CA2382157A1 - Compositions and methods for preparing oligonucleotide solutions - Google Patents

Compositions and methods for preparing oligonucleotide solutions Download PDF

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Publication number
CA2382157A1
CA2382157A1 CA002382157A CA2382157A CA2382157A1 CA 2382157 A1 CA2382157 A1 CA 2382157A1 CA 002382157 A CA002382157 A CA 002382157A CA 2382157 A CA2382157 A CA 2382157A CA 2382157 A1 CA2382157 A1 CA 2382157A1
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Prior art keywords
oligonucleotides
substrate
different
linkers
beads
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CA002382157A
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French (fr)
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CA2382157C (en
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John R. Stuelpnagel
Mark S. Chee
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Illumina Inc
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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
    • C12N15/1093—General methods of preparing gene libraries, not provided for in other subgroups
    • 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
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • G—PHYSICS
    • G11—INFORMATION STORAGE
    • G11C—STATIC STORES
    • G11C7/00—Arrangements for writing information into, or reading information out from, a digital store
    • G11C7/10—Input/output [I/O] data interface arrangements, e.g. I/O data control circuits, I/O data buffers
    • G11C7/1048—Data bus control circuits, e.g. precharging, presetting, equalising
    • H—ELECTRICITY
    • H03—ELECTRONIC CIRCUITRY
    • H03K—PULSE TECHNIQUE
    • H03K19/00—Logic circuits, i.e. having at least two inputs acting on one output; Inverting circuits
    • H03K19/02—Logic circuits, i.e. having at least two inputs acting on one output; Inverting circuits using specified components
    • H03K19/08—Logic circuits, i.e. having at least two inputs acting on one output; Inverting circuits using specified components using semiconductor devices
    • H03K19/094—Logic circuits, i.e. having at least two inputs acting on one output; Inverting circuits using specified components using semiconductor devices using field-effect transistors
    • H03K19/096—Synchronous circuits, i.e. using clock signals
    • H03K19/0966—Self-timed logic
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10S977/00—Nanotechnology
    • Y10S977/70—Nanostructure
    • Y10S977/788—Of specified organic or carbon-based composition
    • Y10S977/789—Of specified organic or carbon-based composition in array format
    • Y10S977/79—Of specified organic or carbon-based composition in array format with heterogeneous nanostructures
    • Y10S977/791—Molecular array
    • Y10S977/792—Nucleic acid array, e.g. human genome array

Abstract

The present invention is directed to methods and compositions for generating a pool of oligonucleotides. The invention finds use in preparing a population or subpopulations of oligonucleotides in solution. The pool of oligonucleotides finds use in a variety of nucleic acid detection and/or amplification assays.

Claims (26)

1. A method of generating a pool of oligonucleotides comprising:
a) providing a substrate and at least first and second different oligonucleotides linked to said substrate through first and second cleavable linkers, respectively; and b) cleaving said first and second linkers, thereby releasing said first and second oligonucleotides from said substrate thereby generating a pool of oligonucleotides comprising said first and second oligonucleotides.
2. A method according to claim 1, wherein said first and second oligonucleotides comprise oligonucleotides of known sequence.
3. A method according to claim 1, wherein said first and second oligonucleotides are labeled.
4. A method according to claim 3, wherein different oligonucleotides bear different labels.
5. A method according to claim 3, wherein said first and second oligonucleotides are attached covalently through said first and second linkers, respectively, to said substrate.
6. A method according to claim 3, wherein said first and second oligonucleotides are synthesized on said substrate.
7. A method according to claim 1, wherein said substrate comprises discrete sites to which said first and second oligonucleotides may be linked.
8. A method according to claim 7, wherein said first and second oligonucleotides are immobilized to first and second beads through said first and second linkers, respectively, and wherein said first and second beads are distributed at said discrete sites.
9. A method according to claim 1, further comprising synthesizing said first and second oligonucleotides on said substrate.
10. The method according to claim 9, wherein said first and second oligonucleotides are synthesized by a synthesis method selected from the group consisting of printing and photolithography.
11. A method for generating a pool of oligonucleotides, said method comprising:
a) providing an array comprising a substrate and a population of oligonucleotides, said population comprising at least first and second subpopulations comprising at least first and second different oligonucleotides, respectively, said first and second oligonucleotides being immobilized to first and second beads, respectively, through first and second cleavable linkers, respectively, said first and second beads being distributed on said substrate; and b) cleaving said first and second linkers, thereby releasing said first and second subpopulations from said first and second beads, thereby generating a pool of oligonucleotides comprising said first and second oligonucleotides.
12. A method according to claim 11, wherein said first and second oligonucleotides comprise known sequence.
13. A method according to claim 11, wherein said first and second oligonucleotides are labeled.
14. A method according to claim 13, wherein said first and second oligonucleotides are labeled with different first and second labels, respectively.
15. A method for generating a pool of oligonucleotides, said method comprising:
a) providing an array comprising a substrate and a population of oligonucleotides, said population comprising at least first and second subpopulations comprising at least first and second different oligonucleotides of known sequence, said first and second oligonucleotides being immobilized directly to a chip through first and second cleavable linkers, respectively; and b) cleaving said first and second linkers, thereby releasing said first and second subpopulations from said chip, thereby generating a pool of oligonucleotides comprising said first and second oligonucleotides.
16. The method according to claim 15, wherein said first and second oligonucleotides are labeled.
17. A composition comprising:
a) a substrate; and b) at least first and second different oligonucleotides of known sequence linked to said substrate through first and second cleavable linkers, respectively.
18. A composition according to claim 17, wherein said substrate comprises discrete sites and said first and second oligonucleotides are immobilized to first and second beads, respectively, through said first and second linkers, respectively, wherein said first and second beads are distributed at said discrete sites.
19. A composition according to claim 18 further comprising at least one linker cleaving agent.
20. A composition according to claim 19, wherein at least said first linker comprises a restriction endonuclease cleavage site and said linker cleaving agent comprises at least one restriction endonuclease.
21. A composition according to claim 17, further comprising at least one solution-phase oligonucleotide.
22. The composition according to claim 21, wherein said first and second oligonucleotides comprise first and second labels, respectively.
23. The composition according to claim 22, wherein said first and second labels are different.
24. A kit comprising:
a) a substrate;
b) at least first and second different oligonucleotides of known sequence linked to said substrate through first and second cleavable linkers, respectively; and c) at least one linker cleaving agent.
25. A kit according to claim 24, wherein said first and second different oligonucleotides comprise first and second labels, respectively.
26. A kit according to claim 25, wherein said first and second labels are different.
CA2382157A 1999-08-18 2000-08-18 Compositions and methods for preparing oligonucleotide solutions Expired - Lifetime CA2382157C (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US14934499P 1999-08-18 1999-08-18
US60/149,344 1999-08-18
PCT/US2000/040684 WO2001012862A2 (en) 1999-08-18 2000-08-18 Compositions and methods for preparing oligonucleotide solutions

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CA2382157A1 true CA2382157A1 (en) 2001-02-22
CA2382157C CA2382157C (en) 2012-04-03

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EP (1) EP1218545B1 (en)
AT (1) ATE542916T1 (en)
AU (1) AU775380B2 (en)
CA (1) CA2382157C (en)
DK (1) DK1218545T3 (en)
WO (1) WO2001012862A2 (en)

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