DK2348125T3 - Fremgangsmåde til syntese af et bifunktionelt kompleks - Google Patents

Fremgangsmåde til syntese af et bifunktionelt kompleks Download PDF

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DK2348125T3
DK2348125T3 DK10184069.2T DK10184069T DK2348125T3 DK 2348125 T3 DK2348125 T3 DK 2348125T3 DK 10184069 T DK10184069 T DK 10184069T DK 2348125 T3 DK2348125 T3 DK 2348125T3
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oligonucleotide
codon
reaction
tag
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DK10184069.2T
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Per-Ola Freskgard
Mikkel Dybro Lundorf
Eva Kampmann Olsen
Soren Nyboe Jakobsen
Christian Sams
Henrik Pedersen
Thomas Franch
Alex Haahr Gouliaev
Jakob Felding
Anette Holtmann
Sanne Schrøder Glad
Kim Birkebaek Jensen
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Nuevolution As
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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
    • C12N15/1068—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
    • 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
    • C12N15/1065—Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/10—Nucleotidyl transfering
    • C12Q2521/101—DNA polymerase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/50—Other enzymatic activities
    • C12Q2521/501—Ligase
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B50/00—Methods of creating libraries, e.g. combinatorial synthesis
    • C40B50/08—Liquid phase synthesis, i.e. wherein all library building blocks are in liquid phase or in solution during library creation; Particular methods of cleavage from the liquid support
    • C40B50/10—Liquid phase synthesis, i.e. wherein all library building blocks are in liquid phase or in solution during library creation; Particular methods of cleavage from the liquid support involving encoding steps
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B50/00—Methods of creating libraries, e.g. combinatorial synthesis
    • C40B50/14—Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
    • C40B50/16—Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support involving encoding steps

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Organic Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biomedical Technology (AREA)
  • General Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Plant Pathology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
  • Organic Low-Molecular-Weight Compounds And Preparation Thereof (AREA)
  • Immobilizing And Processing Of Enzymes And Microorganisms (AREA)
  • Saccharide Compounds (AREA)
  • Enzymes And Modification Thereof (AREA)

Claims (17)

