Massive Parallel Method For Decoding Dna And Rna - EP3034627

The patent EP3034627 was granted to The Trustees OF Columbia University IN The City OF NEW York on Jan 30, 2019. The application was originally filed on Oct 5, 2001 under application number EP15195765A. The patent is currently recorded with a legal status of "Revoked".

EP3034627

THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
Application Number
EP15195765A
Filing Date
Oct 5, 2001
Status
Revoked
Jan 6, 2023
Publication Date
Jan 30, 2019
External Links
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ILLUMINAOct 29, 2019MAIWALDADMISSIBLE

Patent Citations (12) New

Patent citations refer to prior patents cited during different phases such as opposition or international search.

Citation PhasePublication Number
DESCRIPTIONUS5047519
DESCRIPTIONUS5302509
OPPOSITIONUS5151507
OPPOSITIONUS5547839
OPPOSITIONUS5608063
OPPOSITIONWO0053805
OPPOSITIONWO9106678
SEARCHUS6074823
SEARCHWO0006770
SEARCHWO0053805
SEARCHWO0192284
SEARCHWO9106678

Non-Patent Literature (NPL) Citations (68) New

NPL citations refer to non-patent references such as research papers, articles, or other publications cited during examination or opposition phases.

Citation PhaseReference Text
DESCRIPTION- ANTAO VP; LAI SY; TINOCO I JR., "A thermodynamic study of unusually stable RNA and DNA hairpins", NUCLEIC ACIDS RES., (1991), vol. 19, pages 5901 - 5905
DESCRIPTION- AXELROD VD; VARTIKYAN RM; AIVAZASHVILI VA; BEA EALASHVILI RS, "Specific termination of RNA polymerase synthesis as a method of RNA and DNA sequencing", NUCLEIC ACIDS RES., (1978), vol. 5, no. 10, pages 3549 - 3563
DESCRIPTION- BADMAN ER; COOKS RG., "A Parallel Miniature Cylindrical Ion Trap Array", ANAL. CHEM., (2000), vol. 72, no. 14, pages 3291 - 3297
DESCRIPTION- BOWLING JM; BRUNER KL; CMARIK JL; TIBBETTS C, "Neighboring nucleotide interactions during DNA sequencing gel electrophoresis", NUCLEIC ACIDS RES., (1991), vol. 19, pages 3089 - 3097
DESCRIPTION- BURGESS K; JACUTIN SE; LIM D; SHITANGKOON A, "An approach to photolabile, fluorescent protecting groups", J. ORG. CHEM., (1997), vol. 62, no. 15, pages 5165 - 5168
DESCRIPTION- CHEE M; YANG R; HUBBELL E; BERNO, A; HUANG, XC.; STERN D; WINKLER, J; LOCKHART DJ; MORRIS M S; FODOR, SP, "Accessing genetic information with high-density DNA arrays", SCIENCE, (1996), vol. 274, pages 610 - 614
DESCRIPTION- DIZIDIC I; CARROL, DI; STILLWELL, RN; HORNING, MG, "Atmospheric pressure ionization (API) mass spectrometry: formation of phenoxide ions from chlorinated aromatic compounds", ANAL. CHEM., (1975), vol. 47, pages 1308 - 1312
DESCRIPTION- FUJI K; NAKANO S; FUJITA E, "An improved method for methoxymethylation of alcohols under mild acidic conditions", SYNTHESIS, (1975), pages 276 - 277
DESCRIPTION- IRELAND RE; VARNEY MD, "Approach to the total synthesis of chlorothricolide-synthesis of (+/-)-19.20-dihydro-24-0-methylchlorothricolide, methyl-ester, ethyl carbonate", J. ORG. CHEM., (1986), vol. 51, pages 635 - 648
DESCRIPTION- JU J; RUAN C; FULLER CW; GLAZER AN; MATHIES RA, "Energy transfer fluorescent dye-labeled primers for DNA sequencing and analysis", PROC. NATL. ACAD. SCI. USA, (1995), vol. 92, pages 4347 - 4351
