WO2009077173A3 - Dna-encoded chemical libraries - Google Patents
Dna-encoded chemical libraries Download PDFInfo
- Publication number
- WO2009077173A3 WO2009077173A3 PCT/EP2008/010770 EP2008010770W WO2009077173A3 WO 2009077173 A3 WO2009077173 A3 WO 2009077173A3 EP 2008010770 W EP2008010770 W EP 2008010770W WO 2009077173 A3 WO2009077173 A3 WO 2009077173A3
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- complementary
- region
- single strand
- coding
- initial
- 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.)
- Ceased
Links
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
- C12N15/102—Mutagenizing nucleic acids
- C12N15/1031—Mutagenizing nucleic acids mutagenesis by gene assembly, e.g. assembly by oligonucleotide extension PCR
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
- C12N15/1034—Isolating an individual clone by screening libraries
- C12N15/1068—Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
Landscapes
- Health & Medical Sciences (AREA)
- Genetics & Genomics (AREA)
- Life Sciences & Earth Sciences (AREA)
- Chemical & Material Sciences (AREA)
- Engineering & Computer Science (AREA)
- General Engineering & Computer Science (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Biomedical Technology (AREA)
- Organic Chemistry (AREA)
- Biotechnology (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Crystallography & Structural Chemistry (AREA)
- Plant Pathology (AREA)
- Molecular Biology (AREA)
- Microbiology (AREA)
- Physics & Mathematics (AREA)
- Biochemistry (AREA)
- General Health & Medical Sciences (AREA)
- Biophysics (AREA)
- Bioinformatics & Computational Biology (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Abstract
A method of preparing a DNA-encoded chemical library comprising members which comprise a chemical moiety, a linking moiety and a DNA moiety, comprising for each member the steps of: (I) coupling a initial building block to a initial coding single strand oligomer via a linking moiety to form a initial conjugate, the initial coding single strand oligomer comprising a first primer region, an initial coding region and a first annealing region; (II) optionally coupling a middle building block and middle coding single strand oligomer to said initial conjugate to form a middle conjugate, the coupling take place in either order, wherein: (a) the middle building block is coupled to the residue of the initial building block; and (b) the middle coding single strand oligomer comprises a middle coding region and second annealing region, and is coupled by: (i) annealing a complementary single strand oligomer which comprises a chemical modifier, a complementary first annealing region, a complementary middle coding region and a complementary second annealing region by interaction between the first annealing region and the complementary first annealing region; (ii) treating the conjugate formed with a DNA polymerase to elongate the initial coding single strand oligomer to be complementary to the complementary middle coding region and the complementary second annealing region; (iii) removing the complementary single strand oligomer by denaturing the DNA and capturing the complementary single strand oligomer via the chemical modifier; (III) coupling a final building block and final coding single strand oligomer to the initial or middle conjugate as appropriate to form a final conjugate, the coupling take place in either order, wherein: (a) the final building block is coupled to the residue of the initial building block, or may be additionally or alternatively be coupled to the residue of the middle building block (if present); and (b) the final coding single strand oligomer comprises a final coding region and a second primer region, and is coupled by: (i) annealing a complementary single strand oligomer which comprises a complementary first or second annealing region as appropriate, a complementary final coding region and a complementary second primer region, by interaction between the first or second annealing region and the complementary first or second annealing region, as appropriate; (ii) treating the conjugate formed with a DNA polymerase to elongate the initial coding single strand oligomer to be complementary to the complementary final coding region and the complementary second primer region, and to elongate the complementary coding strand to be complementary to the initial coding single strand oligomer.
