High throughput assay system
First Claim
1. 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 and which binds to said target(s), exposing the s ple 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, and detecting said bound protection fragment(s).
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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).
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Citations
41 Claims
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1. 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 and which binds to said target(s), exposing the s ple 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, and detecting said bound protection fragment(s).
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2. A method of detecting at least one nucleic acid target, comprising contacting sample which may comprise said target(s) with a nuclease protection fragment(s) specific for and which binds to said target(s), thereby forming a nuclease protection fragment/target duplex, 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 a portion(s) of said duplex, under conditions effective for hybridization, and detecting any bound protected portion(s).
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37. 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 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,
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, and detecting said bound protection fragment(s).
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38. A kit useful for the detection of at least one nucleic acid target in a sample, comprising
a) at least one nuclease protection fragment specific for said nucleic acid(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, and c) a container comprising at least one biflnctional 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.
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40. A kit useful for the detection of at least one nucleic acid target in a sample, comprising
a) a surface, comprising multiple spatially discrete regions, at least two of which are substantially identical, each region comprising at least two different oligonucleotide anchors, b) a container comprising at least one bifunctional linker molecule, which has a first portion specific for one of said oligonucleotide anchors and a second portion that comprises a probe which is specific for a nuclease protection fragment which is specific for one of said nucleic acids, and c) 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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41. A kit useful for the detection of at least one nucleic acid target in a sample, comprising
a) a surface, comprising multiple spatially discrete regions, at least two of which are substantially identical, each region comprising at least two different oligonucleotide anchors, and b) a set of instructions for i) performing a nuclease protection procedure on said nucleic acid(s) of interest, using a nuclease protection fragment(s) specific for said nucleic acid(s), and ii) attaching to at least one of said oligonucleotide anchors a 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 at least one of said nuclease protection fragments.
Specification