DK2861756T3 - Kinetisk udelukkelsesamplifikation af nukleinsyrebiblioteker - Google Patents

Kinetisk udelukkelsesamplifikation af nukleinsyrebiblioteker Download PDF

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DK2861756T3
DK2861756T3 DK13731229.4T DK13731229T DK2861756T3 DK 2861756 T3 DK2861756 T3 DK 2861756T3 DK 13731229 T DK13731229 T DK 13731229T DK 2861756 T3 DK2861756 T3 DK 2861756T3
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amplification
nucleic acids
target nucleic
sites
array
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DK13731229.4T
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Min-Jui Richard Shen
Jonathan Mark Boutell
Kathryn M Stephens
Mostafa Ronaghi
Kevin L Gunderson
Bala Murali Venkatesan
M Shane Bowen
Kandaswamy Vijayan
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Illumina Inc
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    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844Nucleic acid amplification reactions
    • C12Q1/6848Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
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    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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    • C12Q1/6844Nucleic acid amplification reactions
    • BPERFORMING OPERATIONS; TRANSPORTING
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    • C12Q1/6869Methods for sequencing
    • C12Q1/6874Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
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    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
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    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
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    • BPERFORMING OPERATIONS; TRANSPORTING
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    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583Features relative to the processes being carried out
    • B01J2219/00603Making arrays on substantially continuous surfaces
    • B01J2219/00605Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00608DNA chips
    • BPERFORMING OPERATIONS; TRANSPORTING
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    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583Features relative to the processes being carried out
    • B01J2219/00603Making arrays on substantially continuous surfaces
    • B01J2219/00605Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00614Delimitation of the attachment areas
    • B01J2219/00621Delimitation of the attachment areas by physical means, e.g. trenches, raised areas
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
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    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583Features relative to the processes being carried out
    • B01J2219/00603Making arrays on substantially continuous surfaces
    • B01J2219/00605Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00632Introduction of reactive groups to the surface
    • B01J2219/00637Introduction of reactive groups to the surface by coating it with another layer
    • BPERFORMING OPERATIONS; TRANSPORTING
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    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583Features relative to the processes being carried out
    • B01J2219/00603Making arrays on substantially continuous surfaces
    • B01J2219/00653Making arrays on substantially continuous surfaces the compounds being bound to electrodes embedded in or on the solid supports
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
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    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583Features relative to the processes being carried out
    • B01J2219/00603Making arrays on substantially continuous surfaces
    • B01J2219/00675In-situ synthesis on the substrate
    • BPERFORMING OPERATIONS; TRANSPORTING
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    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00718Type of compounds synthesised
    • B01J2219/0072Organic compounds
    • B01J2219/00722Nucleotides
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    • C12Q2565/00Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/50Detection characterised by immobilisation to a surface
    • C12Q2565/513Detection characterised by immobilisation to a surface characterised by the pattern of the arrayed oligonucleotides
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    • C12Q2565/00Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/50Detection characterised by immobilisation to a surface
    • C12Q2565/537Detection characterised by immobilisation to a surface characterised by the capture oligonucleotide acting as a primer

Claims (15)