DESCRIPTION- LEE LG; CONNELL CR; WOO SL; CHENG RD; MCARDLE BF; FULLER CW; HALLORAN ND; WILSON RK, "DNA sequencing with dye-labeled terminators and T7 DNA -polymerase-effect of dyes and dNTPs on incorporation of dye-terminators and probability analysis of termination fragments", NUCLEIC ACIDS RES., (1992), vol. 20, pages 2471 - 2483
DESCRIPTION- LEE LG; SPURGEON SL; HEINER CR; BENSON SC; ROSENBLUM BB; MENCHEN SM; GRAHAM RJ; CONSTANTINESCU A; UPADHYA KG; CASSEL JM, "New energy transfer dyes for DNA sequencing", NUCLEIC ACIDS RES., (1997), vol. 25, pages 2816 - 2822
DESCRIPTION- METZKER ML; RAGHAVACHARI R; RICHARDS S; JACUTIN SE; CIVITELLO A; BURGESS K; GIBBS RA, "Termination of DNA synthesis by novel 3'-modified-deoxyribonucleoside 5'-triphosphates", NUCLEIC ACIDS RES., (1994), vol. 22, pages 4259 - 4267
DESCRIPTION- O'CONNOR PM; JACKMAN J; BAE I; MYERS TG; FAN S; MUTOH M; SCUDIERO DA; MONKS A; SAUSVILLE EA; WEINSTEIN JN, "Characterization of the p53 tumor suppressor pathway in cell lines of the National Cancer Institute anticancer drug screen and correlations with the growth-inhibitory potency of 123 anticancer agents", CANCER RES., (1997), vol. 57, pages 4285 - 4300, XP002920858
DESCRIPTION- PELLETIER H; SAWAYA MR; KUMAR A; WILSON SH; KRAUT J, "Structures of ternary complexes of rat DNA polymerase B, a DNA template-primer, and ddCTP", SCIENCE, (1994), vol. 264, pages 1891 - 1903
DESCRIPTION- PENNISI E., "DOE Team Sequences Three Chromosomes", SCIENCE, (2000), vol. 288, pages 417 - 419
DESCRIPTION- PILLAI VNR, "Photoremovable Protecting Groups in Organic Synthesis", SYNTHESIS, (1980), pages 1 - 62
DESCRIPTION- ROLLAF F., "Sodium-borohydride reactions under phase-transfer conditions - reduction of azides to amines", J. ORG. CHEM., (1982), vol. 47, pages 4327 - 4329
DESCRIPTION- RONAGHI M; UHLEN M; NYREN P, "A sequencing Method based on real-time pyrophosphate", SCIENCE, (1998), vol. 281, pages 364 - 365
DESCRIPTION- ROSENBLUM BB; LEE LG; SPURGEON SL; KHAN SH; MENCHEN SM; BEINER CR; CHEN SM, "New dye-labeled terminators for improved DNA sequencing patterns", NUCLEIC ACIDS RES., (1997), vol. 25, pages 4500 - 4504
DESCRIPTION- ROSES A., "Pharmacogenetics and the practice of medicie", NATURE, (2000), vol. 405, pages 857 - 865
DESCRIPTION- SCHENA M; SHALON D; DAVIS, R; BROWN P.O., "Quantitative monitoring of gene expression patterns with a cDNA microarray", SCIENCE, (1995), vol. 270, pages 467 - 470
DESCRIPTION- SIMPSON PC; ADAM DR; WOOLLEY T; THORSEN T; JOHNSTON R; SENSABAUGH GF; MATHIES RA, "High-throughput genetic analysis using microfabricated 96-sample capillary array electrophoresis microplates", PROC. NATL. ACAD. SCI. U. S. A., (1998), vol. 95, pages 2256 - 2261
DESCRIPTION- SMITH LM; SANDERS JZ; KAISER RJ; HUGHES P; DODD C; CONNELL CR; HEINER C; KENT SBH; HOOD LE, "Fluorescence detection in automated DNA sequencing analysis", NATURE, (1986), vol. 321, pages 674 - 679
DESCRIPTION- VELCULESCU VE; ZHANG, I; VOGELSTEIN, B.; KINZLER KW, "Serial Analysis of Gene Expression", SCIENCE, (1995), vol. 270, pages 484 - 487
DESCRIPTION- WELCH MB; BURGESS K, "Synthesis of fluorescent, photolabile 3'-O-protected nucleoside triphosphates for the base addition sequencing scheme", NUCLEOSIDES AND NUCLEOTIDES, (1999), vol. 18, pages 197 - 201, XP009010274
