WO2000079008B1 - High throughput assay system - Google Patents

High throughput assay system

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Publication number
WO2000079008B1
WO2000079008B1 PCT/US2000/016952 US0016952W WO0079008B1 WO 2000079008 B1 WO2000079008 B1 WO 2000079008B1 US 0016952 W US0016952 W US 0016952W WO 0079008 B1 WO0079008 B1 WO 0079008B1
Authority
WO
WIPO (PCT)
Prior art keywords
specific
detection
target
sample
anchors
Prior art date
Application number
PCT/US2000/016952
Other languages
French (fr)
Other versions
WO2000079008A9 (en
WO2000079008A3 (en
WO2000079008A2 (en
Inventor
Richard M Kris
Stephen Felder
Original Assignee
Richard M Kris
Stephen Felder
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority to EA200200062A priority Critical patent/EA007338B1/en
Application filed by Richard M Kris, Stephen Felder filed Critical Richard M Kris
Priority to AU54980/00A priority patent/AU775659B2/en
Priority to JP2001505351A priority patent/JP2003504011A/en
Priority to MXPA01013355A priority patent/MXPA01013355A/en
Priority to CN008092702A priority patent/CN1390263B/en
Priority to EP00939977A priority patent/EP1190095A2/en
Priority to CA2377567A priority patent/CA2377567C/en
Publication of WO2000079008A2 publication Critical patent/WO2000079008A2/en
Publication of WO2000079008A3 publication Critical patent/WO2000079008A3/en
Publication of WO2000079008B1 publication Critical patent/WO2000079008B1/en
Priority to NO20016261A priority patent/NO20016261L/en
Publication of WO2000079008A9 publication Critical patent/WO2000079008A9/en
Priority to HK03104782.1A priority patent/HK1052536A1/en

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    • 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
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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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

85AMENDED CLAIMS[received by the International Bureau on 07 May 2001 (07 05 01), original claims 1-21 replaced by new claims 1-49 (11 pages)]
1. A method of detecting at least one target, comprising a) contacting a sample which may comprise said target(s) with a combination which compπses, before the addition of said sample, l) a surface, compπsing multiple spatially discrete regions, at least two of which are substantially identical, each region compπsing ii) at least eight different oligonucleotidc anchors, each in association with iij) a bifunctional linker which has a first portion that is specific for the o gonucleotide anchor, and a second portion that compπses a probe which is specific for said target(s), wherein the target(s) is a protection fragroent(s) and is amplified by PCR before said samρle(s) is contacted with said combinauon, under conditions effective for said target(s) to bind to said combination, b) contacting said corabinanon and any bound targets with a labeled detection probe, and c) detecting said detection probe.
2. The method of claim 1 , wherein said target(s) are amplified by PCR using two PCR pπmers, either or both of which comprises a chemical modification which allows the pπmer to attach to a solid surface.
3. The method of claim 1 , wherein said larget(s) are amplified by PCR using two PCR pπmers, either or both of which compπses one or more restriction enzyme sites.
4. The method of claim 1, wherein said target(s) are amplified by PCR using two PCR pπmers, either or both of which compπses one or more peptide sequences which can be cleaved by a protease 86
5. The method of claim 1, wherein said targeι(s) are amplified by PCR using two PCR pπmers, either or both of which compnses a sequence which is specific for said detection probe.
6. A method of detecting at least one target, compnsing a) contacting a sample which may comprise said target(s) with a combination which comprises, before the addition of said sample, i) a surface, compπsing multiple spatially discrete regions, at least two of which are substantially identical, each region comprising i) at least eight different oligonucleotide anchors, each in association with iii) a bifujictional linker which has a first portion that is specific for the oligonucleotide anchor, and a second portion that compπses a probe which is specific for said target(s), under conditions effective for said target(s) to bind to said combination, b) contacting said combination and any bound targets with a labeled detection probe, and c) detecting said detection probe, wherein said labeled detecuon probe comprises an upcσnveπing phosphore.
7. The method of claim 6, wherein said combination and any bound targets are contacted with at least two different labeled detection probes, each of which labeled probe comprises a different upconverting phosphore.
