Arrays, computer program products and methods for in silico array-based comparative binding assays

• US 7,994,296 B2
• Filed: 08/10/2004
• Issued: 08/09/2011
• Est. Priority Date: 03/27/2002
• Status: Expired due to Fees

• Current Assignee: PerkinElmer Health Sciences, Inc. (Revvity, Inc.)
• Original Assignee: PerkinElmer Health Sciences, Inc. (Revvity, Inc.)
• Inventors: Shah, Shishir
• Primary Examiner(s): BAUSCH, SARAE L
• Application Number:
  US10/916,269
• Publication Number:
  US 20050014184A1
• Time in Patent Office: 2,555 Days
• Field of Search: None
• US Class Current: 536/23.1
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2545/101 with an internal standard/control
• CPC Class Codes: C12Q 2545/114 involving a quantitation step
• CPC Class Codes: C12Q 2565/513 characterised by the pattern of the arrayed oligonucleotides
• CPC Class Codes: C40B 30/04 by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
• CPC Class Codes: G01N 33/6845 Methods of identifying protein-protein interactions in protein mixtures
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Abstract

The invention provides computer systems, computer program products and methods for in silico array-based methods for determining the relative amount of biological molecules (e.g., nucleic acid sequences) in two or more samples. The invention also provides novel arrays comprising immobilized calibration molecules (e.g., nucleic acids) for normalizing the results of array-based binding assays (e.g., hybridization reactions).

Claims

1. An array for determining the relative amount of a biological molecule in a sample, the array comprising a plurality of biological molecules immobilized to a plurality of discrete and known spots on a substrate surface to form the array of biological molecules, wherein the array of spots comprises a plurality of test spots comprising different biological molecules and at least one calibration spot, and the at least one calibration spot comprises a mixture of the plurality of different biological molecules present in the test spots and wherein each of the discrete and known spots comprises a biological molecule that is a marker for each said spot on the array to provide a plurality of markers on the array.

2. The array of claim 1, wherein the calibration spot comprises an equimolar mixture of all the biological molecules spotted on the array.

3. The array of claim 1, comprising at least a second calibration spot comprising an equimolar dilution of the mixture of biological molecules spotted on a first calibration spot.

4. The array of claim 3, comprising a plurality of calibration spots, wherein each calibration spot represents a different equimolar dilution of the mixture of biological molecules spotted on the array.

5. The array of claim 3, wherein the array comprises a first substrate surface comprising a first array and a second substrate surface comprising a second array, wherein the first and second arrays are separated by a hydrophobic barrier such that a first sample can be applied to the first array at the same time a second sample is applied to the second array without the two samples mixing together, and the first and the second arrays comprise the same calibration spots.

6. The array of claim 3, wherein the biological molecule comprises a nucleic acid.

7. The array of claim 6, wherein the nucleic acid comprises a DNA or an RNA.

9. The array of claim 1, wherein the calibration spot comprises a mixture of all the biological molecules spotted on the array that is not equimolar.

10. The array of claim 3, wherein the array comprises a first substrate surface comprising a first array and a second substrate surface comprising a second array, wherein the first and second arrays are not separated by a hydrophobic barrier, and the first and the second arrays comprise the same calibration spots.

11. The array of claim 7, wherein the DNA is genomic DNA.

12. The array of claim 11, wherein the plurality of array-immobilized nucleic acids comprises genomic DNA cloned in a construct comprising a vector.

13. The array of claim 12, wherein the vector comprises an artificial chromosome.

14. The array of claim 13, wherein the artificial chromosome comprises a bacterial artificial chromosome (BAC).

15. The array of claim 13, wherein the artificial chromosome is selected from the group consisting of a human artificial chromosome (HAC), a yeast artificial chromosome (YAC), a transformation-competent artificial chromosome (TAC) and a bacteriophage P1-derived artificial chromosome (PAC).

16. The array of claim 13, wherein the plurality of array-immobilized nucleic acids are cloned in a construct comprising a vector selected from the group consisting of a cosmid vector, a plasmid vector and a viral vector.

17. The array of claim 11, wherein the genomic nucleic acid comprises a substantially complete chromosome or a known subset of a chromosome.

