WO2003050290A3 - Phosphoromonothioate and phosphorodithioate oligonucleotide aptamer chip for functional proteomics - Google Patents

Phosphoromonothioate and phosphorodithioate oligonucleotide aptamer chip for functional proteomics Download PDF

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Publication number
WO2003050290A3
WO2003050290A3 PCT/US2002/025049 US0225049W WO03050290A3 WO 2003050290 A3 WO2003050290 A3 WO 2003050290A3 US 0225049 W US0225049 W US 0225049W WO 03050290 A3 WO03050290 A3 WO 03050290A3
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WIPO (PCT)
Prior art keywords
phosphoromonothioate
oligonucleotide aptamer
functional proteomics
aptamer chip
phosphorodithioate oligonucleotide
Prior art date
Application number
PCT/US2002/025049
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French (fr)
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WO2003050290A2 (en
Inventor
David Nmi Gorenstein
Bruce A Luxon
Norbert Nmi Herzog
Xian Bin Yang
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Univ Texas
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Publication date
Application filed by Univ Texas filed Critical Univ Texas
Priority to EP02798407A priority Critical patent/EP1534301A4/en
Priority to AU2002363923A priority patent/AU2002363923A1/en
Publication of WO2003050290A2 publication Critical patent/WO2003050290A2/en
Publication of WO2003050290A3 publication Critical patent/WO2003050290A3/en

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    • C12N15/09—Recombinant DNA-technology
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    • C12N15/1048—SELEX
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    • C12N15/115—Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith ; Nucleic acids binding to non-nucleic acids, e.g. aptamers
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Abstract

An apparatus and method for monitoring biological interactions is disclosed. The apparatus includes a substrate, a modified nucleotide aptamer attached to the substrate, a target molecule or portion thereof, wherein the interaction between the modified nucleotide aptamer and the target molecule or portion thereof is detected.
PCT/US2002/025049 2001-11-15 2002-08-07 Phosphoromonothioate and phosphorodithioate oligonucleotide aptamer chip for functional proteomics WO2003050290A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP02798407A EP1534301A4 (en) 2001-11-15 2002-08-07 Phosphoromonothioate and phosphorodithioate oligonucleotide aptamer chip for functional proteomics
AU2002363923A AU2002363923A1 (en) 2001-11-15 2002-08-07 Phosphoromonothioate and phosphorodithioate oligonucleotide aptamer chip for functional proteomics

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Application Number Priority Date Filing Date Title
US33488701P 2001-11-15 2001-11-15
US60/334,887 2001-11-15

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WO2003050290A2 WO2003050290A2 (en) 2003-06-19
WO2003050290A3 true WO2003050290A3 (en) 2005-04-07

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EP (1) EP1534301A4 (en)
AU (1) AU2002363923A1 (en)
WO (1) WO2003050290A2 (en)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN105087595B (en) * 2014-05-16 2018-06-05 深圳市第二人民医院 The aptamer of people NF-kB and its application