8. The method of claim 6, wherein said target(s) is a nuclease protection ■fragment.
9. The method of claim S, wherein said combination and any bound targets are contacted with at least two labeled detection probes, each of which labeled probe comprises a different upconveπmg phosphore. 87
10. A method of detecting at least one target, compπsing a) contacting a sample which may comprise said target(s) with a combination which comprises, before the addition of said sample,
I) a surface, compnsing multiple spatially discrete regions, at least two of which are substantially identical, each region compπsing ii) at least eight different oligonucleotide anchors, each m association with ni) a bifunctional linker which has a first poπion that is specific for the oligonucleotide anchor, and a second portion that compnses a probe which is specific for said target(s), under conditions effective for said target(s) to bind to said combination, b) contacting said combination and any bound targets w th a detection linker, which comprises a moiety specific for said target and a moiety specific for a repoπer reagent, which interacts with said detection linker and which compπses a signaling entity, c) contacting said detection linker with said repoπer reagent, and d) detecting said signaling entity
11. The method of claim 10, wherein said target(s) is a nuclease protection fragment.
12. The method of claim 10, which is a method for detecting at least two targets, further comprising b) contacting said combination and any bound targets with at least two detection linkers, each of which compπses a moiety specific for one of said targets and a moiety specific for a common reporter reagent, 88
c) contacting sa d detection linkers with said common repoπer reagent, which interacts with said detection linkers and which compnses a signaling entity, and d) detecting said signaling entity.
13. The method of claim 12, wherem said targets are nuclease protection fragments
14. The method of claim 12, wherem said signaling entity comprises an upconvertmg phosphore
15. A method of detecting at least two RNAs, compπsing a) incubating a sample which may co pπse said RNAs with two or more protection f agments under conditions which are effecnve for hybπdization of said protection fragments to said RNAs, wherein each of said protection fragments compπses a common 3' overhanging sequence which is not specific for said RNAs, b) subjecting said incubated sample to treatment with one or more nucle ses effecnve for digesting nucleic acid other than the porπon of said protection fragments which have hybridized to said RNAs and, optionally, the portions of said RNAs which have been hybπdized, c) removing nucleic acid material other than said protection fragments which have hybπdized to said RNAs, to provide a sample containing the protection f agments, d) contacting said sample containing the protection fragments with a combination which compnses, before the addition of said sample, i) a surface, compns g muluple spatially discrete regions, at least two of which are substantially identical, each region comprising n) at least eight different oligonucleotide anchors, each in association with 89
iii) a bifunctional linker which has a first portion that is specific for the oligonucleotide anchor, and a second ponion that comprises a probe which is specific for at least one of said protection f agments, under conditions effective for said protection fragments to bind to said combination, e) contacting said combination and any bound protection fragments with at least two detection linkers, each of which comprises a moiety specific for one of said protection fragments and a moiety specific for said common 3' overhanging sequence, f) contacting said detection linkers with a repoπer reagent which is specific for said common reporter reagent and which compπses a signaling entity, and g) detecting said signaling entity.
16. The method of claim 15, wherein said signaling entity comprises an upconveπiπg phosphore.
17. The method of claim 15, wherein one or more of said detection linkers is diluted with blocked detection linker.
18. A method of detecting at least one nucleic acid target, compπsmg a) contacting a sample which may compnse said target(s) with a nuclease protection fragment(s) specific for and which b ds 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 combmation which compπses, before the addition of said sample, i) a surface, comprising multiple spatially discrete regions, at least two of which are substantially identical, each region compnsing ii) at least two different anchors, each in association with in) a bifunctional linker which has a first ponion that is specific for the anchor, and a second ponion that comprises a probe which is specific for said nuclease protection fragroent(s), 90
under conditions effective for said nuclease protection fragment(s) to bind to said combinanon, 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 repoπer reagent, and c) detecting said detection hnker(s).
19. The method of claim 18, wherein said repoπer reagent interacts with said detection linker(s) and comprises a signaling entity, further comprising d) contacting said detection iinker(s) with said repoπer reagent, and e) detecting said signaling entity.