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US824907P | 2007-12-19 | 2007-12-19 | |
| US61/008,249 | 2007-12-19 |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| WO2009077173A2 WO2009077173A2 (en) | 2009-06-25 |
| WO2009077173A3 true WO2009077173A3 (en) | 2009-10-29 |
Family
ID=40790879
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| PCT/EP2008/010770 Ceased WO2009077173A2 (en) | 2007-12-19 | 2008-12-17 | Dna-encoded chemical libraries |
Country Status (1)
| Country | Link |
|---|---|
| WO (1) | WO2009077173A2 (en) |
Cited By (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US8932992B2 (en) | 2001-06-20 | 2015-01-13 | Nuevolution A/S | Templated molecules and methods for using such molecules |
| US9096951B2 (en) | 2003-02-21 | 2015-08-04 | Nuevolution A/S | Method for producing second-generation library |
| US9109248B2 (en) | 2002-10-30 | 2015-08-18 | Nuevolution A/S | Method for the synthesis of a bifunctional complex |
| US9121110B2 (en) | 2002-12-19 | 2015-09-01 | Nuevolution A/S | Quasirandom structure and function guided synthesis methods |
| US9574189B2 (en) | 2005-12-01 | 2017-02-21 | Nuevolution A/S | Enzymatic encoding methods for efficient synthesis of large libraries |
Families Citing this family (36)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2003078625A2 (en) | 2002-03-15 | 2003-09-25 | Nuevolution A/S | An improved method for synthesising templated molecules |
| US10730906B2 (en) | 2002-08-01 | 2020-08-04 | Nuevolutions A/S | Multi-step synthesis of templated molecules |
| ATE447626T1 (en) | 2003-09-18 | 2009-11-15 | Nuevolution As | METHOD FOR OBTAINING STRUCTURAL INFORMATION FROM ENCODED MOLECULES AND FOR SELECTING COMPOUNDS |
| EP2361930A3 (en) | 2007-03-26 | 2011-10-26 | Dako Denmark A/S | Multimers of MHC-peptide complexes and uses thereof in Borrelia infectious diseases |
| WO2009003493A2 (en) | 2007-07-03 | 2009-01-08 | Dako Denmark A/S | Mhc multimers, methods for their generation, labeling and use |
| EP2197908A2 (en) | 2007-09-27 | 2010-06-23 | Dako Denmark A/S | Mhc multimers in tuberculosis diagnostics, vaccine and therapeutics |
| WO2010009735A2 (en) | 2008-07-23 | 2010-01-28 | Dako Denmark A/S | Combinatorial analysis and repair |
| WO2010037402A1 (en) | 2008-10-02 | 2010-04-08 | Dako Denmark A/S | Molecular vaccines for infectious disease |
| US11992518B2 (en) | 2008-10-02 | 2024-05-28 | Agilent Technologies, Inc. | Molecular vaccines for infectious disease |
| ES2842527T3 (en) | 2009-02-13 | 2021-07-14 | X Chem Inc | Methods for creating and analyzing DNA-encoded libraries |
| US8329239B2 (en) * | 2009-03-03 | 2012-12-11 | Givandan S.A. | Off-taste masking |
| CA2832672A1 (en) | 2010-04-16 | 2011-10-20 | Nuevolution A/S | Bi-functional complexes and methods for making and using such complexes |
| WO2012019765A1 (en) * | 2010-08-10 | 2012-02-16 | European Molecular Biology Laboratory (Embl) | Methods and systems for tracking samples and sample combinations |
| WO2013036810A1 (en) | 2011-09-07 | 2013-03-14 | X-Chem, Inc. | Methods for tagging dna-encoded libraries |
| ES2675167T3 (en) * | 2012-07-13 | 2018-07-09 | X-Chem, Inc. | DNA-encoded libraries that have non-polymerase readable oligonucleotide linkages |
| GB201322692D0 (en) | 2013-12-20 | 2014-02-05 | Philochem Ag | Production of encoded chemical libraries |
| EP3102241B1 (en) | 2014-02-03 | 2019-04-17 | Eidgenössiche Technische Hochschule Zürich | Small molecule drug conjugates |
| GB201404552D0 (en) * | 2014-03-14 | 2014-04-30 | Philochem Ag | Purification of dna-conjugate products |
| DK3152232T3 (en) * | 2014-06-06 | 2020-02-24 | Immudex Aps | Determination of antigen recognition by bar coding of MHC multimers |
| WO2015188839A2 (en) | 2014-06-13 | 2015-12-17 | Immudex Aps | General detection and isolation of specific cells by binding of labeled molecules |
| US20180340174A1 (en) | 2014-11-11 | 2018-11-29 | Nanocore Aps | Method for identification of molecules with desired characteristics |