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Publication number Priority date Publication date Assignee Title
US6423493B1 (en) * 1998-10-26 2002-07-23 Board Of Regents The University Of Texas System Combinatorial selection of oligonucleotide aptamers
US20060172925A1 (en) * 1998-10-26 2006-08-03 Board Of Regents, The University Of Texas System Thio-siRNA aptamers
US20040242521A1 (en) * 1999-10-25 2004-12-02 Board Of Regents, The University Of Texas System Thio-siRNA aptamers
AU2003263853A1 (en) * 2002-08-16 2004-03-03 Board Of Regents The University Of Texas System Compositions and methods related to flavivirus envelope protein domain iii antigens
EP1572978A4 (en) * 2002-10-16 2006-05-24 Univ Texas Bead bound combinatorial oligonucleoside phosphorothioate and phosphorodithioate aptamer libraries
US6936496B2 (en) 2002-12-20 2005-08-30 Hewlett-Packard Development Company, L.P. Nanowire filament
WO2005037053A2 (en) * 2003-05-23 2005-04-28 Board Of Regents - The University Of Texas System High throughput screening of aptamer libraries for specific binding to proteins on viruses and other pathogens
US7910523B2 (en) * 2003-05-23 2011-03-22 Board Of Regents, The University Of Texas System Structure based and combinatorially selected oligonucleoside phosphorothioate and phosphorodithioate aptamer targeting AP-1 transcription factors
US20050250094A1 (en) * 2003-05-30 2005-11-10 Nanosphere, Inc. Method for detecting analytes based on evanescent illumination and scatter-based detection of nanoparticle probe complexes
WO2005010016A2 (en) * 2003-07-24 2005-02-03 Board Of Regents Thioaptamers enable discovery of physiological pathways and new therapeutic strategies
US7132298B2 (en) * 2003-10-07 2006-11-07 Hewlett-Packard Development Company, L.P. Fabrication of nano-object array
US7223611B2 (en) * 2003-10-07 2007-05-29 Hewlett-Packard Development Company, L.P. Fabrication of nanowires
US7407738B2 (en) * 2004-04-02 2008-08-05 Pavel Kornilovich Fabrication and use of superlattice
US20050239134A1 (en) * 2004-04-21 2005-10-27 Board Of Regents, The University Of Texas System Combinatorial selection of phosphorothioate single-stranded DNA aptamers for TGF-beta-1 protein
US20050241959A1 (en) * 2004-04-30 2005-11-03 Kenneth Ward Chemical-sensing devices
US7683435B2 (en) 2004-04-30 2010-03-23 Hewlett-Packard Development Company, L.P. Misalignment-tolerant multiplexing/demultiplexing architectures
US7247531B2 (en) 2004-04-30 2007-07-24 Hewlett-Packard Development Company, L.P. Field-effect-transistor multiplexing/demultiplexing architectures and methods of forming the same
US20060024814A1 (en) * 2004-07-29 2006-02-02 Peters Kevin F Aptamer-functionalized electrochemical sensors and methods of fabricating and using the same
AU2005282380A1 (en) * 2004-09-07 2006-03-16 Archemix Corp. Aptamer medicinal chemistry
JPWO2006062127A1 (en) * 2004-12-10 2008-06-12 シスメックス株式会社 Diagnosis support information output device and diagnosis support information output program for immune system abnormal disease
US7375012B2 (en) * 2005-02-28 2008-05-20 Pavel Kornilovich Method of forming multilayer film
WO2006125094A2 (en) * 2005-05-18 2006-11-23 Board Of Regents, The University Of Texas System Combinatorial selection of phosphorothioate aptamers for rnases
EP2147010A1 (en) 2007-04-18 2010-01-27 Roche Diagnostics GmbH Nucleotide with an alpha-phosphate mimetic
