Dual resonance energy transfer nucleic acid probes

• US 7,399,591 B2
• Filed: 02/02/2006
• Issued: 07/15/2008
• Est. Priority Date: 06/25/2001
• Status: Expired due to Fees

• Current Assignee: Georgia Tech Research Corporation (University System of Georgia)
• Original Assignee: Georgia Tech Research Corporation (University System of Georgia)
• Inventors: Tsourkas, Andrew, Bao, Gang, Xu, Yangquing
• Primary Examiner(s): Martinell; James
• Application Number:
  US11/346,072
• Publication Number:
  US 20060127940A1
• Time in Patent Office: 894 Days
• Field of Search: None
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer
• CPC Class Codes: C12Q 2525/301 Hairpin oligonucleotides
• CPC Class Codes: C12Q 2565/101 Interaction between at least two labels

Abstract

Dual nucleic acid probes with resonance energy transfer moieties are provided. In particular, fluorescent or luminescent resonance energy transfer moieties are provided on hairpin stem-loop molecular beacon probes that hybridize sufficiently near each other on a subject nucleic acid, e.g. mRNA, to generate an observable interaction. The invention also provides lanthanide chelate luminescent resonance energy transfer moieties on linear and stem-loop probes that hybridize sufficiently near each other on a subject nucleic acid to generate an observable interaction. The invention thereby provides detectable signals for rapid, specific and sensitive hybridization determination in vivo. The probes are used in methods of detection of nucleic acid target hybridization for the identification and quantification of tissue and cell-specific gene expression levels, including response to external stimuli, such as drug candidates, and genetic variations associated with disease, such as cancer.

Claims

1. A composition comprising:

(a) a stem-loop donor molecular beacon; and

(b) a stem-loop acceptor molecular beacon, wherein resonance energy transfer occurs between the donor molecular beacon and the acceptor molecular beacon when the donor and acceptor molecular beacons hybridize adjacent to each other on a target nucleic acid and are exposed to an exciting amount of electromagnetic radiation, and

(c) means for delivering the stem-loop donor molecular beacon and the stem-loop donor molecular beacons into a cell.

2. The composition of claim 1, wherein the donor molecular beacon comprises a resonance energy transfer donor moiety or a luminescence resonance energy transfer donor moiety.

3. The composition of claim 2, wherein the donor molecular beacon comprises a quencher that reduces emissions from the donor moiety when the donor molecular beacon is not hybridized to the target nucleic acid.

4. The composition of claim 2, wherein the donor moiety comprises a fluorophore, Europium, Terbium, or a lanthanide chelate.

5. The composition of claim 1, wherein the acceptor molecular beacon comprises a resonance energy transfer acceptor moiety or a luminescence resonance energy transfer acceptor moiety.

6. The composition of claim 5, wherein the acceptor moiety comprises a fluorophore or a phycobiliprotein.

7. The composition of claim 1, wherein acceptor molecular beacon comprises a quencher that reduces emissions from the acceptor moiety when the acceptor molecular beacon is not hybridized to the target nucleic acid.

8. The composition of claim 1, wherein emission from the acceptor molecular beacon produces a detectable signal resulting from resonance energy transfer.

9. The composition of claim 1, wherein the energy to excite the donor molecular beacon has a negligible capacity to directly excite the acceptor molecular beacon.

10. The composition of claim 1, wherein unquenched emission from the donor moiety or acceptor moiety is distinguishable from emissions from the acceptor moiety resulting from resonance energy transfer.

11. A composition comprising:

(a) a shared-stem acceptor molecular beacon; and

(b) a shared-stem donor molecular beacon, wherein fluorescence resonance energy transfer occurs between the acceptor molecular beacon and the donor molecular beacon when the acceptor and donor molecular beacons hybridize adjacent to each other on a target nucleic acid and are exposed to an exciting amount of electromagnetic radiation.

12. The composition of claim 11, wherein the donor molecular beacon comprises a resonance energy transfer donor moiety or a luminescence resonance energy transfer donor moiety.

13. The composition of claim 12, wherein the donor molecular beacon comprises a quencher that reduces emissions from the donor moiety when the donor molecular beacon is not hybridized to the target nucleic acid.

14. The composition of claim 12, wherein the donor moiety comprises a fluorophore, Europium, Terbium, or a lanthanide chelate.

15. The composition of claim 11, wherein the acceptor molecular beacon comprises a resonance energy transfer acceptor moiety or a luminescence resonance energy transfer acceptor moiety.

16. The composition of claim 15, wherein the acceptor moiety comprises a fluorophore or a phycobiliprotein.

17. The composition of claim 11, wherein acceptor molecular beacon comprises a quencher that reduces emissions from the acceptor moiety when the acceptor molecular beacon is not hybridized to the target nucleic acid.

18. The composition of claim 11, wherein emission from the acceptor molecular beacon produces a detectable signal.

19. The composition of claim 11, wherein the energy to excite the donor molecular beacon has a negligible capacity to directly excite the acceptor molecular beacon.