1. Fremgangsmåde til amplificering af nukleinsyrer, som omfatter (a) tilvejebringelse af (i) et array af amplifikationsteder med et eller flere indfangningsmidler og (ii) et amplifikationsreagens, der omfatter en opløsning, der omfatter et antal af forskellige målnukleinsyrer, hvor antallet af de forskellige målnukleinsyrer i opløsningen overstiger antallet af amplifikationssteder i arrayet, hvor de forskellige målnukleinsyrer har fluidisk adgang til antallet af amplifikationssteder, og hvor hvert af amplifikationsstederne er i stand til at blive besat af adskillige målnukleinsyrer af antallet af forskellige målnukleinsyrer; og (b) reaktion af amplifikationsreagenset med arrayet af amplifikationssteder, således at et antal af amplifikationssteder hvert omfatter klonale amplikoner fra en individuel målnukleinsyre fra opløsningen, hvor reaktionen omfatter samtidigy (i) transport af de forskellige målnukleinsyrer til amplifikationsstederne til podning i amplifikationsstederne og (ii) amplificering af målnukleinsyrerne, der er podet i amplifikationsstederne, hvor amplifikationshastigheden overstiger podningshastigheden, således at de dannede amplikoner forhindrer, at yderligere målnukleinsyrer podes i hvert af antallet af amplifikationssteder, og derved forhindrer, at de amplificeres i hvert af antallet af amplifikationssteder.
2. Fremgangsmåde ifølge krav 1, hvor hvert af amplifikationsstederne omfatter et antal af indfangningsmidler, der er i stand til at binde til de forskellige målnukleinsyrer i opløsningen.
3. Fremgangsmåde ifølge krav 1 eller 2, hvor arrayet af amplifikationssteder omfatter et array af træk på en overflade, og eventuelt hvor arealet for hvert af trækkene er større end diameteren af det udelukkede volumen af målnukleinsyrerne, der transporteres til amplifikationsstederne.
4. Fremgangsmåde ifølge krav 3, hvor trækkene er ikke-fortløbende og er adskilt af mellemrumsområder af overfladen, der mangler indfangningsmidlerne.
5. Fremgangsmåde ifølge krav 3 eller 4, hvor hvert af trækkene omfatter et korn, en brønd, en kanal, en kam, et fremspring eller en kombination deraf.
6. Fremgangsmåde ifølge krav 1 eller 2, hvor arrayet af amplifikationssteder omfatter korn i opløsning eller korn på en overflade.
7. Fremgangsmåde ifølge krav 2, hvor indfangningsmidlerne omfatter indfangningsnukleinsyrer, der er komplementære til de forskellige målnukleinsyrer, og eventuelt hvor de forskellige målnukleinsyrer omfatter universelle sekvenser, der er komplementære til indfangningsnukleinsyrerne.
8. Fremgangsmåde ifølge et hvilket som helst af ovennævnte krav, hvor hvert af amplifikationsstederne omfatter et antal primere, der anvendes til frembringelse af amplikonerne i (b).
9. Fremgangsmåde ifølge krav 8, hvor arrayet af amplifikationssteder omfatter et array af træk på en overflade, hvor trækkene er ikke-fortløbende og er adskilt af mellemrumsområder af overfladen, der mangler primerne, der anvendes til frembringelse af amplikonerne i (b).
10. Fremgangsmåde ifølge et hvilket som helst af ovennævnte krav, hvor amplifikationsreagenset yderligere omfatter rekombinase og et enkeltstrenget bindingsprotein, og eventuelt hvor amplifikationsreagenset yderligere omfatter et middel til molekylær sammenklumpning.
11. Fremgangsmåde ifølge et hvilket som helst af ovennævnte krav, hvor amplificeringen af målnukleinsyrerne, der transporteres til amplifikationsstederne, ikke indbefatter en denatureringscyklus.
12. Fremgangsmåde ifølge et hvilket som helst af ovennævnte krav, hvor antallet af amplifikationssteder, der omfatter en klonal population af amplikoner, overstiger 40 % af amplifikationsstederne, som de forskellige målnukleinsyrer har fluidisk adgang til.
13. Fremgangsmåde ifølge et hvilket som helst af ovennævnte krav, hvor de forskellige målnukleinsyrer transporteres aktivt til amplifikationsstederne assisteret af påføring af et elektrisk felt.
14. Fremgangsmåde ifølge krav 13, hvor det elektriske felt øges, efterhånden som reaktionen forløber over tid.
15. Fremgangsmåde ifølge krav 13 hvor arrayet af amplifikationssteder omfatter et array af ikke-fortløbende træk på en overflade, hvilke træk er adskilt af mellemrumsområder af overfladen, eventuelt hvor arealet for hvert af trækkene er større end diameteren af det udelukkede volumen af målnukleinsyrerne, der transporteres til amplifikationsstederne, eventuelt hvor de forskellige målnukleinsyrer aktivt frastødes fra mellemrumsområder ved forstærkning af et andet elektrisk felt.
DK13731229.4T 2012-06-15 2013-06-12 Kinetisk udelukkelsesamplifikation af nukleinsyrebiblioteker DK2861756T3 (da)

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US201261660487P 2012-06-15 2012-06-15
US201261715478P 2012-10-18 2012-10-18
US13/783,043 US8895249B2 (en) 2012-06-15 2013-03-01 Kinetic exclusion amplification of nucleic acid libraries
PCT/US2013/045491 WO2013188582A1 (en) 2012-06-15 2013-06-12 Kinetic exclusion amplification of nucleic acid libraries

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