US20090286286A1 (en) * 2007-11-06 2009-11-19 Ambergen , Inc. Methods for controlling amplification
ES2936256T3 (en) 2008-02-01 2023-03-15 Massachusetts Gen Hospital Use of microvesicles in the diagnosis, and prognosis of diseases and medical conditions
US11266736B2 (en) 2008-04-17 2022-03-08 Vin De Bona Trading Company Pte Ltd Method of painting micro vesicles
KR20120037992A (en) 2009-07-16 2012-04-20 더 제너럴 하스피탈 코포레이션 Nucleic acid analysis
EP2475988B1 (en) 2009-09-09 2018-11-14 The General Hospital Corporation Use of microvesicles in analyzing nucleic acid profiles
US20130029339A1 (en) 2009-09-09 2013-01-31 The General Hospital Corporation Use of microvesicles in analyzing kras mutations
US20140045915A1 (en) 2010-08-31 2014-02-13 The General Hospital Corporation Cancer-related biological materials in microvesicles
US20130295574A1 (en) 2010-11-10 2013-11-07 Exosome Diagnostics, Inc. Method for Isolation of Nucleic Acid Containing Particles and Extraction of Nucleic Acids Therefrom
ES2744589T3 (en) 2011-05-11 2020-02-25 Exosome Diagnostics Inc Nucleic acid extraction from heterogeneous biological materials
CA2839896A1 (en) 2011-06-21 2012-12-27 Alnylam Pharmaceuticals, Inc. Assays and methods for determining activity of a therapeutic agent in a subject
WO2013028788A1 (en) 2011-08-22 2013-02-28 Exosome Diagnostics, Inc. Urine biomarkers
CN104995311A (en) 2012-08-30 2015-10-21 外来体诊断公司 Controls for nucleic acid assays
US9982292B2 (en) 2012-09-28 2018-05-29 Src, Inc. Detecting chemical and biological agents using textile-based sensors
CA2887058C (en) 2012-10-03 2022-02-22 Exosome Diagnostics, Inc. Use of microvesicles in diagnosis, prognosis, and treatment of medical diseases and conditions
DK2906717T3 (en) 2012-10-11 2019-04-01 Vin De Bona Trading Company Pte Ltd PROCEDURE FOR PAINTING MICROVESICS
CA2920429C (en) 2013-08-06 2021-11-16 Exosome Diagnostics, Inc. Urine biomarker cohorts, gene expression signatures, and methods of use thereof
ES2825708T3 (en) 2014-07-17 2021-05-17 Univ Pennsylvania Methods for using exosomes to monitor transplanted organ status
US10655097B2 (en) 2014-12-22 2020-05-19 Saint-Gobain Performance Plastics Corporation T-cell culture double bag assembly
US10280390B2 (en) 2014-12-22 2019-05-07 Saint-Gobain Performance Plastics Corporation System for culture of cells in a controlled environment
US9926524B2 (en) 2014-12-22 2018-03-27 Saint-Gobain Performance Plastics Corporation Gas permeable material
WO2018055080A1 (en) 2016-09-22 2018-03-29 INSERM (Institut National de la Santé et de la Recherche Médicale) Methods and pharmaceutical compositions for reprograming immune environment in a subject in need thereof
MX2019006825A (en) * 2016-12-12 2019-10-30 Univ Colorado Regents Use of biological rna scaffolds with in vitro selection to generate robust small molecule binding aptamers for genetically encodable biosensors.
WO2019014486A1 (en) 2017-07-12 2019-01-17 Exosome Diagnostics, Inc. Methods for isolating and enriching populations of biofluid- derived extracellular vesicles, and methods of use thereof
US20200339987A1 (en) 2017-11-09 2020-10-29 Alnylam Pharmaceuticals, Inc. Assays and methods for determining expression of the lect2 gene
WO2020106853A1 (en) 2018-11-20 2020-05-28 Exosome Diagnostics, Inc. Compositions and methods for internal controls of microvesicle isolations

