Methods of making and using composite arrays for the detection of a plurality of target analytes
The invention relates to sensor compositions comprising a composite array of individual arrays, to allow for simultaneous processing of a number of samples. The invention further provides methods of making and using the composite arrays. The invention further provides a hybridization chamber for use with a composite array.
1. A method of detecting the presence or absence of a plurality of different target analytes, comprising
(a) providing a first substrate with a surface comprising a plurality of assay wells, wherein said assay wells contain sample solutions each having a plurality of different target analytes;
(b) providing a second substrate comprising a plurality of array locations, each array location comprising a plurality of discrete sites on a projection, wherein said sites comprise different bioactive agents;
(c) dipping the projections of said second substrate into said assay wells such that each array location of said second substrate contacts sample solution in a different well of said first substrate under conditions suitable for binding of said different target analytes to said different bioactive agents, thereby processing said sample solutions in parallel; and
(d) detecting the presence or absence of said target analytes.
2. The method of claim 1 , wherein said target analytes comprise nucleic acids or nucleic acid analogs.
3. The method of claim 2 , wherein said nucleic acids comprise single nucleotide polymorphisms.
4. The method of claim 3 , wherein said nucleic acids comprise single nucleotide polymorphisms obtained by multiplex PCR amplification.
5. The method of claim 2 , wherein said nucleic acids are labeled with fluorochromes during PCR amplification.
6. The method of claim 1 , wherein said bioactive agents are selected from the group consisting of peptides, peptide structural analogs, saccharides, fatty acids, steroids, purines, and pyrimidines.
7. The method of claim 1 , wherein said array locations comprise from 10,000,000 to 2,000,000,000 bioactive agents per square centimeter.
8. The method of claim 1 , wherein said array locations comprise from 100,000 to about 10,000,000 bioactive agents per square centimeter.
9. The method of claim 1 , wherein said array locations comprise from 10,000 to about 100,000 bioactive agents per square centimeter.
10. The method of claim 1 , wherein said bioactive agents are directly coupled to said array locations.
11. The method of claim 1 , wherein said bioactive agents are attached to microspheres and wherein said microspheres. are associated with said array locations.
12. The method of claim 1 , wherein said target analytes comprise decoder binding ligands.
13. The method of claim 1 , wherein said target analyte is labeled.
14. The method of claim 13 , wherein said label comprises an optical label.
15. The method of claim 14 , wherein said optical label comprises. a fluorochrome.
16. The method of claim 1 , wherein said detecting is done through the use of a change in optical signature.
17. The method of claim 1 , further comprising quantitating differences in concentrations of said target analytes.
18. The method of claim 17 , further comprising quantitating a specific mRNA.
19. The method of claim 18 , comprising quantitating said specific mRNA in the presence of total cellular mRNA.
20. The method of claim 1 , wherein said assay wells comprise wells of a microtiter plate.
21. The method of claim 1 , wherein said plurality of assay wells comprises 96 wells.
22. The method of claim 1 , wherein said plurality of assay wells comprises 384 wells.
23. The method of claim 1 , wherein said plurality of assay wells comprises 1536 wells.
24. The method of claim 1 , wherein optical signals generated at said discrete sites upon binding of said different target analytes to said different bioactive agents are detected.
25. The method of claim 24 , wherein said different target analytes comprise labels and wherein said optical signal occurs as a result of said labels recruited to said sites by said target analytes binding said different bioactive agents.
26. The method of claim 24 , wherein an enzyme generates species at said discrete sites that are optically detectable.
27. The method of claim 1 , further comprising using said projections to stir said sample solutions in said assay wells.