20. The composition of claim 11, wherein unquenched emission from the donor moiety or acceptor moiety is distinguishable from emissions from the acceptor moiety resulting from resonance energy transfer.

21. A method for detecting expression of a target nucleic acid in a cell comprising:

(a) delivering a stem-loop acceptor molecular beacon and a stem-loop donor molecular beacon to an interior of a cell;

(b) exposing the molecular beacons with an exciting amount of electromagnetic energy so that fluorescence resonance energy transfer occurs between the acceptor molecular beacon and the donor molecular beacon when the acceptor and donor molecular beacons hybridize adjacent to each other on the target nucleic acid; and

(c) detecting a signal resulting from fluorescence resonance energy transfer between the stem-loop donor molecular beacon and the stem-loop acceptor molecular beacon in response to the exciting amount of electromagnetic energy wherein a detectable signal indicates the presence of the target nucleic acid.

22. The method of claim 21, wherein the target nucleic acid comprises RNA.

23. The method of claim 21, wherein the molecular beacons are shared-stem molecular beacons.

24. A method for detecting cancer comprising:

(a) delivering a stem-loop acceptor molecular beacon and a stem-loop donor molecular beacon to an interior of a cell suspected of being cancerous, wherein the molecular beacons specifically hybridize to a subject nucleic acid that is differentially expressed in cancer cells compared to non-cancer cells;

(b) exposing the molecular beacons with an exciting amount of radiation so that fluorescence resonance energy transfer occurs between the acceptor molecular beacon and the donor molecular beacon when the acceptor and donor molecular beacons hybridize adjacent to each other on the subject nucleic acid; and

(c) detecting emissions from the acceptor molecular beacon resulting from resonance energy transfer, wherein a detectable signal is indicative of cancer.

25. The method of claim 24, wherein the cancer is pancreatic cancer.

26. The method of claim 24, wherein the subject nucleic acid encodes an oncogene or tumor suppressor gene.

27. The method of claim 26, wherein the oncogene or tumor suppressor gene is selected from the group consisting of K-ras, p53, p16, MADH4, DPC4, BRCA2, MKK4, STK 11, TGFBR1, and TGFBR2.

28. The method of claim 24, wherein the subject nucleic acid can be used for the direct detection of an infectious disease agent or quantification of an infectious agent.

29. The method of claim 24, wherein detectable emissions indicate the location the subject nucleic acid.

30. The method of claim 24, wherein the molecular beacons are shared-stem molecular beacons.

31. A method for identifying compounds that increase or decrease expression of a subject nucleic acid comprising:

(a) delivering stem-loop acceptor molecular beacons and a stem-loop donor molecular beacons to an interior of a cell suspected of being cancerous;

(b) exposing the molecular beacons to an exciting amount of electromagnetic radiation so that fluorescence resonance energy transfer occurs between the acceptor molecular beacons and the donor molecular beacons when the acceptor and donor molecular beacons hybridize adjacent to each other on the subject nucleic acid;

(c) detecting a first signal from the acceptor molecular beacons resulting from resonance energy transfer;

(d) contacting the cell comprising the molecular beacons with a test compound;

(e) detecting a second signal from the acceptor molecular beacons resulting from resonance energy transfer, wherein in an increased second signal compared to the first signal indicates that the test compound increases expression of the target nucleic acid and a decreased second signal compared to the first signal indicates that the test compound decreases expression of the subject nucleic acid.

32. The method of claim 31, wherein the subject nucleic acid encodes an oncogene or tumor suppressor gene.

33. The method of claim 31, wherein the molecular beacons are shared-stem molecular beacons.

34. The method of claim 31, wherein the test compound comprises hormones or growth factors.

35. A system for detecting a target nucleic acid comprising:

(a) a stem-loop donor molecular beacon;

(b) a stem-loop acceptor molecular beacon, wherein resonance energy transfer occurs between the donor molecular beacon and the acceptor molecular beacon when the donor and acceptor molecular beacons hybridize adjacent to each other on a target nucleic acid and are exposed to an exciting amount of electromagnetic radiation;

(c) means for exciting the molecular beacons;

(d) means for detecting emissions from the molecular beacons; and

(e) means for delivering the beacons inside the cell.

36. The system of claim 35, wherein the means for exciting the molecular beacons comprises a laser, a one-photon excitation device, or a two-photon excitation device.

37. A kit comprising:

a) a stem-loop acceptor molecular beacon that specifically hybridizes to a target nucleic acid;

b) a stem-loop donor molecular beacon that specifically hybridizes to the target nucleic acid,

wherein fluorescence resonance energy transfer occurs between the acceptor molecular beacon and the donor molecular beacon when the acceptor and donor molecular beacons hybridize adjacent to each other on a target nucleic acid and are exposed to an exciting amount of electromagnetic radiation; and

c) instructions for detecting the target nucleic acid using the molecular beacons.

38. The kit of claim 37, wherein the molecular beacons are shared-stem molecular beacons.

39. The kit of claim 37, further comprising a means for delivering the molecular beacons into a cell.