System and method for the detection of analytes

• US 20050064452A1
• Filed: 04/26/2004
• Published: 03/24/2005
• Est. Priority Date: 04/25/2003
• Status: Abandoned Application

• Current Assignee: Board of Regents of the University of Texas System (University of Texas System)
• Original Assignee: Board of Regents of the University of Texas System (University of Texas System)
• Inventors: Willson, C. Grant, Schmid, Matthew J.
• Application Number:
  US10/832,469
• Publication Number:
  US 20050064452A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2565/102 Multiple non-interacting labels
• CPC Class Codes: C12Q 2565/549 characterised by the capture oligonucleotide being a reporter labelled capture oligonucleotide

Abstract

A system and method for the detection of an analyte using multiplexing of the sensing elements is described. In one embodiment, a sensor array includes sensing elements, and probes bound to one or more sensing elements. The sensor array is formed from a supporting member to which a plurality of sensing elements may be coupled. The sensing element may have a predefined shape, size or location. A signal may be produced when a target analyte interacts with a probe. In one embodiment, the identity of the target may be determined by the detection of the signals produced and the shapes of the sensing elements. Each analyte may be given a unique code that is represented by one or more sensing elements.

Claims

1. An analyte detection device comprising a plurality of sensing elements, wherein one or more probes are coupled to each of the sensing elements, and wherein at least one of the probes is configured to interact with an analyte, and wherein at least one sensing element is configured to produce a signal when the analyte interacts with a probe coupled to the sensing element, and wherein the sensing elements produce detectable signals in a predetermined pattern, and wherein the predetermined pattern represents a code that identifies the analyte.

2. The device of claim 1, wherein the sensing elements are positioned on a supporting member at predetermined locations.

3. The device of claim 1, wherein the sensing elements are particles positioned in cavities formed on a supporting member at predetermined locations of the supporting member.

4. The device of claim 1, wherein the sensing elements are positioned on a supporting member in an array.

5. The device of claim 1, wherein each of the sensing elements comprise one or more probes coupled to a supporting member at discrete predetermined locations.

6. The device of claim 1, wherein each of the sensing elements has a shape that is different from the other sensing elements.

7. The device of claim 1, wherein each of the sensing elements has a size that is different from the other sensing elements.

8. The device of claim 1, wherein each of the sensing elements has a shape and/or size that is different from the other sensing elements.

9. The device of claim 1, wherein each of the sensing elements is capable of interacting with more than one analyte.

10. The device of claim 1, wherein each of the sensing elements comprises a polymer, wherein one or more probes are coupled to the polymer.

11. The device of claim 1, wherein each of the sensing elements comprises a mixture of one or more probes in a liquid medium.

12. The device of claim 1, wherein one or more probes comprise a nucleic acid.

13. The device of claim 1, wherein one or more probes comprise deoxyribonucleic acid.

14. The device of claim 1, wherein one or more probes comprise single stranded deoxyribonucleic acid.

15. The device of claim 1, wherein one or more probes comprise ribonucleic acid.

16. The device of claim 1, wherein one or more probes comprise an oligonucleotide.

17. The device of claim 1, wherein one or more probes comprise an oligopeptide.

18. The device of claim 1, wherein one or more probes comprise an oligonucleotide complementary with one or more single nucleotide polymorphisms of a reference DNA sequence.

19. The device of claim 1, wherein one or more probes comprise an oligonucleotide complementary with one or more single nucleotide polymorphisms of a reference DNA sequence.

20. The device of claim 1, wherein the analyte detection device is capable of determining the identify of more analytes than sensing elements.

21. The device of claim 1, wherein one or more probes comprise an oligonucleotide complementary with one or more single nucleotide polymorphisms of a reference DNA sequence, and wherein the number of sensing elements in the system is less than the number of possible single nucleotide polymorphisms of the reference DNA sequence, and wherein the analyte detection device is capable of determining the presence of analytes having all possible single nucleotide polymorphisms of a reference DNA sequence.

22. The device of claim 1, wherein the predetermined pattern represents a binary code.

23. The device of claim 1, wherein the number of analytes detectable by the analyte detection device is 2ⁿ where n is the number of sensing elements.

24. The device of claim 1, wherein the number of analytes detectable by the analyte detection device is 2ⁿ-2, where n is the number of sensing elements.

25. A method of identifying an analyte, comprising:

adding a sample that comprises one or more analytes to an analyte detection device, wherein the analyte detection device comprises;

a plurality of sensing elements, wherein one or more probes are coupled to each of the sensing elements, and wherein at least one of the probes is configured to interact with an analyte, and wherein at least one sensing element is configured to produce a signal when the analyte interacts with a probe coupled to the sensing element;

determining a pattern produced by one or more sensing elements producing a signal;

determining the code represented by the pattern; and

determining the identity of the analyte based on the determined code.