DESCRIPTION- YAMAKAWA H; OHARA 0, "A DNA cycle sequencing reaction that minimizes compressions on automated fluorescent sequencers", NUCLEIC. ACIDS. RES., (1997), vol. 25, pages 1311 - 1312
DESCRIPTION- ZHANG B.; LIU H.; KARGER BL.; FORET F., "Microfabricated devices for capillary electrophoresis-electrospray mass spectrometry", ANAL. CHEM., (1999), vol. 71, pages 3258 - 3264
DESCRIPTION- ZHU Z; CHAO J; YU H; WAGGONER AS, "Directly labeled DNA probes using fluorescent nucleotides with different length linkers", NUCLEIC ACIDS RES., (1994), vol. 22, pages 3418 - 3422, XP002074425
DESCRIPTION- KHETERPAL I; SCHERER J; CLARK SM; RADHAKRISHNAN A; JU J; GINTHER CL; SENSABAUGH GF; MATHIES RA, "DNA Sequencing Using a Four-Color Confocal Fluorescence Capillary Array Scanner", ELECTROPHORESIS, (1996), vol. 17, doi:doi:10.1002/elps.1150171209, pages 1852 - 1859, XP000901208
DESCRIPTION- HUNG SC; JU J; MATHIES RA; GLAZER AN., "Cyanine dyes with high absorption cross section as donor chromophores in energy transfer primers", ANAL BIOCHEM., (1996), vol. 243, no. 1, doi:doi:10.1006/abio.1996.0477, pages 15 - 27, XP002055578
DESCRIPTION- HYMAN ED, "A new method of sequencing DNA", ANALYTICAL BIOCHEMISTRY, (1988), vol. 174, doi:doi:10.1016/0003-2697(88)90041-3, pages 423 - 436, XP024825574
DESCRIPTION- KHOUKHI N; VAULTIER M; CARRIE R, "Synthesis and reactivity of methyl-azido butyrates and ethyl-azido valerates and of the corresponding acid chlorides as useful reagents for the aminoalkylation", TETRAHEDRON, (1987), vol. 43, doi:doi:10.1016/S0040-4020(01)81492-7, pages 1811 - 1822, XP022057548
DESCRIPTION- KAMAL A; LAXMAN E; RAO NV, "A mild and rapid regeneration of alcohols from their allylic ethers by chlorotrimethylsilane/sodium iodide", TETRAHEDRON LETTERS, (1999), vol. 40, doi:doi:10.1016/S0040-4039(98)02314-4, pages 371 - 372, XP004152555
DESCRIPTION- LIU H.H.; FELTON C.; XUE Q.F.; ZHANG B.; JEDRZEJEWSKI P.; KARGER B.L.; FORET F., "Development of multichannel Devices with an Array of Electrospray tips for high-throughput mass spectrometry", ANAL. CHEM., (2000), vol. 72, doi:doi:10.1021/ac000115l, pages 3303 - 3310, XP002163521
DESCRIPTION- BADMAN ER; COOKS RG, "Cylindrical Ion Trap Array with Mass Selection by Variation in Trap Dimensions", ANAL. CHEM., (2000), vol. 72, no. 20, doi:doi:10.1021/ac000377n, pages 5079 - 5086, XP055089302
DESCRIPTION- WOOLLEY AT; SENSABAUGH GF; MATHIES RA, "High-Speed DNA Genotyping Using Microfabricated Capillary Array Electrophoresis Chips", ANAL. CHEM., (1997), vol. 69, no. 11, doi:doi:10.1021/ac961237+, pages 2181 - 2186, XP000696550
DESCRIPTION- SALAS-SOLANO O; CARRILHO E; KOTLER L; MILLER AW; GOETZINGER W; SOSIC Z; KARGER BL, "Routine DNA sequencing of 1000 bases in less than one hour by capillary electrophoresis with replaceable linear polyacrylamide solutions", ANAL. CHEM., (1998), vol. 70, doi:doi:10.1021/ac980457f, pages 3996 - 4003, XP001088167
DESCRIPTION- FU DJ; TANG K; BRAUN A; REUTER D; DARNHOFER-DEMAR B; LITTLE DP; O'DONNELL MJ; CANTOR CR; KOSTER H, "Sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry", NAT BIOTECHNOL., (1998), vol. 16, doi:doi:10.1038/nbt0498-381, pages 381 - 384, XP001118386
