Method of detecting an analyte in a sample using semiconductor nanocrystals as a detectable label

• US 6,274,323 B1
• Filed: 05/05/2000
• Issued: 08/14/2001
• Est. Priority Date: 05/07/1999
• Status: Expired due to Term

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Quantum Dot Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Daniels, R. Hugh, Empedocles, Stephen A., Bruchez, Marcel P., Zehnder, Donald A., Wong, Edith Y., Phillips, Vince E.
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): STRZELECKA, TERESA E
• Application Number:
  US09/566,014
• Time in Patent Office: 466 Days
• Field of Search: 435/6, 435/7.92, 435/7.93
• US Class Current: 435/6.11
• CPC Class Codes: B82Y 15/00 Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
• CPC Class Codes: G01N 2458/00 Labels used in chemical analysis of biological material
• CPC Class Codes: G01N 33/533 with fluorescent label
• CPC Class Codes: G01N 33/54346 Nanoparticles
• CPC Class Codes: G01N 33/588 with semiconductor nanocrystal label, e.g. quantum dots
• CPC Class Codes: Y10S 977/924 using nanostructure as support of dna analysis

Abstract

The use of semiconductor nanocrystals as detectable labels in various chemical and biological applications is disclosed. The methods find use for detecting a single analyte, as well as multiple analytes by using more than one semiconductor nanocrystal as a detectable label, each of which emits at a distinct wavelength.

Claims

1. A method of detecting a target polynucleotide analyte in a sample containing or suspected of containing the polynucleotide analyte, comprising the steps of:

(a) providing the sample on a solid support;

(b) combining with said sample a specific-binding molecule, wherein (i) said specific-binding molecule comprises a first member of a binding pair, (ii) the specific-binding molecule is a polymerase chain reaction (PCR) amplification product, which product comprises said first member of the binding pair, and (iii) said combining is performed under conditions that allow formation of a first complex comprising said specific-binding molecule and said polynucleotide analyte, when present;

(c) removing any unbound specific-binding molecule;

(d) combining said first complex with a second member of the binding pair, wherein (i) said second member of the binding pair is linked to a first semiconductor nanocrystal; and

(ii) said combining is performed under conditions that allow formation of a second complex comprising the first complex and the second member of the binding pair; and

(e) detecting the presence of the second complex, if present, by monitoring a spectral emission mediated by the first semiconductor nanocrystal in the second complex, wherein the emission indicates the presence of polynucleotide analyte in the sample.

2. The method of claim 1, wherein the polynucleotide analyte is contained within a chromosome or chromosomal fragment.

3. The method of claim 1, wherein the polynucleotide analyte is a DNA molecule.

4. The method of claim 1, wherein the polynucleotide analyte is an RNA molecule.

5. The method of claim 1, wherein the specific-binding molecule is an aptamer.

6. The method of claim 1, wherein the first member of the binding pair is biotin and the second member of the binding pair is avidin or streptavidin.

7. The method of claim 1, wherein the first member of the binding pair is digoxygenin and the second member of the binding pair is an antibody directed against digoxygenin.

8. The method of claim 1, wherein the first member of the binding pair is flourescein and the second member of the binding pair is an antibody directed against flourescein.

9. The method of claim 1, wherein there is a second target polynucloetide analyte, wherein the method further comprises:

combining with said sample a second specific-binding molecule, wherein (i) said second specific-binding molecule comprises a first member of a second binding pair, (ii) the second specific-binding molecule is a second polymerase chain reaction (PCR) amplification product, which second amplification product comprises the first member of the second binding pair, and (iii) said combining is performed under conditions that allow formation of a third complex comprising said second specific-binding molecule and said second polynucleotide analyte, when the second target analyte is present;

removing any unbound second specific-binding molecule;

combining said third complex with a second member of the second binding pair, wherein (i) said second member of the second binding pair is linked to a second semiconductor nanocrystal that has a second emission spectrum distinct from that of the first semiconductor nanocrystal; and

(ii) said combining is performed under conditions that allow formation of a fourth complex comprising the third complex and the second member of the second binding pair; and

detecting the presence of the fourth complex, if present, by monitoring the second spectral emission mediated by the second semiconductor nanocrystal in the fourth complex, wherein the second emission indicates the presence of the second target polynucleotide analyte in the sample.

10. The method of claim 1, wherein the first member of the binding pair is selected from the group consisting of a polynucleotide, a hapten and a biotin.