| US11576892B2 (en) | 2015-08-18 | 2023-02-14 | Novation Pharmaceuticals Inc. | Benzopyran derivatives and uses thereof |
| CN105218405B (en) * | 2015-11-04 | 2017-07-28 | 上海泰坦科技股份有限公司 | The synthesis technique of (R, S) 2 [[base of 5 (9 fluorenylmethyloxycarbonyl amino) dibenzo [A, D] cycloheptane 2] oxygen] acetic acid |
| GB201603789D0 (en) | 2016-03-04 | 2016-04-20 | Apta Biosciences Ltd | Oligonucleotides and methods for preparing |
| CN115820806A (en) | 2016-06-16 | 2023-03-21 | 哈斯达克科学公司 | Combinatorial synthesis of oligonucleotide-guided and documented encoded probe molecules |
| WO2018089641A2 (en) * | 2016-11-10 | 2018-05-17 | The Scripps Research Institute | Encode solid phase compound library with polynucleotide based barcoding |
| WO2018204420A1 (en) | 2017-05-02 | 2018-11-08 | Haystack Sciences Corporation | Molecules for verifying oligonucleotide directed combinatorial synthesis and methods of making and using the same |
| RU2020112854A (en) | 2017-11-30 | 2021-12-30 | Арракис Терапьютикс, Инк. | PHOTOPROBES BINDING NUCLEIC ACIDS AND METHODS OF THEIR APPLICATION |
| CN108178790B (en) * | 2018-01-18 | 2021-09-07 | 上海药明康德新药开发有限公司 | Method for separating cell membrane to screen transmembrane protein by using DNA coding compound library |
| WO2019149198A1 (en) * | 2018-01-31 | 2019-08-08 | 成都先导药物开发股份有限公司 | Dna-encoded compound library and compound screening method |
| WO2019236644A1 (en) * | 2018-06-05 | 2019-12-12 | Arrakis Therapeutics, Inc. | Encoded libraries and methods of use for screening nucleic acid targets |
| WO2020047095A1 (en) * | 2018-08-28 | 2020-03-05 | The Scripps Research Institute | Use of non-covalent immobilization in dna encoded libraries |
| GB201821109D0 (en) | 2018-12-21 | 2019-02-06 | Philochem Ag | Nucleic acid encoded chemical libraries |
| CN112575389B (en) * | 2019-09-30 | 2023-09-19 | 成都先导药物开发股份有限公司 | Liquid chromatography purification method of DNA coding compound library |
| EP4232578A1 (en) | 2020-10-23 | 2023-08-30 | ETH Zurich | Self-purified nucleic acid encoded libraries |
| WO2024254528A1 (en) * | 2023-06-09 | 2024-12-12 | Arc Institute | Methods of screening for sting inhibitors |
Citations (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2004083427A2 (en) * | 2003-03-20 | 2004-09-30 | Nuevolution A/S | Ligational encoding of small molecules |
-
2008
- 2008-12-17 WO PCT/EP2008/010770 patent/WO2009077173A2/en not_active Ceased
Patent Citations (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2004083427A2 (en) * | 2003-03-20 | 2004-09-30 | Nuevolution A/S | Ligational encoding of small molecules |
Non-Patent Citations (8)
| Title |
|---|
| BULLER F ET AL: "Design and synthesis of a novel DNA-encoded chemical library using Diels-Alder cycloadditions", BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, PERGAMON, ELSEVIER SCIENCE, GB, vol. 18, no. 22, 15 November 2008 (2008-11-15), pages 5926 - 5931, XP025627172, ISSN: 0960-894X, [retrieved on 20080715] * |
| GARTNER Z J ET AL: "DNA-templated organic synthesis and selection of a library of macrocycles", SCIENCE, AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE, US, WASHINGTON, DC, vol. 305, no. 5690, 10 September 2004 (2004-09-10), pages 1601 - 1605, XP002397753, ISSN: 0036-8075 * |
| HALPIN DAVID R ET AL: "DNA display II. Genetic manipulation of combinatorial chemistry libraries for small-molecule evolution", PLOS BIOLOGY, PUBLIC LIBRARY OF SCIENCE, US, vol. 2, no. 7, 1 July 2004 (2004-07-01), pages 1022 - 1030, XP002424416, ISSN: 1544-9173 * |
| MANNOCCI LUCA ET AL: "High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 105, no. 46, November 2008 (2008-11-01), pages 17670 - 17675, XP002541365, ISSN: 0027-8424 * |
| MELKKO ET AL: "Lead discovery by DNA-encoded chemical libraries", DRUG DISCOVERY TODAY, ELSEVIER, RAHWAY, NJ, US, vol. 12, no. 11-12, 1 June 2007 (2007-06-01), pages 465 - 471, XP022095609, ISSN: 1359-6446 * |
| MELKKO S ET AL: "Encoded self-assembling chemical libraries", NATURE BIOTECHNOLOGY MAY 2004 NATURE PUBLISHING GROUP US, vol. 22, no. 5, May 2004 (2004-05-01), pages 568 - 574, XP002541364 * |