DESCRIPTION- TABOR S; RICHARDSON C.C., "DNA sequence analysis with a modified bacteriophage T7 DNA polymerase", PROC. NATL. ACAD. SCI. U.S.A., (1987), vol. 84, doi:doi:10.1073/pnas.84.14.4767, pages 4767 - 4771, XP000051702
DESCRIPTION- WOOLLEY AT; MATHIES RA, "Ultra-high-speed DNA fragment separations using microfabricated capillary array electrophoresis chips", PROC. NATL. ACAD. SCI. USA., (1994), vol. 91, doi:doi:10.1073/pnas.91.24.11348, pages 11348 - 11352, XP002940483
DESCRIPTION- TABOR S.; RICHARDSON, CC, "A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy- and dideoxyribonucleotides", PROC. NATL. ACAD. SCI. U.S.A., (1995), vol. 92, doi:doi:10.1073/pnas.92.14.6339, pages 6339 - 6343, XP000606203
DESCRIPTION- OLEJNIK J; SONAR S; KRZYMANSKA-OLEJNIK E; ROTHSCHILD KJ, "Photocleavable biotin derivatives: a versatile approach for the isolation of biomolecules", PROC. NATL. ACAD. SCI. USA., (1995), vol. 92, doi:doi:10.1073/pnas.92.16.7590, pages 7590 - 7594, XP055366666
DESCRIPTION- ZHANG XH; CHIANG VL, "Single-stranded DNA ligation by T4 RNA ligase for PCR cloning of 5'-noncoding fragments and coding sequence of a specific gene", NUCLEIC ACIDS RES., (1996), vol. 24, doi:doi:10.1093/nar/24.5.990, pages 990 - 991, XP002983384
DESCRIPTION- JU J; GLAZER AN; MATHIES RA, "Cassette labeling for facile construction of energy transfer fluorescent primers", NUCLEIC ACIDS RES., (1996), vol. 24, doi:doi:10.1093/nar/24.6.1144, pages 1144 - 1148, XP002937505
DESCRIPTION- OLEJNIK J; LUDEMANN HC; KRZYMANSKA-OLEJNIK E; BERKENKAMP S; HILLENKAMP F; ROTHSCHILD KJ, "Photocleavable peptide-DNA conjugates: synthesis and applications to DNA analysis using MALDI-MS", NUCLEIC ACIDS RES., (1999), vol. 27, doi:doi:10.1093/nar/27.23.4626, pages 4626 - 4631, XP002220753
DESCRIPTION- PROBER JM; TRAINOR GL; DAM RJ; HOBBS FW; ROBERTSON CW; ZAGURSKY RJ; COCUZZA AJ; JENSEN MA; BAUMEISTER K, "A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides", SCIENCE, (1987), vol. 238, doi:doi:10.1126/science.2443975, pages 336 - 341, XP000604017
DESCRIPTION- SAXON E; BERTOZZI CR, "Cell surface engineering by a modified Staudinger reaction", SCIENCE, (2000), vol. 287, doi:doi:10.1126/science.287.5460.2007, pages 2007 - 2010, XP002188901
DESCRIPTION- CARUTHERS MH., "Gene synthesis machines: DNA chemistry and its uses", SCIENCE, (1985), vol. 230, doi:doi:10.1126/science.3863253, pages 281 - 285, XP008012652
DESCRIPTION- CANARD B; CARDONA B; SARFATI RS, "Catalytic editing properties of DNA polymerases", PROC. NATL. ACAD. SCI. USA, (1995), vol. 92, doi:doi:org/10.1073/pnas.92.24.10859, pages 10859 - 10863, XP055488231
EXAMINATION- PELLETIER H ET AL, "Structures of ternary complexes of rat DNA polymerase [beta], a DNA template-primer, and ddCTP", INSPEC, THE INSTITUTION OF ELECTRICAL ENGINEERS, STEVENAGE, GB, (19940624), Database accession no. 4729992
EXAMINATION- SCIENCE USA, (1994), vol. 264, no. 5167, ISSN 0036-8075, pages 1891 - 1903
OPPOSITION- ALBERTS et al., Molecular Biology of the Cell, 3rd ed., New York, (19940000), pages 98 - 103, XP055656993
OPPOSITION- M. B. WELCH et al., "Syntheses of Nucleosides Designed for Combinatorial DNA Sequencing", Chem. Eur. J., (19990000), vol. 5, no. 3, pages 951 - 960, XP002570325
