Microarrays for analyte detection

• US 7,867,754 B1
• Filed: 04/11/2007
• Issued: 01/11/2011
• Est. Priority Date: 08/01/2002
• Status: Expired due to Fees

• Current Assignee: Purdue Research Foundation (The Trustees of Purdue University (d/b/a Purdue University))
• Original Assignee: Purdue Research Foundation (The Trustees of Purdue University (d/b/a Purdue University))
• Inventors: Inerowicz, Halina Dorota, Howell, Stephen Wayne, Reifenberger, Ronald George, Regnier, Fred E.
• Primary Examiner(s): Yu; Melanie J
• Application Number:
  US11/786,757
• Time in Patent Office: 1,371 Days
• Field of Search: 435/7.1, 435/283.1, 435/287.1, 435/288.7, 435/287.2, 436/518, 436/164, 422/50, 422/68.1, 422/82.05
• US Class Current: 435/287.1
• CPC Class Codes: G01N 27/3276 being a hybridisation with immobilised receptors using a FET type sensor G01N27/4145; concerning the hybridisation C12Q1/68

Abstract

Method and device for detection of analytes, particularly biohazards. A microarray containing immobilized sensing molecules captures complementary analytes on a redundant patterned substrate. Pattern analysis is performed using a computer algorithm.

Claims

1. A method for detecting an analyte comprising:

providing a substrate surface comprising a microarray comprising multiple positive array elements arranged on the substrate surface in a periodic pattern of array elements, said positive array elements comprising a sensing molecule that targets the analyte;

flowing a sample comprising the analyte over the substrate surface such that the sample sequentially contacts positive array elements in the microarray under conditions to cause the analyte to interact with the sensing molecules;

detecting interactions between the analyte and the sensing molecule;

determining whether the arrangement of the detected interactions on the substrate surface forms a periodic pattern;

calculating the periodicity of the pattern of detected interactions; and

comparing the periodicity of the pattern of detected interactions with the periodicity of the pattern of positive array elements, to determine whether the periodicities are essentially the same;

wherein a determination that the periodicities are essentially the same is indicative of the presence of analyte in the sample.

2. The method of claim 1 wherein the substrate surface is disposed in a channel.

3. The method of claim 2 wherein the sample is introduced into the channel as a point source.

4. The method of claim 1 further comprising analyzing sequentially contacted positive array elements to determine concentration of the analyte in the sample.

5. The method of claim 1 wherein the substrate surface comprises alternating regions in which the microarray is present or absent, such that the sample flow sequentially contacts the alternating regions.

6. The method of claim 5 further comprising analyzing the sequentially contacted microarray regions to determine the concentration of analyte in the sample.

7. The method of claim 5 further comprising analyzing the sequentially contacted microarray regions to determine the level of nonspecific binding of sample components to array elements.

8. The method of claim 1 wherein the microarray further comprises multiple null array elements that do not specifically target the analyte, and wherein the shape of the positive array elements on the substrate surface is different from the shape of the null array elements.

9. The method of claim 1 wherein the pattern periodicity is detected using a computer algorithm.

10. The method of claim 1 wherein the substrate surface comprises a plurality of different microarrays.

11. The method of claim 10 wherein the positive array elements in a first microarray comprise a first sensing molecule, and wherein the positive elements in a second microarray comprise a second sensing molecule.

12. The method of claim 1 wherein the sensing molecule is a biomolecule.

13. The method of claim 12 wherein the biomolecule comprises a protein, glycoprotein, nucleic acid or carbohydrate.

14. The method of claim 1 wherein the analyte is a biomolecule.

15. The method of claim 1 wherein the analyte is a pathogenic organism.

21. The method of claim 1 wherein the periodicity is a two-dimensional periodicity.

22. The method of claim 21 wherein the periodicity is a square periodicity.

23. The method of claim 1 wherein the periodicity is a linear periodicity.

24. The method of claim 1 wherein the periodicity cannot be detected without the aid of a computer algorithm.

25. The method of claim 9 wherein the periodicity is detected using a Fourier transform.

16. A method for detecting an analyte comprising:

providing a device comprising a channel comprising a surface comprising a microarray comprising positive array elements comprising a sensing molecule that targets the analyte, said positive array elements arranged on the channel surface in a periodic pattern of array elements, said microarray transecting the channel and disposed along a length of the channel;

flowing a sample comprising the analyte through the channel such that the sample flow sequentially contacts the microarray under conditions to cause the analyte to interact with the sensing molecules;

detecting interactions between the analyte and the sensing molecule;

determining whether the arrangement of the detected interactions on the substrate surface forms a periodic pattern;

calculating the periodicity of the pattern of detected interactions; and

comparing the periodicity of the pattern of detected interactions with the periodicity of the pattern of positive array elements, to determine whether the periodicities are essentially the same;

wherein a determination that the periodicities are essentially the same is indicative of the presence of analyte in the sample.

17. The method of claim 16 wherein the sample is introduced into the channel as a point source.

18. The method of claim 16 comprising analyzing sequentially contacted positive array elements to determine concentration of the analyte in the sample.

19. The method of claim 16 wherein the channel comprises a first branch comprising a surface comprising a plurality of microarrays comprising multiple positive array elements comprising a first sensing molecule that targets a first analyte, the positive array elements arranged on the branch surface in a first periodic pattern of array elements;

and a second branch comprising a surface comprising a plurality of microarrays comprising multiple positive array elements comprising a second sensing molecule that targets a second analyte, the positive array elements arranged on the branch surface in a second periodic pattern of array elements; and

wherein the step of flowing a sample through the channel comprises flowing a sample comprising the first and second analyte through the channel such that the sample flow enters the first and second branches and sequentially contacts the microarray elements under conditions to cause the analyte to interact with the sensing molecules; and

wherein the detecting, determining, calculating and comparing steps are performed separately for each branch.

20. The method of claim 19 wherein the concentration of the first analyte in the sample is at least an order of magnitude higher than the concentration of the second analyte, and wherein more of the sample flow is directed to the second branch than the first branch.