DK2622073T5 - Fremgangsmåde til fremstilling af et beriget bibliotek - Google Patents
Fremgangsmåde til fremstilling af et beriget bibliotek Download PDFInfo
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- DK2622073T5 DK2622073T5 DK11749853.5T DK11749853T DK2622073T5 DK 2622073 T5 DK2622073 T5 DK 2622073T5 DK 11749853 T DK11749853 T DK 11749853T DK 2622073 T5 DK2622073 T5 DK 2622073T5
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- Prior art keywords
- nucleic acid
- binding
- dna
- target
- acid molecule
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Classifications
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- 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
- C12N15/1075—Isolating an individual clone by screening libraries by coupling phenotype to genotype, not provided for in other groups of this subclass
-
- 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
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Claims (13)
1: En fremgangsmåde til fremstilling af et beriget bibliotek omfattende specifik nukleinsyre sekvensinformation, der tillader at identificere mindst en bindingsenhed, der binder til mindst ét mål, hvor den specifikke bindingsenhed har været til stede i et in vitro display- bibliotek, og hvor fremgangsmåden omfatter trinene: (i) : fremstilling af et in vitro display-bibliotek med mindst 100 forskellige bindingsenheder Bn, hvor n = 100 eller mere, hvor hver bindingsenhed er fæstnet til et nukleinsyremolekyle, og nukleinsyremolekylet omfatter specifik nukleinsyresekvensinformation, der gør det muligt at identificere bindingsenheden - hvorved når man kender nukleinsyremolekylets specifikke nukleinsyresekvensinformation, kender man direkte strukturen af den specifikke bindingsenhed, der er fæstnet til nukleinsyremolekylet, hvor strukturen af bindingsenheden fæstnet til nukleinsyremolekylet heri betegnes B-struktur; (ii) : fremstilling af nukleinsyremolekyler med mindst et mål Tn, hvor n = 1 eller mere, fæstnet til et nukleinsyremolekyle, og hvor nukleinsyremolekylet omfatter specifik nukleinsyresekvensinformation, der tillader at identificere det specifikke mål, hvor målet er i stand til at binde til mindst en af bindingsenhederne til stede i biblioteket i trin (i) - strukturen af målet fæstnet til nukleinsyremolekylet heri betegnes T-struktur; og (iii) : blanding afen opløsning omfattende X, hvor X er et tal større end 104, antal B-strukturer i biblioteket i trin (i) med en opløsning omfattende Y, hvor Y er et tal større end 102, antal T-strukturer i trin (ii) under bindingsbetingelser, der er betingelser, hvor en B-struktur indeholdende en bindingsenhed, der er i stand til at binde til et målmolekyle, binder mere effektivt til den tilsvarende T-struktur end en B-struktur indeholdende en bindingsenhed, der ikke er i stand til at binde til det samme mål gør, og hvor man opnår binding af mindst en af bindingsenhederne til mindst et mål og hvorved skabes et kompleks omfattende en B-struktur bundet til en T-struktur, heri betegnet BBoundToT-struktur; (iv) : anvendelse af et in vitro opdelingssystem - under bindingsbetingelser, der er betingelser, hvor en B-struktur indeholdende en bindingsenhed, der er i stand til at binde til et målmolekyle, binder mere effektivt til den tilsvarende T-struktur end en B-struktur indeholdende en bindingsenhed, der ikke er i stand til at binde til det samme mål gør - hvor opdelingssystemet omfatter mindst 2 gange flere individuelle rum end Y-antallet af T-strukturer, til stede i trin (iii) under betingelser, hvor B-strukturerne, T-strukturerne og BBoundToT-strukturerne indtræder tilfældigt i de enkelte rum; og (v) : fusion af nukleinsyremolekylerne af en B-struktur og en T-struktur, der begge er tilstede indenfor det samme individuelle rum - hvilket er fusion af nukleinsyremolekylet af B-strukturen til nukleinsyremolekylet af T- struktur - denne struktur er heri betegnet BTFused-struktur, og BTFuSed-strukturen omfatter den specifikke nukleinsyresekvensinformation, der tillader at identificere bindingsenheden fra trin (i) og den specifikke nukleinsyresekvensinformation, der tillader at identificere det specifikke mål i trin (ii); og (vi) : kombination af indholdet af de enkelte rum i trin (v) under betingelser, hvor der ikke er fusion af nukleinsyremolekylerne af en B-struktur og en T-struktur -hvorved der ikke dannes nogen ny BTFused-struktur der ikke allerede er dannet i trin (v) - for at få et bibliotek af BTFused-strukturer, hvor biblioteket er et beriget bibliotek af arter af BTFused-strukturer stammende fra bindende par af mål og bindingsenheder i sammenligning med BTFused-strukturer stammende fra ikke-bindende par af mål og bindingsenheder; og hvor BsoundToT-strukturerne forbliver suspenderet i opløsning i de enkelte rum i trin (iv); og/eller hvor fremgangsmåden ikke er afhængig afmålimmobilisering på en fast bærer; og hvor BTFuSed-strukturerne, der er til stede i det berigede bibliotek i trin (vi) intensiveres.