1. En split-og-mix fremgangsmåde til opnåelse af et eller flere bifunktionelle komplekser, hvert bifunktionelt kompleks omfattende en display-molekyle del og en kodende del omfattende et oligonukleotid, hvor et foreløbigt bifunktionelt kompleks omfattende et kemisk reaktionssted og et primingssted egnet til enzymatisk addition afen tag reageres ved det kemiske reaktionssted med en eller flere reaktanter, og hvor respektive tag(s), der identificerer reaktanten eller reaktanterne, tilvejebringes ved primingsstedet under anvendelse af et eller flere enzymer.
2. En split-og-mix fremgangsmåde til syntese af et eller flere bifunktionelle komplekser, hvert bifunktionelt kompleks omfattende et display-molekyle og en oligonukleotid-identifier, hvilket display-molekyle er bundet af en bindingsdel til oligonukleotid-identifieren, hvilken fremgangsmåde omfatter de trin, at man a) tilvejebringer et foreløbigt bifunktionelt kompleks omfattende et kemisk reaktionssted og et primingssted egnet til enzymatisk addition afen oligonukleotid-tag, b) reagerer det kemiske reaktionssted med en eller flere reaktanter, og c) reagerer primingsstedet enzymatisk med en eller flere oligonukleotid-tags, der identificerer den ene eller flere reaktanter, hvor to oligonukleotid-tags, der skal ligeres sammen, holdes sammen af et komplementerende oligonukleotid, som komplementerer enderne af de to oligonukleotider.
3. En fremgangsmåde til syntese af et bibliotek af forskellige bifunktionelle komplekser ved gentagelse af fremgangsmåden ifølge et hvilket som helst af kravene 1 eller 2 til syntese af de pågældende, forskellige bifunktionelle komplekser, hvilken fremgangsmåde omfatter de trin, at man reagerer forskellige reaktanter med det kemiske reaktionssted, eller med et foreløbigt bifunktionelt kompleks syntetiseret i en tidligere synteserunde.
4. Fremgangsmåden ifølge krav 3, hvor biblioteket indeholder fra 105 til 106 forskellige bifunktionelle komplekser, eller fra 105 til 108 forskellige bifunktionelle komplekser, eller fra 105 til 1010 forskellige bifunktionelle komplekser, eller fra 105 til 1014 forskellige bifunktionelle komplekser.
5. Fremgangsmåden ifølge krav 4, hvor identifier-oligonukleotidet i de bifunktionelle komplekser er dobbeltstrenget, hvor den pågældende dobbeltstrengede form opnås ved en forlængelsesproces under anvendelse af en primer og en polymerase, der er i stand til at forlænge den pågældende primer.
6. Fremgangsmåden ifølge krav 3, hvor der udføres en enkelt selektionsrunde mod et specifikt mål, eller hvor der udføres flere selektionsrunder mod et specifikt mål.
7. Fremgangsmåden ifølge krav 6, hvor målet er valgt fra gruppen bestående af et protein, et peptid, et kulhydrat, et polysaccharid, et glycoprotein, et hormon, en receptor, et antigen, et antistof, et virus, et substrat, en metabolit, en transition-state analog, en co-faktor, en inhibitor, et lægemiddel, et farvestof, et næringsmiddel, en vækstfaktor, en celle, og et væv.
8. Fremgangsmåden ifølge et hvilket som helst af kravene 6 og 7, hvor biblioteket partitioneres og et eller flere bifunktionelle komplekser selekteres, hvor de selekterede display-molekyler i de pågældende bifunktionelle komplekser har en affinitet for det pågældende mål.
9. Fremgangsmåden ifølge et hvilket som helst af kravene 5 og 6, hvor identifier-oligonukleotidet i syntetiserede eller selekterede molekyler amplificeres ved anvendelse af PCR.
10. Fremgangsmåden ifølge krav 9, hvor identifier-oligonukleotider, der identificerer selekterede og/eller amplificerede display-molekyler, sekventeres.
11. Fremgangsmåden ifølge et hvilket som helst af kravene 1 og 2, hvor en eller to reaktanter anvendes i syntesen af display-molekylet.
12. Fremgangsmåden ifølge et hvilket som helst af kravene 1 og 2, hvor reaktionen mellem en eller flere reaktanter foregår efter addition af en eller flere tags eller samtidig med addition af en eller flere tags.
13. Fremgangsmåden ifølge et hvilket som helst af kravene 1 og 2, hvor en beskyttelsesgruppe, der beskytter det kemiske reaktionssted og/eller reaktant(er), der skal reageres, fjernes inden en reaktion.
14. Fremgangsmåden ifølge krav 3, hvor identifier-oligonukleotider i de syntetiserede, bifunktionelle komplekser, inden et selektionstrin, omdannes til en dobbeltstrenget form under anvendelse af en polymerase.
15. Fremgangsmåden ifølge et hvilket som helst af kravene 1 og 2, hvor mindst nogle reaktantreaktioner foregår i et organisk solvent.
16. Fremgangsmåden ifølge et hvilket som helst af kravene 1 og 2, hvor de anvendte oligonukleotider er syntetiseret ved standard phosphoramidit-kemi.
17. Fremgangsmåden ifølge krav 3, hvor målet er immobiliseret.
DK10184069.2T 2002-10-30 2003-10-30 Fremgangsmåde til syntese af et bifunktionelt kompleks DK2348125T3 (da)

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
US42216702P 2002-10-30 2002-10-30
DKPA200201652 2002-10-30
US43442502P 2002-12-19 2002-12-19
DKPA200201955 2002-12-19
US48619903P 2003-07-11 2003-07-11
DKPA200301064 2003-07-11
EP03757752A EP1558744B1 (en) 2002-10-30 2003-10-30 Enzymatic encoding

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DK2348125T3 true DK2348125T3 (da) 2017-10-02

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DK17177016.7T DK3299463T3 (da) 2002-10-30 2003-10-30 Enzymatisk kodning
DK10184069.2T DK2348125T3 (da) 2002-10-30 2003-10-30 Fremgangsmåde til syntese af et bifunktionelt kompleks
DK10183942.1T DK2348124T3 (da) 2002-10-30 2003-10-30 Syntese af et bifunktionelt kompleks
DK03757752.5T DK1558744T3 (da) 2002-10-30 2003-10-30 Enzymatisk kodning

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US (8) US8206901B2 (da)
EP (4) EP2348125B1 (da)
JP (3) JP4895608B2 (da)
CN (3) CN102838654B (da)
AT (1) ATE513055T1 (da)
AU (1) AU2003273792B2 (da)
CA (2) CA2544153C (da)
DK (4) DK3299463T3 (da)
ES (3) ES2452566T3 (da)
HU (1) HUE033651T2 (da)
IL (2) IL207673A0 (da)
LT (1) LT2348125T (da)
NZ (1) NZ538993A (da)
PT (3) PT2348125T (da)
SI (3) SI2348124T1 (da)
WO (1) WO2004039825A2 (da)
ZA (1) ZA200502624B (da)

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