20. The method of claim 18, wherein the anchors are oligonucleotide anchors.
21. A method of detecting at least two nucleic acid targets, comprising a) contacting a sample which may comprise said targets with nuclease protection f agments 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 li) at least two different anchors, each in associanon with iii) a bifunctional linker which has a first portion that is specific for the anchor, and a second portion that compπses a probe which is specific for one of said nuclease protection f agments, 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. 91
22. The method of claim 21 , wherein said repoπer reagent interacts with said detection Unker(s) and comprises a signaling entity, further comprising d) contacnng said detection linker(s) with said repoπer reagent, and e) detecting said signaling entity.
23. The method of claim 21, wherein the anchors are oligonucleotide anchors.
24. A method of detecting at least two nucleic acid targets of interest in a sample which may compnse said targets, comprising a) incubating said sample with two or more protection fragments under conditions which are effecnve 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 interesi which have been hybridized, c) removing nucleic acid mateπal 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, l) a surface, comprising multiple spanally discrete regions, at least two of which are substantially identical, each region compnsing 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 compπses 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.
25. The method of claim 24, further comprising f) contacting said detection linkers with a reporter reagent which is specific for said common 3' overhanging sequence and which compnses a signaling entity, and g) detecting said signaling entity.
26. The method of claim 24, wherein the anchors are oligonucleotide anchors.
27. The method of claim 26, wherein one or more of the detection linkers is diluted with blocked detection linker.
28. The method of claim 23, 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 compπses a probe which is specific for a different nuclease protecuon fragment
29. The method of claim 18, wherem said anchors have been dissociated f om bifunctional linkers having a different target specificity .
30. The method of claim 18, wherein said combinanon compπses a large number of said regions, and wherein the method is high throughput.
31. A kit useful for the detection of at least one nucleic acid target in a sample, which compπses a) at least one nuclease protection f agment specific for at least one of said targets, but not for any of the oligonucleotide anchors m said kit, b) a surface, compπsing multiple spatially discrete regions, at least two of which are substantially identical, each region comprising at least two different oligonucleonde anchors, c) a container compπsing 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.
32. A k t useful for the detection of at least one nucleic acid target in a sample, which comprises: 93
a) at least one nuclease protecnon fragment specific for at least one of said targets, but not for any of the other oligonucleotides in said kit, 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 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.
33. The method of claim 18, wherein each region comprises at least eight different anchors.
34. The method of claim 21, wherein each region comprises at least eight different anchors.
35. The method of claim 24, wherein each region comprises at least eight different anchors.
36. A method of detecting at least one nucleic acid target, comprising a) contacting a sample which may comprise said targei(s) with a nuclease protection itagmenι(s) specific for and which binds to said target(s) and exposing the resultant product to a nuclease effective to digest single sirand 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 taτget(s) which are protected by said nuclease protection fragments, under conditions effective for said protected ρortions(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. 94
37. The method of claim 36- wherein said reporter reagent interacts with said detection lιnker(s) and comprises a signaling entity, further compnsing d) contacting said detection linker(s) with said reporter reagent, and e) detecting said signaling entity.
38. The method of claun 36, wherein each region compπses at least eight different anchors.
39. 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 m 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 rwo 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.
40. The method of claim 39, 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.
41. The method of claim 39, further comprising c) contacting said combination and any bound targets with at least one detection probe.
42. The method of claim 41, 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, 95
and the first and second detection probes are detected simultaneously or sequentially.
43. The method of claim 39, wherem said target(s) is a nuclease protection fragment(s) specific for a nucleic acid(s) of interest.
44. The method of claun 40, wherein said target(s) is a nuclease protection fragmenι(s) specific for a nucleic acιd(s) of interest.
45. The method of claim 42, wherein said target(s) is a nuclease protection fragment(s) specific for a nucleic acid(s) of interest.
46. The method of claim 39, wherein each region comprises at least eight different anchors.
47. The kit of claim 31 , wherein each region comprises at least eight different anchors.
48. The kit of claim 31 , further comprising e) one or more nucleases effective for digesting single strand nucleic acid and/or the RNA strand of a DNA/RNA duplex.
49. 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.
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