26. The method of claim 25, further comprising adding a tag to one or more analytes in the sample.

27. The method of claim 25, further comprising adding a tag to one or more analytes in the sample, wherein the tag is a fluorescent tag.

28. The method of claim 25, further comprising adding a visualization agent after the sample has been added to the analyte detection device.

29. The method of claim 25, wherein determining the code represented by the pattern comprises looking at the sensing elements with a magnification device.

30. The method of claim 25, wherein the sensing elements are positioned on a supporting member at predetermined locations.

31. The method of claim 25, wherein the sensing elements are particles positioned in cavities formed on a supporting member at predetermined locations of the supporting member.

32. The method of claim 25, wherein the sensing elements are positioned on a supporting member in an array.

33. The method of claim 25, wherein each of the sensing elements comprise one or more probes coupled to a supporting member at discrete predetermined locations, and wherein determining the code represented by the pattern comprises determining the location of the sensing elements producing a signal.

34. The method of claim 25, wherein each of the sensing elements has a shape that is different from the other sensing elements, and wherein determining a pattern comprises determining the shape of each of the sensing elements producing a signal.

35. The method of claim 25, wherein each of the sensing elements has a size that is different from the other sensing elements, and wherein determining a pattern comprises determining the size of each of the sensing elements producing a signal.

36. The method of claim 25, wherein each of the sensing elements has a shape and/or size that is different from the other sensing elements, and wherein determining a pattern comprises determining the shape and/or size of each of the sensing elements producing a signal.

37. The method of claim 25, wherein each of the sensing elements is capable of interacting with more than one analyte.

38. The method of claim 25, wherein each of the sensing elements comprises a polymer, wherein one or more probes are coupled to the polymer.

39. The method of claim 25, wherein each of the sensing elements comprises a mixture of one or more probes in a liquid medium.

40. The method of claim 25, wherein one or more probes comprise a nucleic acid.

41. The method of claim 25, wherein one or more probes comprise deoxyribonucleic acid.

42. The method of claim 25, wherein one or more probes comprise single stranded deoxyribonucleic acid.

43. The method of claim 25, wherein one or more probes comprise ribonucleic acid.

44. The method of claim 25, wherein one or more probes comprise an oligonucleotide.

45. The method of claim 25, wherein one or more probes comprise an oligopeptide.

46. The method of claim 25, wherein one or more probes comprise an oligonucleotide complementary with one or more single nucleotide polymorphisms of a reference DNA sequence.

47. The method of claim 25, wherein the analyte detection device is capable of determining the identify of more analytes than sensing elements.

48. The method of claim 25, wherein one or more probes comprise an oligonucleotide complementary with one or more single nucleotide polymorphisms of a reference DNA sequence, and wherein the number of sensing elements in the system is less than the number of possible single nucleotide polymorphisms of the reference DNA sequence, and wherein the analyte detection device is capable of determining the presence of analytes having all possible single nucleotide polymorphisms of a reference DNA sequence.

49. The method of claim 25, wherein the predetermined pattern represents a binary code.

50. The method of claim 25, wherein the number of analytes detectable by the analyte detection device is 2ⁿ, where n is the number of sensing elements.

51. The method of claim 25, wherein the number of analytes detectable by the analyte detection device is 2ⁿ-2, where n is the number of sensing elements.

52. An analyte detection device comprising a plurality of sensing elements, wherein one or more oligonucleotide probes are coupled to each of the sensing elements, and wherein at least one of the oligonucleotide probes is configured to interact with an oligonucleotide analyte, and wherein at least one sensing element is configured to produce a signal when the oligonucleotide analyte interacts with an oligonucleotide probe coupled to the sensing element, and wherein the sensing elements produce detectable signals in a predetermined pattern, and wherein the predetermined pattern represents a code that identifies the oligonucleotide analyte.

53-96. -96. (canceled)

97. An analyte detection device comprising a plurality of groups of oligonucleotide probes coupled to a supporting member, each group of oligonucleotide probes coupled to a discrete location of the supporting member, and wherein at least one group of oligonucleotide probes are configured to produce a signal when an oligonucleotide analyte interacts with at least one of the oligonucleotide probes in the group, and wherein one or more groups of oligonucleotide probes produces a detectable signal in a predetermined pattern, and wherein the predetermined pattern represents a code that identifies the oligonucleotide analyte.

98. An analyte detection device comprising a plurality of sensing elements, each of the sensing elements having a shape that differs from the other sensing elements, wherein one or more probes are coupled to each of the sensing elements, and wherein at least one of the probes is configured to interact with an analyte, and wherein at least one sensing element is configured to produce a signal when the analyte interacts with a probe coupled to the sensing element, and wherein the sensing elements produce detectable signals in a predetermined pattern, and wherein the predetermined pattern represents a code that identifies the analyte.

99-143. -143. (canceled)