High throughput assay system

• US 6,238,869 B1
• Filed: 06/21/1999
• Issued: 05/29/2001
• Est. Priority Date: 12/19/1997
• Status: Expired due to Term

• Current Assignee: High Throughput Genomics, Inc.
• Original Assignee: High Throughput Genomics, Inc.
• Inventors: Kris, Richard M, Felder, Stephen
• Primary Examiner(s): Brusca, John S.
• Assistant Examiner(s): KIM, YOUNG J
• Application Number:
  US09/337,325
• Time in Patent Office: 708 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 435/196, 435/199, 436/501
• US Class Current: 435/6.12
• CPC Class Codes: B01J 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00547 Bar codes
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00644 the porous medium being present in discrete locations, e.g. gel pads
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00662 Two-dimensional arrays within two-dimensional arrays
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6874 : involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2521/325 : Single stranded exonuclease
• CPC Class Codes: C12Q 2537/125 : Sandwich assay format
• CPC Class Codes: C12Q 2565/513 : characterised by the pattern of the arrayed oligonucleotides
• CPC Class Codes: C12Q 2565/519 : characterised by the capture moiety being a single stranded oligonucleotide
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: C40B 70/00 : Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes

Abstract

The present invention relates to compositions, apparatus and methods useful for concurrently performing multiple, high throughput, biological or chemical assays, using repeated arrays of probes. A combination of the invention comprises a surface, which comprises a plurality of test regions, at least two of which, and in a preferred embodiment, at least twenty of which, are substantially identical, wherein each of the test regions comprises an array of generic anchor molecules. The anchors are associated with bifunctional linker molecules, each containing a portion which is specific for at least one of the anchors and a portion which is a probe specific for a target of interest. The resulting array of probes is used to analyze the presence or test the activity of one or more target molecules which specifically interact with the probes. In one embodiment of the invention, the test regions (which can be wells) are further subdivided into smaller subregions (indentations, or dimples).

Claims

1. A method of detecting at least one nucleic acid target, comprising

a) contacting a sample which may comprise said target(s) with a nuclease protection fragment(s) specific for and which binds to said target(s), exposing the sample to a nuclease effective to digest remaining single strand nucleic acid, and then contacting the resultant sample with a combination which comprises, before the addition of said sample,

i) a surface, comprising multiple spatially discrete regions, at least two of which are substantially identical, each region comprising

ii) at least two different anchors, each in association with

iii) a bifunctional linker which has a first portion that is specific for the anchor, and a second portion that comprises a probe which is specific for said nuclease protection fragment(s),

under conditions effective for said nuclease protection fragment(s) to bind to said combination,

b) contacting said combination and any bound nuclease protection fragment(s) with at least one detection linker, which comprises a first moiety specific for one of said bound nuclease protection fragment(s) and a second moiety specific for a reporter reagent, and

c) detecting said detection linker(s).

2. The method of claim 1, wherein said reporter reagent interacts with said detection linker(s) and comprises a signaling entity, further comprising

c) contacting said detection linker(s) with said reporter reagent, and

d) detecting said signaling entity.

3. The method of claim 1, wherein the anchors are oligonucleotide anchors.

12. The method of claim 1, wherein said anchors have been dissociated from bifunctional linkers having a different target specificity.

13. The method of claim 1, wherein said combination comprises a large number of said regions, and wherein the method is high throughput.

16. The method of claim 1, wherein each region comprises at least eight different anchors.

4. A method of detecting at least two nucleic acid targets, comprising

a) contacting a sample which may comprise said targets with nuclease protection fragments specific for and which bind to said targets, exposing the sample to a nuclease effective to digest remaining single strand nucleic acid, and then contacting the resultant sample with a combination which comprises, before the addition of said sample,

i) a surface, comprising multiple spatially discrete regions, at least two of which are substantially identical, each region comprising

ii) at least two different anchors, each in association with

iii) a bifunctional linker which has a first portion that is specific for the anchor, and a second portion that comprises a probe which is specific for one of said nuclease protection fragments,

under conditions effective for said nuclease protection fragments to bind to said combination,

b) contacting said combination and any bound nuclease protection fragments with at least two detection linkers, each of which comprises a first moiety specific for one of said nuclease protection fragments and a second moiety specific for a common reporter reagent, and

c) detecting said detection linkers.

5. The method of claim 4, wherein said reporter reagent interacts with said detection linker(s) and comprises a signaling entity, further comprising

c) contacting said detection linker(s) with said reporter reagent, and

d) detecting said signaling entity.

6. The method of claim 4, wherein the anchors are oligonucleotide anchors.

11. The method of claim 6, wherein at least one of said anchors is in association with a plurality of bifunctional linkers, each of which has a first portion that is specific for the anchor, and a second portion which comprises a probe which is specific for a different nuclease protection fragment.

17. The method of claim 4, wherein each region comprises at least eight different anchors.

7. A method of detecting at least two nucleic acid targets of interest in a sample which may comprise said targets, comprising

a) incubating said sample with two or more protection fragments under conditions which are effective for hybridization of said protection fragments to said nucleic acids of interest in said sample, wherein each of said protection fragments comprises a common 3′

overhanging sequence which is not specific for said nucleic acids of interest,

b) subjecting said incubated sample to treatment with one or more nucleases effective for digesting nucleic acid other than the portions of said protection fragments which have hybridized to the nucleic acids of interest and, optionally, the portions of said nucleic acids of interest which have been hybridized,

c) removing nucleic acid material other than said protection fragments which have hybridized to said nucleic acids of interest, to provide a sample containing the protection fragments, then

d) contacting said sample containing the protection fragments with a combination which comprises, before the addition of said sample,

i) a surface, comprising multiple spatially discrete regions, at least two of which are substantially identical, each region comprising

ii) at least two different anchors, each in association with

iii) a bifunctional linker which has a first portion that is specific for the anchor, and a second portion that comprises a probe which is specific for one of said protection fragments,

under conditions effective for said protection fragments to bind to said combination, and

e) contacting said combination and any bound protection fragments with at least two detection linkers, each of which comprises a first moiety specific for one of said protection fragments and a second moiety specific for said common 3′

overhanging sequence.

