Systems, tools and methods of assaying biological materials using spatially-addressable arrays

• US 7,608,396 B2
• Filed: 04/06/2006
• Issued: 10/27/2009
• Est. Priority Date: 11/08/1999
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies Europe BV (Agilent Technologies, Inc.)
• Original Assignee: Agilent Technologies Europe BV (Agilent Technologies, Inc.)
• Inventors: Delenstarr, Glenda C.
• Primary Examiner(s): Kim; Young J
• Application Number:
  US11/400,717
• Publication Number:
  US 20060246494A1
• Time in Patent Office: 1,300 Days
• Field of Search: None
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2523/101 Crosslinking agents, e.g. psoralen
• CPC Class Codes: C12Q 2537/137 a displacement step
• CPC Class Codes: C12Q 2565/133 conformational analysis
• CPC Class Codes: C12Q 2565/514 characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array
• CPC Class Codes: C40B 40/00 Libraries per se, e.g. arrays, mixtures

Abstract

Systems, tools and methods are used to perform complex sandwich hybridization assays of biological material. The tools comprise biological solution probes having a first region for hybridizing to capture probes on a universal assay apparatus, and a second region for hybridizing to a sample target. The solution probe assembles the target to the apparatus by hybridizing the second region to the target and the first region to the capture probe. Multiple biological samples, having a plurality of targets per sample, can be multiplexed on the same universal array. The customized solution probe addresses and assembles a predetermined target-sample combination onto the array at a corresponding capture probe address location. Specificity and sensitivity of the assay are provided by the incorporation of a modified monomer in the capture probe and a similarly modified monomer complement in the first region of the solution probe. The modified monomers preferentially hybridize with each other.

Claims

1. An assay system comprising:

an apparatus having a plurality of first probes attached to a substrate, each of said first probes comprising a sequence of nucleotides having a first polarity and a first nucleotide having a second polarity; and

a plurality of second probes, each of said second probes comprising a first region and a second region, wherein said first region is complementary to the first probe and comprises a sequence of nucleotides that has said first polarity and a second nucleotide having said second polarity, and wherein said second region binds to a biological material to be assayed;

wherein said second polarity is reversed relative to said first polarity; and

wherein said first nucleotide base pairs with said second nucleotide.

2. The assay system of claim 1, wherein the biological material to be assayed comprises a group selected from oligonucleotides, cDNAs, RNAs, PCR products, proteins, amino acids, antigens, antibodies, receptors, and ligands.

3. The assay system of claim 1, wherein the second region of the second probe comprises a group selected from oligonucleotides, cDNAs, RNAs, PCR products, proteins, amino acids, antigens, antibodies, receptors, and ligands that binds with the biological material to be assayed.

4. The assay system of claim 1, wherein the each first probe further comprises a first member of a specific binding pair, and the first region of each second probe comprises a second member of the specific binding pair, the first member and the second member cross-link.

5. The assay system of claim 1, wherein the first probes are located in an array of features on the substrate, at least some of the first probes being different from others in the plurality of first probes, a different first probe being located at a different feature address of the array, and

wherein one or both of the first region and the second region of at least some of the second probes is different from respective other first regions and other second regions of the second probes, such that some of the second probes of the plurality are different from each other, a biological material to be assayed being addressable to a respective feature address on the array by a respective second probe according to the first region and the respective first probe.

6. An assay system comprising:

an array apparatus that comprises a plurality of first probes on a substrate in an array of features, at least some first probes being different from others in the plurality of first probes, a different first probe being located at a different feature and being a different address on the array, wherein each of said at least some first probes comprises a first nucleotide with a reversed polarity relative to other nucleotides of said first probe; and

a plurality of second probes, each second probe comprising a first region and a second region, one or both of the first region and the second region being different from respective other first regions and other second regions of at least some of the second probes, such that some of the second probes in the plurality of second probes are different, the first region of the second probe binding with a respective first probe,

wherein the first region of at least some second probes comprises a second nucleotide with the same polarity as said reversed polarity of said first nucleotide;

wherein said second nucleotide preferentially binds to the first nucleotide of the first probes instead of to a complementary nucleotide whose polarity has not been reversed, and

wherein the second region of the second probes binds with a specific target of a biological material to be assayed to address the specific target to a feature address on the array corresponding to the respective first probe.

7. The assay system of claim 6, wherein the second region of at least some second probes is different from the second region of other second probes, the first region being the same on the at least some second probes, the different second regions binding with different portions of the specific target to address the different portions of the specific target to a same feature address on the array corresponding to the respective first probe.

8. The assay system of claim 7, wherein the specific target is addressable to the same feature address using different second probes.

9. The assay system of claim 6, wherein the second region of at least some second probes is different from the second region of other second probes, the first region being different on the second probes, the different second region binding with a different specific target, such that the different specific targets are addressable to different feature addresses on the array corresponding to the first region of the respective different second probes and the respective first probes.

10. The assay system of claim 6, wherein the second region of at least some second probes is the same and binds with a same specific target, the same specific target being in a plurality of different biological samples, the first region being different on the second probes, such that the different biological samples are distinguishable according to where the corresponding same specific target is addressed on the array by the first regions of the respective second probes and the respective first probes.

11. The assay system of claim 6, wherein the second region of at least some second probes is different and binds with a different specific target, the first region being different on the second probes, the different specific targets being in a plurality of different biological samples, such that each different specific target and each different sample are distinguishable according to where the different specific targets are addressed on the array by the different first regions of the respective different second probes and the respective different first probes.