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5756291A (en) * 1992-08-21 1998-05-26 Gilead Sciences, Inc. Aptamers specific for biomolecules and methods of making
WO2000024404A1 (en) * 1998-10-26 2000-05-04 Board Of Regents The University Of Texas System Thio-modified aptamer synthetic methods and compositions

Family Cites Families (47)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US521088A (en) * 1894-06-05 Mechanism for shocking cornstalks
US5273879A (en) * 1987-07-23 1993-12-28 Syntex (U.S.A.) Inc. Amplification method for polynucleotide assays
US5218088A (en) * 1989-11-02 1993-06-08 Purdue Research Foundation Process for preparing dithiophosphate oligonucleotide analogs via nucleoside thiophosphoramidite intermediates
US5620963A (en) * 1991-10-15 1997-04-15 Isis Pharmaceuticals, Inc. Oligonucleotides for modulating protein kinase C having phosphorothioate linkages of high chiral purity
US5635488A (en) * 1991-10-15 1997-06-03 Isis Pharmaceuticals, Inc. Compounds having phosphorodithioate linkages of high chiral purity
US5587361A (en) * 1991-10-15 1996-12-24 Isis Pharmaceuticals, Inc. Oligonucleotides having phosphorothioate linkages of high chiral purity
CA2084987C (en) * 1990-06-11 2007-02-13 Larry Gold Nucleic acid ligands
US6346611B1 (en) * 1990-06-11 2002-02-12 Gilead Sciences, Inc. High affinity TGfβ nucleic acid ligands and inhibitors
US5270163A (en) * 1990-06-11 1993-12-14 University Research Corporation Methods for identifying nucleic acid ligands
US5795721A (en) * 1990-06-11 1998-08-18 Nexstar Pharmaceuticals, Inc. High affinity nucleic acid ligands of ICP4
US5660985A (en) * 1990-06-11 1997-08-26 Nexstar Pharmaceuticals, Inc. High affinity nucleic acid ligands containing modified nucleotides
US5853984A (en) * 1990-06-11 1998-12-29 Nexstar Pharmaceuticals, Inc. Use of nucleic acid ligands in flow cytometry
US5705337A (en) * 1990-06-11 1998-01-06 Nexstar Pharmaceuticals, Inc. Systematic evolution of ligands by exponential enrichment: chemi-SELEX
IE920561A1 (en) * 1991-02-21 1992-08-26 Gilead Sciences Aptamer specific for thrombin and methods of use
US5840867A (en) * 1991-02-21 1998-11-24 Gilead Sciences, Inc. Aptamer analogs specific for biomolecules
US5582981A (en) * 1991-08-14 1996-12-10 Gilead Sciences, Inc. Method for identifying an oligonucleotide aptamer specific for a target
US5639603A (en) * 1991-09-18 1997-06-17 Affymax Technologies N.V. Synthesizing and screening molecular diversity
US5607923A (en) * 1991-10-15 1997-03-04 Isis Pharmaceuticals, Inc. Oligonucleotides for modulating cytomegalovirus having phosphorothioate linkages of high chiral purity
WO1993008296A1 (en) * 1991-10-15 1993-04-29 Isis Pharmaceuticals, Inc. Oligonucleotides having chiral phosphorus linkages
US5599797A (en) * 1991-10-15 1997-02-04 Isis Pharmaceuticals, Inc. Oligonucleotides having phosphorothioate linkages of high chiral purity
US5661134A (en) * 1991-10-15 1997-08-26 Isis Pharmaceuticals, Inc. Oligonucleotides for modulating Ha-ras or Ki-ras having phosphorothioate linkages of high chiral purity
US5576302A (en) * 1991-10-15 1996-11-19 Isis Pharmaceuticals, Inc. Oligonucleotides for modulating hepatitis C virus having phosphorothioate linkages of high chiral purity
FR2687679B1 (en) * 1992-02-05 1994-10-28 Centre Nat Rech Scient OLIGOTHIONUCLEOTIDES.
US5516664A (en) * 1992-12-23 1996-05-14 Hyman; Edward D. Enzymatic synthesis of repeat regions of oligonucleotides
NZ267842A (en) * 1993-05-28 1997-09-22 Baylor College Medicine Apparatus for measuring molecular mass (by mass spectrometry) in which the sample is ionised on the sample holder and desorbed therefrom by laser pulses
US5801154A (en) * 1993-10-18 1998-09-01 Isis Pharmaceuticals, Inc. Antisense oligonucleotide modulation of multidrug resistance-associated protein
WO1995026204A1 (en) * 1994-03-25 1995-10-05 Isis Pharmaceuticals, Inc. Immune stimulation by phosphorothioate oligonucleotide analogs
US5658738A (en) * 1994-05-31 1997-08-19 Becton Dickinson And Company Bi-directional oligonucleotides that bind thrombin