8. The method of claim 7, further comprising

f) contacting said detection linkers with a reporter reagent which is specific for said common 3′ overhanging sequence and which comprises a signaling entity, and

g) detecting said signaling entity.

9. The method of claim 7, wherein the anchors are oligonucleotide anchors.

10. The method of claim 9, wherein one or more of the detection linkers is diluted with blocked detection linker.

18. The method of claim 7, wherein each region comprises at least eight different anchors.

14. A kit useful for the detection of at least one nucleic acid target in a sample, which comprises

a) at least one nuclease protection fragment specific for at least one of said targets, but not for any of the oligonucleotide anchors in said kit,

b) a surface, comprising multiple spatially discrete regions, at least two of which are substantially identical, each region comprising at least two different oligonucleotide anchors,

c) a container comprising at least one bifunctional linker molecule, which has a first portion specific for at least one of said oligonucleotide anchors and a second portion that comprises a probe which is specific for, and in said detection binds to, at least one of said nuclease protection fragments, and

d) at least one detection linker, which has a first moiety specific for one of said nuclease protection fragments and a second moiety specific for a reporter reagent.

30. The kit of claim 14, wherein each region comprises at least eight different anchors.

31. The kit of claim 14, further comprising

e) one or more nucleases effective for digesting single strand nucleic acid and/or the RNA strand of a DNA/RNA duplex.

15. A kit useful for the detection of at least one nucleic acid target in a sample, which comprises:

b) at least one bifunctional linker which has a first portion that is specific for an oligonucleotide anchor, and a second portion which is specific for, and in said detection binds to, at least one of said nuclease protection fragments, and

a) at least one nuclease protection fragment specific for at least one of said targets, but not for any of the other oligonucleotides in said kit,

c) at least one detection linker, which has a first moiety specific for one of said nuclease protection fragments and a second moiety specific for a reporter reagent.

19. A method of detecting at least one nucleic acid target, comprising contacting a sample which may comprise said target(s) with a nuclease protection fragment(s) specific for said target(s) and exposing the resultant product to a nuclease effective to digest single strand nucleic acid, and then contacting the resultant sample with a combination which comprises, before the addition of said sample,

i) a surface comprising multiple spatially discrete regions, at least two of which are substantially identical, each region comprising

ii) at least two different anchors, each in association with

iii) a bifunctional linker which has a first portion that is specific for the anchor, and a second portion that comprises a probe which is specific for portions of said nucleic acid target(s) which are protected by said nuclease protection fragments,

under conditions effective for said protected portions(s) to bind to said combination,

b) contacting said combination and any bound protected portion(s) with at least one detection linker, which comprises a first moiety specific for one of said bound protected portion (s) and a second moiety specific for a reporter reagent, and

c) detecting said detection linker.

20. The method of claim 19, wherein said reporter reagent interacts with said detection linker(s) and comprises a signaling entity, further comprising

d) contacting said detection linker(s) with said reporter reagent, and

e) detecting said signaling entity.

21. The method of claim 19, wherein each region comprises at least eight different anchors.

22. A method of detecting at least one target, comprising

a) contacting a sample which may comprise said target(s) with a combination which comprises, before the addition of said sample,

i) a surface, comprising multiple spatially discrete regions, at least two of which are substantially identical, each region comprising

ii) at least two different loci of anchors, the anchors at each locus each in association with

iii) a bifunctional linker which has a first portion that is specific for the anchor, and a second portion that comprises a probe which is specific for said target(s),

under conditions effective for said target(s) to bind to said combination, and

wherein two or more of the anchors located at at least one locus of a region are in association with different bifunctional linkers, having different target specificities.

23. The method of claim 22, further comprising

b) contacting said combination and any bound targets with at least one detection linker, which comprises a first moiety specific for one of said bound target(s) and a second moiety specific for a reporter reagent.

24. The method of claim 22, further comprising

c) contacting said combination and any bound targets with at least one detection probe.

25. The method of claim 24, wherein

a first detection probe binds to a first target bound to the combination at a first locus,

a second detection probe binds to a second target bound to the combination at the same locus,

and the first and second detection probes are detected simultaneously or sequentially.

26. The method of claim 22, wherein said target(s) is a nuclease protection fragment(s) specific for a nucleic acid(s) of interest.

27. The method of claim 23, wherein said target(s) is a nuclease protection fragment(s) specific for a nucleic acid(s) of interest.

28. The method of claim 25, wherein said target(s) is a nuclease protection fragment(s) specific for a nucleic acid(s) of interest.

29. The method of claim 22, wherein each region comprises at least eight different anchors.

32. A kit useful for the detection of at least one nucleic acid target, comprising

a) at least one nuclease protection fragment specific for said target(s), but not for any of the oligonucleotide anchors in said kit,

b) a surface, comprising multiple spatially discrete regions, at least two of which are substantially identical, each region comprising at least two different oligonucleotide anchors,

c) a container comprising at least one bifunctional linker molecule, which has a first portion specific for at least one of said oligonucleotide anchors and a second portion that comprises a probe which is specific for, and in said detection binds to, at least one of said nuclease protection fragments,

d) at least one detection linker, which has a first moiety specific for one of said nuclease protection fragments and a second moiety specific for a reporter reagent, and

e) one or more nucleases effective for digesting single strand nucleic acid and/or the RNA strand of a DNA/RNA duplex.