OPPOSITION- M. L. METZKER et al., "Termination of DNA synthesis by novel 3'-modified-deoxyribonucleoside 5'-triphosphates", Nucleic Acids Research, (19940000), vol. 22, no. 20, pages 4259 - 4267, XP002191232
OPPOSITION- N. RAMZAEVA et al., "7-SUBSTITUTED 7-DEAZA-2'-DEOXYGUANOSINES: REGIOSELECTIVE HALOGENATION OF PYRROLOÚ2,3-D3⁄4PYRIMIDINE NUCLEOSIDES", Helvetica Chimica Acta, (19950000), vol. 78, pages 1083 - 1090, XP000655172
OPPOSITION- N. RAMZAEVA et al., "7-DEAZAGUANINE DNA: OLIGONUCLEOTIDES WITH HYDROPHOBIC OR CATIONIC SIDE CHAINS", Helvetica Chimica Acta, (19970000), vol. 80, pages 1809 - 1822, XP002064597
OPPOSITION- SEELA et al., "OLIGONUCLEOTIDE DUPLEX STABILITY CONTROLLED BY THE 7-SUBSTITUENTS OF 7-DEAZAGUANINE BASES", Bioorganic & Mechanical Chemistry Letters, (19950000), vol. 5, no. 24, pages 3049 - 3052, XP000655156
OPPOSITION- R. GIGG et al., "The Allyl Ether as a Protecting Group in Carbohydrate Chemistry. Part II", Journal of the Chemical Society, (19680000), pages 1903 - 1911, XP055656997
OPPOSITION- B. B. ROSENBLUM et al., "NEW DYE-LABELED TERMINATORS FOR IMPROVED DNA SEQUENCING PATTERNS", Nucleic Acids Research, (19970000), vol. 25, no. 22, pages 4500 - 4504, XP002201149
OPPOSITION- J. M. PROBER et al., "A SYSTEM FOR RAPID DNA SEQUENCING WITH FLUORESCENT CHAIN- TERMINATING DIDEOXYNUCLEOTIDES", Science, (19870000), vol. 238, no. 4825, pages 336 - 341, XP000604017
OPPOSITION- B. CANARD et al., "Catalytic editing properties of DNA polymerases (pucleotide analogues/termination/active site/mechanism)", PNAS, (19950000), vol. 92, pages 10859 - 10863, XP055488231
SEARCH- HULTMAN T ET AL, "DIRECT SOLID PHASE SEQUENCING OF GENOMIC AND PLASMID DNA USING MAGNETIC BEADS AS SOLID SUPPORT", NUCLEIC ACIDS RESEARCH, INFORMATION RETRIEVAL LTD, GB, (19890711), vol. 17, no. 13, ISSN 0305-1048, pages 4937 - 4946, XP000371656 [A] 1-15 * abstract *
SEARCH- METZKER M L ET AL, "TERMINATION OF DNA SYNTHESIS BY NOVEL 3'-MODIFIED-DEOXYRIBONUCLEOSIDE 5'-TRIPHOSPHATES", NUCLEIC ACIDS RESEARCH, INFORMATION RETRIEVAL LTD, GB, (19940101), vol. 22, no. 20, ISSN 0305-1048, pages 4259 - 4267, XP001068669 [A] 1-15 * figure 2 *
SEARCH- RAJASEKHARAN PILLAI V N, "Photoremovable Protecting Groups in Organic Synthesis", SYNTHESIS, GEORG THIEME VERLAG, STUTTGART, DE, (19800101), vol. 1, no. 1, doi:10.1055/S-1980-28908, ISSN 0039-7881, pages 1 - 26, XP002099233 [A] 1-15 * item 9 *
SEARCH- JU JINGYUE ET AL, "Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, NATIONAL ACADEMY OF SCIENCES, US, (20060101), vol. 103, no. 52, doi:10.1073/PNAS.0609513103, ISSN 0027-8424, pages 19635 - 19640, XP002461564 [T] * figure 1 *
SEARCH- RONAGHI ET AL, "A SEQUENCING METHOD BASED ON REAL-TIME PYROPHOSPHATE", SCIENCE, AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE, US, (19980717), vol. 281, doi:10.1126/SCIENCE.281.5375.363, ISSN 0036-8075, pages 363 - 365, XP002135869 [A] 1-15 * figure 1 *
SEARCH- MICHAEL A. JENSEN ET AL, "DMSO and Betaine Greatly Improve Amplification of GC-Rich Constructs in De Novo Synthesis", PLOS ONE, (20100611), vol. 5, no. 6, doi:10.1371/journal.pone.0011024, page e11024, XP055265247 [T] * abstract *

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