US5556752A (en) * 1994-10-24 1996-09-17 Affymetrix, Inc. Surface-bound, unimolecular, double-stranded DNA
DE4438918A1 (en) * 1994-11-04 1996-05-09 Hoechst Ag Modified oligonucleotides, their preparation and their use
EP0807171A1 (en) * 1994-12-22 1997-11-19 HYBRIDON, Inc. Synthesis of stereospecific oligonucleotide phosphorothioates
US6111095A (en) * 1995-06-07 2000-08-29 Merck & Co., Inc. Capped synthetic RNA, analogs, and aptamers
US5734041A (en) * 1995-10-20 1998-03-31 Mcgill University Preparation of chiral phosphorothioate oligomers
US5804445A (en) * 1996-01-11 1998-09-08 Board Of Regents, The University Of Texas System High affinity mutants of nuclear factor-interleukin 6 and methods of use therefor
NZ516848A (en) * 1997-06-20 2004-03-26 Ciphergen Biosystems Inc Retentate chromatography apparatus with applications in biology and medicine
EP1042351A4 (en) * 1997-11-10 2003-06-25 Gen Hospital Corp Detection systems for registering protein interactions and functional relationships
US6242246B1 (en) * 1997-12-15 2001-06-05 Somalogic, Inc. Nucleic acid ligand diagnostic Biochip
US6551795B1 (en) * 1998-02-18 2003-04-22 Genome Therapeutics Corporation Nucleic acid and amino acid sequences relating to pseudomonas aeruginosa for diagnostics and therapeutics
US6180348B1 (en) * 1998-04-20 2001-01-30 Weihua Li Method of isolating target specific oligonucleotide ligands
US20010034330A1 (en) * 1998-08-10 2001-10-25 Charlotte Kensil Innate immunity-stimulating compositions of CpG and saponin and methods thereof
US6514948B1 (en) * 1999-07-02 2003-02-04 The Regents Of The University Of California Method for enhancing an immune response
EP1133988A1 (en) * 2000-03-11 2001-09-19 Biognostik Gesellschaft für biomolekulare Diagnostik mbH Mixture comprising an inhibitor or suppressor of a gene and a molecule binding to an expression product of that gene
US6610504B1 (en) * 2000-04-10 2003-08-26 General Atomics Methods of determining SAM-dependent methyltransferase activity using a mutant SAH hydrolase
EP1330306A2 (en) * 2000-10-10 2003-07-30 BioTrove, Inc. Apparatus for assay, synthesis and storage, and methods of manufacture, use, and manipulation thereof
CA2444696A1 (en) * 2001-04-19 2002-10-31 Bristol-Myers Squibb Company Polynucleotides and polypeptides associated with the nf-kb pathway
US6725526B2 (en) * 2002-01-14 2004-04-27 Hitachi Global Storage Technologies Netherlands B.V. Method of forming microsuspension assemblies for direct access storage devices
US6874219B2 (en) * 2003-05-22 2005-04-05 Hitachi Global Storage Technologies Netherlands B.V. System, method, and apparatus for preventing rotation of a disk clamp while being assembled to the hub of a spindle motor in a hard disk drive and fastener centering features

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5756291A (en) * 1992-08-21 1998-05-26 Gilead Sciences, Inc. Aptamers specific for biomolecules and methods of making
WO2000024404A1 (en) * 1998-10-26 2000-05-04 Board Of Regents The University Of Texas System Thio-modified aptamer synthetic methods and compositions

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
CASSIDAY ET AL.: "In vivo recognition of an RNA aptamer by its transcription factor target", BIOCHEMISTRY, vol. 40, no. 8, 1 February 2001 (2001-02-01), pages 2433 - 2438, XP003012377 *
KING D.J.: "Selection, binding and design of phosphorothioate duplex aptamers for the transcription factors NF-IL6 and NF-kB", PHD DISSERTATION, August 2001 (2001-08-01), pages 1 - 109, XP008074388 *
LEBRUSKA ET AL.: "Selection and characterization of an RNA decoy for transcription factor NF-kB", BIOCHEMISTRY, vol. 38, 13 February 1999 (1999-02-13), pages 3168 - 3174, XP002923025 *
See also references of EP1534301A4 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN105087595B (en) * 2014-05-16 2018-06-05 深圳市第二人民医院 The aptamer of people NF-kB and its application

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