for analyzing nucleic acid molecules utilizing sizing techniques 77 1997
6,312,893 Methods and compositions for determining the sequence of nucleic acid molecules 177 1997
6,623,928 Methods and compositions for determining the sequence of nucleic acid molecules 87 2001
6,613,523 Method of DNA sequencing using cleavable tags 15 2001
6,815,212 Methods and compositions for enhancing sensitivity in the analysis of biological-based assays 15 2001
7,052,846 Methods and compositions for analyzing nucleic acid molecules utilizing sizing techniques 8 2003
* 2006/0057,566 METHODS AND COMPOSITIONS FOR ANALYZING NUCLEIC ACID MOLECULES UTILIZING SIZING TECHNIQUES 3 2003
* 7,816,079 Method of DNA sequencing using cleavable tags 0 2003
7,247,434 Methods and compositions for determining the sequence of nucleic acid molecules 0 2003
* 2004/0115,694 Methods and compositions for determining the sequence of nucleic acid molecules 1 2003
7,642,344 Methods and compositions for determining the sequence of nucleic acid molecules 1 2007
 
PRESIDENT AND FELLOWS OF HARVARD COLLEGE (5)
6,548,021 Surface-bound, double-stranded DNA protein arrays 14 1998
6,432,360 Replica amplification of nucleic acid arrays 154 1998
6,485,944 Replica amplification of nucleic acid arrays 191 1999
* 2003/0124,594 Replica amplification of nucleic acid arrays 7 2002
7,785,790 Replica amplification of nucleic acid arrays 119 2007
* Cited By Examiner