11. The method of claim 1, wherein the second member of the binding pair is selected from the group consisting of a polynucleotide, an anti-hapten, avidin, and a streptavidin.

12. The method of claim 1, wherein the first member of the binding pair is a hapten and the second member of the binding pair is an anti-hapten.

13. The method of claim 12, wherein the hapten is digoxigenin, fluorescein, dinitrophenol, bromodeoxyuridine, and mouse immunoglobulin and the antihapten is anti-digoxigenin, anti-fluorescein, anti-dinitrophenol, anti-bromodeoxyuridine, and anti-mouse immunoglobulin, respectively.

14. The method of claim 1, wherein the first and second members of the binding pair are complementary polynucleotide molecules capable of forming nucleic acid duplex.

15. The method of claim 1, wherein the sample is a sample of isolated cells, a tissue sample, or a fluid sample.

16. The method of claim 1, wherein there is a second analyte, wherein the method further comprises:

combining with said sample a second specific-binding molecule, wherein (i) said second specific-binding molecule comprises a first member of a second binding pair, and (ii) said combining is performed under conditions that allow formation of a third complex comprising said second specific-binding molecule and said second analyte when said second analyte, is present;

removing any unbound second specific-binding molecule;

combining said third complex with a second member of the second binding pair, wherein (i) said second member of the second binding pair is linked to a second semiconductor nanocrystal that has a second emission spectrum distinct from that of the first semiconductor nanocrystal; and

(ii) said combining is performed under conditions that allow formation of a fourth complex comprising said third complex and the second member of the second binding pair; and

detecting the presence of the fourth complex, if present, by monitoring the second spectral emission mediated by the second semiconductor nanocrystal in the fourth complex, wherein the second emission indicates the presence of the second target analyte in the sample.

17. The method of claim 16, wherein the second target analyte is a polypeptide analyte.

18. The method of claim 16, wherein the second specific-binding molecule is a polypeptide specific-binding molecule.

19. The method of claim 18, wherein the polypeptide specific-binding molecule is an antibody.

20. The method of claim 1, wherein the specific-binding molecule comprises a plurality of first members of binding pairs, which first members may be the same or different.

21. The method of claim 20, wherein the plurality of first members are the same.

22. The method of claim 1, wherein the PCR is reverse transcriptase-PCR (RT-PCR).

23. The method of claim 9, wherein the PCR is reverse transcriptase-PCR (RT-PCR).

24. The method of claim 9, wherein the first member of the second binding pair is selected from the group consisting of a polynucleotide, a hapten and a biotin.

25. The method of claim 9, wherein the second member of the second binding pair is selected from the group consisting of a polynucleotide, an anti-hapten, an avidin, and a streptavidin.

26. The method of claim 9, wherein the first member of the second binding pair is a biotin and the second member of the second binding pair is avidin or streptavidin.

27. The method of claim 9, wherein the first member of the second binding pair is a hapten and the second member of the second binding pair is an anti-hapten.

28. The method of claim 27, wherein the hapten is digoxigenin, fluorescein, dinitrophenol, bromodeoxyuridine, and mouse immunoglobulin and the antihapten is anti-digoxigenin, anti-fluorescein, anti-dinitrophenol, anti-bromodeoxyuridine, and anti-mouse immunoglobulin, respectively.

29. The method of claim 9, wherein the first and second members of the second binding pair are complementary polynucleotide molecules capable of forming nucleic acid duplex.

30. The method of claim 9, wherein the second specific-binding molecule is an aptamer.

31. The method of claim 9, wherein the sample is a sample of isolated cells, a tissue sample, or a fluid sample.

32. The method of claim 9, wherein the polynucleotide target analytes are present on more than one chromosome or more than one chromosome fragment.

33. The method of claim 9, wherein the polynucleotide target analytes are present on the same chromosome or chromosome fragment.

34. The method of claim 9, wherein each of the polynucleotide target analytes is a DNA molecule.

35. The method of claim 9, wherein each of the polynucleotide target analytes is an RNA molecule.

36. The method of claim 9, wherein the polynucleotide target analytes are a combination of DNA molecules and RNA molecules.

37. The method of claim 9, wherein each specific-binding molecule comprises a plurality of first members of binding pairs, which first members may be the same or different.

38. The method of claim 37, wherein on each specific-binding molecule the plurality of first members are the same.

39. The method of claim 16, wherein each specific-binding molecule comprises a plurality of first members of binding pairs, which first members may be the same or different.

40. The method of claim 39, wherein on each specific-binding molecule the plurality of first members are the same.