2. Fremgangsmåde ifølge krav 1, hvor bindingsenheden i trin (i) er fæstnet til nukleinsyremolekylet ved f.eks. en kovalent binding, og hvor målet i trin (ii) er fæstnet til nukleinsyremolekylet ved en kovalent binding, og hvor nukleinsyremolekylet i B-strukturen er DNA, og nukleinsyremolekylet i T-strukturen er DNA.
3. Fremgangsmåde ifølge krav 2, hvor DNA nukleinsyremolekylet i B-strukturen er et dobbeltstrenget nukleinsyremolekyle, og hvor DNA nukleinsyremolekylet i T-strukturen er et dobbeltstrenget nukleinsyre molekyle.
4. Fremgangsmåde ifølge et hvilket som helst af de foregående krav, hvor nukleinsyremolekylet fæstnet til bindingsenheden i B-strukturen indeholder et PCR initieringssted og hvor nukleinsyremolekylet fæstnet til målet i T-strukturen indeholder et PCR initieringssted.
5. Fremgangsmåde ifølge et hvilket som helst af de foregående krav, hvor in vitro biblioteket i trin (i) omfatter mindst 105 forskellige bindingsenheder Bn, hvor η = 105 eller mere, og hvor bindingsenhederne i trin (i) er kemiske forbindelser med en gennemsnitlig molekylevægt MW under 5000 dalton.
6: Fremgangsmåde ifølge et hvilket som helst af de foregående krav, hvor der er mindst to forskellige mål Tn i trin (ii), hvor n = 2 eller mere.
7: Fremgangsmåde ifølge et hvilket som helst af de foregående krav, hvor mindst ét mål er et protein.
8: Fremgangsmåde ifølge et hvilket som helst af de foregående krav, hvor der i trin (iii) er mindst 105 kopier afen T-struktur af interesse - hvor Ύ" er mindst 105, og hvor koncentrationen af T-strukturer i "blandetrin (iii)" er mindst 10'9 M.
9. Fremgangsmåde ifølge et hvilket som helst af de foregående krav, hvor trin (iii) udføres under bindingsbetingelser, hvor en B-struktur indeholdende en bindingsenhed, der er i stand til at binde til et målmolekyle, binder 100 gange mere effektivt til den tilsvarende T-struktur end en B-struktur indeholdende en bindingsenhed, der ikke er i stand til binde til det samme mål gør.
10: Fremgangsmåde ifølge et hvilket som helst af de foregående krav, hvor fremgangsmåden ifølge krav 1 omfatter et yderligere trin (iii-b), der udføres før trin (iv) ifølge krav 1, der omfatter: (iii-b): fortynding af opløsningen i trin (iii) mindst 100 gange under bindingsbetingelser, der er betingelser, hvor en B-struktur indeholdende en bindingsenhed i stand til at binde til et målmolekyle binder mere effektivt til den tilsvarende T-struktur end en B-struktur indeholdende en bindingsenhed der ikke i stand til at binde til det samme mål gør.
11: Fremgangsmåde ifølge et hvilket som helst af de foregående krav, hvor der i trin (iv) ifølge krav 1 er mindst 100 gange flere individuelle rum end Y-antallet af T-strukturer til stede i trin (iii), og hvor der i trin (iv) ifølge krav 1 er mindst kvadratroden af 10 (3,16) gange flere individuelle rum end X-antallet af B-strukturer i trin (iii).
12: Fremgangsmåde ifølge et hvilket som helst af de foregående krav, hvor in vitro fordelingssystemet i trin (iv) er et vand-i-olie emulsionssystem, og hvor det gennemsnitlige volumen af et rum er mindre end 10'12 liter.
13: Fremgangsmåde ifølge et hvilket som helst af de foregående krav, hvor der er et ekstra trin (vii), omfattende anvendelse af det berigede bibliotek i trin (vi) til at identificere mindst en individuel bindingsenhed, der binder til mindst et mål af interesse.