18. The array of claim 11, wherein the genomic nucleic acid comprises a substantially complete genome or a known subset of a genome.

19. The array of claim 11, wherein the genomic nucleic acid is derived from a genome of a normal cell.

20. The array of claim 11, wherein the genomic nucleic acid is derived from a genome of a mammalian cell.

21. The array of claim 20, wherein the mammalian cell is a human cell.

22. The array of claim 12, wherein the calibration spot nucleic acid comprises vector nucleic acid.

34. The array of claim 1 in which the calibration spot comprises an equimolar mixture of the plurality of different biological molecules present in all of the plurality of test spots.

8. A system for performing comparative binding assays comprising:

(a) an array comprising a first substrate surface comprising a first array and a second substrate surface comprising a second array, wherein the first and second arrays are separated by a hydrophobic barrier such that a first sample can be applied to the first array at the same time a second sample is applied to the second array without the two samples mixing together, and the first and the second arrays comprise the same calibration spots and wherein each of the first and second arrays comprise discrete and known spots comprising a nucleic acid sequence that is a marker for each said spot on the arrays to provide a plurality of markers on the arrays, and wherein at least one of the first and second arrays comprises test spots comprising different nucleic acid sequences, and wherein the calibration spots comprise a mixture of the different nucleic acid sequences from the test spots; and

(b) a device for detecting a detectable label, wherein the device can measure which detectable labels are on which spots on the substrate surface.

35. The system of claim 8, in which the calibration spot comprises an equimolar mixture of the mixture of the different nucleic acid sequences from all of the test spots.

23. An array for determining the relative amount of a nucleic acid in a sample, the array comprising a plurality of nucleic acid molecules immobilized to a plurality of discrete and known spots on a substrate surface to form the array of nucleic acid molecules, wherein the array of spots comprises a plurality of test spots comprising different nucleic acids and at least one calibration spot, and the calibration spot comprises a mixture of the different nucleic acid sequences from the test spots and nucleic acid sequences from a genome other than that spotted on the array or in the sample, and wherein each of the discrete and known spots comprises a nucleic acid sequence that is a marker for each said spot on the array to provide a plurality of markers on the array.

24. The array of claim 23, wherein the genome other than that in the sample or on the array is genomic DNA of Mus or Drosophila.

25. The array of claim 23, wherein detectable label is incorporated into at least one of the array-immobilized nucleic acids.

26. The array of claim 25, wherein the detectable label is incorporated into the test spots and the at least one calibration spot.

27. The array of claim 25, wherein the detectable label is incorporated into the test spot and not into the calibration spot.

28. The array of claim 25, wherein the detectable label is incorporated into the calibration spot and not into the test spot.

29. The array of claim 25, wherein the detectable label is a fluorescent dye.

30. The array of claim 29, wherein the fluorescent dye is a fluorescent cyanine dye.

31. The array of claim 25, wherein the detectable label is radioactive.

32. The array of claim 31, wherein the detectable label is selected from the group consisting of ³²P, ³⁵H, ¹⁴C, ¹²⁵I and ¹³¹I.

36. The array of claim 23, in which the calibration spot comprises an equimolar mixture of all of the plurality of different nucleic acid sequences from the test spots.

37. The array of claim 36, in which the calibration spot comprises an equimolar mixture of all of the plurality of different nucleic acid sequences from the test spots.

33. A device comprising a first array and a second array respectively, the first and second array each comprising a plurality of nucleic acid segments, wherein each nucleic acid segment is immobilized to a discrete and known spot on each of a first substrate surface and a second substrate surface to form the first and the second arrays of nucleic acid segments wherein each said spot comprises a different nucleic acid sequence that is a marker for each said spot on the array to provide a plurality of markers on each array and the nucleic acid segments immobilized on the second array comprise substantially the same plurality of nucleic acid segments immobilized on the first array, each array further comprising at least one calibration spot comprising a mixture of the same plurality of nucleic acid sequence markers present in all of the other spots of the array.

38. The device of claim 33, in which the calibration spot comprises an equimolar mixture of the same plurality of nucleic acid sequence markers present in all of the other spots of the array.