| SCHEUERMANN J ET AL: "DNA-encoded chemical libraries", JOURNAL OF BIOTECHNOLOGY, ELSEVIER SCIENCE PUBLISHERS, AMSTERDAM, NL, vol. 126, no. 4, 1 December 2006 (2006-12-01), pages 568 - 581, XP024956589, ISSN: 0168-1656, [retrieved on 20061201] * |
| TENG S F ET AL: "A STRATEGY FOR THE GENERATION OF BIOMIMETIC LIGANDS FOR AFFINITY CHROMATOGRAPHY. COMBINATORIAL SYNTHESIS AND BIOLOGICAL EVALUATION OF AN IGG BINDING LIGAND", JOURNAL OF MOLECULAR RECOGNITION, HEYDEN & SON LTD., LONDON, GB, vol. 12, no. 1, 1 January 1999 (1999-01-01), pages 67 - 75, XP001084821, ISSN: 0952-3499 * |
Cited By (6)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US8932992B2 (en) | 2001-06-20 | 2015-01-13 | Nuevolution A/S | Templated molecules and methods for using such molecules |
| US9109248B2 (en) | 2002-10-30 | 2015-08-18 | Nuevolution A/S | Method for the synthesis of a bifunctional complex |
| US9284600B2 (en) | 2002-10-30 | 2016-03-15 | Neuvolution A/S | Method for the synthesis of a bifunctional complex |
| US9121110B2 (en) | 2002-12-19 | 2015-09-01 | Nuevolution A/S | Quasirandom structure and function guided synthesis methods |
| US9096951B2 (en) | 2003-02-21 | 2015-08-04 | Nuevolution A/S | Method for producing second-generation library |
| US9574189B2 (en) | 2005-12-01 | 2017-02-21 | Nuevolution A/S | Enzymatic encoding methods for efficient synthesis of large libraries |
Also Published As
| Publication number | Publication date |
|---|---|
| WO2009077173A2 (en) | 2009-06-25 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| WO2009077173A3 (en) | Dna-encoded chemical libraries | |
| WO2008002740A3 (en) | Methods, compositions, and kits for rna extraction | |
| WO2011106724A3 (en) | Fast pcr for str genotyping | |
| WO2013032850A3 (en) | Compositions and methods for high fidelity assembly of nucleic acids | |
| EP1845160A4 (en) | METHOD FOR AMPLIFYING A NUCLEOTIDE SEQUENCE | |
| WO2006102309A3 (en) | Methods, compositions, and kits for detection of micro rna | |
| WO2008052101A3 (en) | Multiplex automated genome engineering | |
| WO2010075188A3 (en) | Multibase delivery for long reads in sequencing by synthesis protocols | |
| ATE464381T1 (en) | LIGATION-BASED RNA AMPLIFICATION | |
| WO2007136874A3 (en) | Genomic library construction | |
| WO2009120374A3 (en) | Methods and compositions for nucleic acid sample preparation | |
| WO2008143627A3 (en) | Targeted whole genome amplification method for identification of pathogens | |
| WO2009114321A3 (en) | Rationally-designed meganucleases for maize genome engineering | |
| WO2006081284A3 (en) | Methods for quantitating small rna molecules | |
| MD4120B1 (en) | Method for the production of wine and wine obtained from such method | |
| WO2007087262A3 (en) | Selective genome amplification | |
| WO2008057502A3 (en) | Content borrowing system and method | |
| WO2009124255A8 (en) | Methods for transcript analysis | |
| WO2008067423A3 (en) | Methods of improving the introduction of dna into bacterial cells | |
| WO2007017229A3 (en) | Method for carrying out the selective evolution of proteins in vitro | |
| WO2008082429A3 (en) | Plant-specific genetic elements and transfer cassettes for plant transformation | |
| WO2010039802A3 (en) | Methods and compositions for isolating nucleic acid | |
| WO2008065200A8 (en) | Dnase expression in recombinant host cells | |
| WO2011095501A8 (en) | Complexitiy reduction method | |
| WO2009153667A3 (en) | Method for the detection of ovarian cancer |
Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| 121 | Ep: the epo has been informed by wipo that ep was designated in this application |
Ref document number: 08862565 Country of ref document: EP Kind code of ref document: A2 |
|
| NENP | Non-entry into the national phase |
Ref country code: DE |
|
| 122 | Ep: pct application non-entry in european phase |
Ref document number: 08862565 Country of ref document: EP Kind code of ref document: A2 |