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| WO2012041633A1 (en) * | 2010-09-27 | 2012-04-05 | Vipergen | A method for making an enriched library |
| EP2931948B1 (en) * | 2012-12-05 | 2019-08-14 | The Regents of The University of California | Screening of nucleic acid agents via particle display |
| CN104630202A (zh) * | 2013-11-13 | 2015-05-20 | 北京大学 | 一种能够减小微量核酸物质整体扩增时产生偏倚的扩增方法 |
| GB201420852D0 (en) * | 2014-11-24 | 2015-01-07 | Genevillage Kft | Method |
| WO2017031378A1 (en) * | 2015-08-18 | 2017-02-23 | Krusemark Casey J | Systems and methods for proteomic activity analysis using dna-encoded probes |
| EP3452591B1 (en) | 2016-05-02 | 2023-08-16 | Encodia, Inc. | Macromolecule analysis employing nucleic acid encoding |
| WO2017218293A1 (en) | 2016-06-16 | 2017-12-21 | Richard Edward Watts | Oligonucleotide directed and recorded combinatorial synthesis of encoded probe molecules |
| US11795580B2 (en) | 2017-05-02 | 2023-10-24 | Haystack Sciences Corporation | Molecules for verifying oligonucleotide directed combinatorial synthesis and methods of making and using the same |
| JP7390027B2 (ja) | 2017-10-31 | 2023-12-01 | エンコディア， インコーポレイテッド | 核酸エンコーディングおよび／または標識を使用する解析のためのキット |
| WO2019109046A1 (en) | 2017-11-30 | 2019-06-06 | Arrakis Therapeutics, Inc. | Nucleic acid-binding photoprobes and uses thereof |
| CA3127137A1 (en) | 2019-01-22 | 2020-07-30 | Vipergen Aps | A method for screening of an in vitro display library within a cell |
| CN114072499B (zh) | 2019-04-30 | 2024-08-06 | Encodia公司 | 用于制备分析物的方法和相关试剂盒 |
| CN112941634B (zh) * | 2019-12-10 | 2023-09-26 | 成都先导药物开发股份有限公司 | 通过dna编码化合物库筛选同时结合多个生物靶标的化合物的方法 |
| EP4330678A1 (en) * | 2021-04-26 | 2024-03-06 | Ecole Polytechnique Federale De Lausanne (Epfl) | High complexity microcompartment-based interaction screening |
| GB202317973D0 (en) | 2023-11-24 | 2024-01-10 | Nuclera Ltd | Use of DNA encoded libraries |
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| US4683202A (en) | 1985-03-28 | 1987-07-28 | Cetus Corporation | Process for amplifying nucleic acid sequences |
| CA2346989A1 (en) | 1998-10-19 | 2000-04-27 | The Board Of Trustees Of The Leland Stanford Junior University | Dna-templated combinatorial library chemistry |
| EP1423400B2 (en) | 2001-03-19 | 2013-05-22 | President and Fellows of Harvard College | Evolving new molecular function |
| IL159268A0 (en) | 2001-06-20 | 2004-06-01 | Nuevolution As | Templated molecules and methods for using such molecules |
| US11118215B2 (en) * | 2003-09-18 | 2021-09-14 | Nuevolution A/S | Method for obtaining structural information concerning an encoded molecule and method for selecting compounds |
| EP1694693A2 (en) * | 2003-12-17 | 2006-08-30 | Praecis Pharmaceuticals Inc. | Methods for synthesis of encoded libraries |
| US7968287B2 (en) * | 2004-10-08 | 2011-06-28 | Medical Research Council Harvard University | In vitro evolution in microfluidic systems |
| US20060099626A1 (en) * | 2004-10-27 | 2006-05-11 | Harbury Pehr B | DNA-templated combinatorial library device and method for use |
| AU2005300886B2 (en) * | 2004-11-08 | 2009-11-12 | Vipergen Aps | Structural nucleic acid guided chemical synthesis |
| ATE420170T1 (de) | 2004-11-22 | 2009-01-15 | Peter Birk Rasmussen | Matrizengerichtete split-and-mix-synthese von bibliotheken kleiner moleküle |
| DE602008003757D1 (de) | 2007-02-23 | 2011-01-13 | New England Biolabs Inc | Auswahl und anreicherung von proteinen durch in-vitro-untergliederung |
| EP2210104A4 (en) * | 2007-11-01 | 2011-02-23 | Univ Arizona State | CELL-FREE PROCEDURE FOR DETECTING PROTEIN-LIGAND INTERACTIONS |
| US8153446B2 (en) | 2008-05-23 | 2012-04-10 | Kent State University | Fluorogenic compounds converted to fluorophores by photochemical or chemical means and their use in biological systems |
| CN102549427A (zh) * | 2009-07-07 | 2012-07-04 | 新加坡科技研究局 | 鉴定结合配偶体对的方法 |
| WO2012041633A1 (en) * | 2010-09-27 | 2012-04-05 | Vipergen | A method for making an enriched library |
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| DK3399035T3 (da) | 2021-05-17 |
| IL224694A0 (en) | 2013-07-31 |
| DK2622073T3 (da) | 2018-07-30 |
| JP6193761B2 (ja) | 2017-09-06 |
| CN103119165A (zh) | 2013-05-22 |
| JP2013540440A (ja) | 2013-11-07 |
| EP3399035B1 (en) | 2021-02-17 |
| CA2808656C (en) | 2019-12-03 |
| WO2012041633A1 (en) | 2012-04-05 |
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