Screening using polarization anisotropy in FRET emissions

• US 20060234279A1
• Filed: 04/04/2006
• Published: 10/19/2006
• Est. Priority Date: 04/04/2005
• Status: Abandoned Application

• Current Assignee: Blueshift Biotechnologies, Inc. (Danaher Corporation)
• Original Assignee: Blueshift Biotechnologies, Inc. (Danaher Corporation)
• Inventors: Miller, Steven C., Shumate, Christopher B., Comita, Paul B., Cromwell, Evan F.
• Application Number:
  US11/398,496
• Publication Number:
  US 20060234279A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: G01N 2500/00 Screening for compounds of potential therapeutic value
• CPC Class Codes: G01N 33/542 with steric inhibition or signal modification, e.g. fluorescent quenching

Abstract

Methods and apparatus are described for detecting specific binding between first and second chemical entities. The first chemical entity in association with a first fluorophore is immobilized. The second chemical entity is allowed to bind with the immobilized first chemical entity. The second chemical entity is or becomes coupled to a second fluorophore, which forms a FRET pair with the first fluorophore. The bound chemical entities are exposed to radiation at an excitation frequency for either the first or the second fluorophore, and polarization anisotropy of a FRET fluorescent signal from the bound chemical entities is measured to detect specific binding between the first and second chemical entities. Techniques are also disclosed for detecting whether a FRET interaction is occurring between a first chemical entity including a donor fluorophore and a second chemical entity including an acceptor fluorophore, using simultaneous anisotropy measurements at the wavelengths of the donor and acceptor fluorophores.

Claims

1. A method for detecting specific binding between a first chemical entity and a second chemical entity, the method comprising:

immobilizing the first chemical entity in association with a first fluorophore;

allowing the second chemical entity to bind with the immobilized first chemical entity, wherein the second chemical entity is or becomes coupled to a second fluorophore, which forms a FRET pair with the first fluorophore;

exposing the bound chemical entities to radiation at an excitation frequency for either the first or the second fluorophore; and

measuring polarization anisotropy of a FRET fluorescent signal from the bound chemical entities to detect specific binding between the first and second chemical entities.

2. The method of claim 1, further comprising measuring donor emission lifetime of at least one of the first or second fluorophores.

3. The method of claim 1, wherein both the first fluorophore and the second fluorophore have a high intrinsic anisotropy.

4. The method of claim 1, wherein the polarization anisotropy is measured at a single wavelength.

5. The method of claim 1, wherein at least one of the first and second chemical entities is a biomolecule.

6. The method of claim 5, wherein the biomolecule is a protein.

7. The method of claim 1 wherein the first and second fluorophores are the same (homo-FRET).

8. The method of claim 1, wherein one of the first and second chemical entities comprises a protein and the other of the first and second chemical entities comprises a nucleic acid.

9. The method of claim 1, further comprising performing a defined treatment on at least one of the first and second chemical entities, wherein the specific binding between the first and second chemical entities only occurs when the defined treatment results in at least one of the first and second chemical entities entering a particular state.

10. The method of claim 1, wherein the polarization anisotropy is measured at a first wavelength and a second wavelength.

11. The method of claim 10, further comprising comparing the anisotropy of the first and second wavelengths to determine whether a FRET interaction is occurring.

12. The method of claim 10, further comprising using the anisotropy at a first wavelength as a reference to determine a change in the anisotropy of the second wavelength.

13. The method of claim 10, wherein the anisotropies of the first and second wavelengths are measured simultaneously.

14. The method of claim 10, wherein the anisotropies of the first and second wavelengths are measured sequentially in a time frame that is short with respect to a systematic measured change in signal readout.

15. The method of claim 10, further comprising measuring a polarization anisotropy of a reference source.

16. The method of claim 15, wherein the reference source is a laser excitation source for one of the fluorophores.

17. The method of claim 15, wherein the reference source is an excitation source other than a laser excitation source for fluorescence.

18. The method of claim 15, further comprising comparing the anisotropy of the first and second wavelengths to the anisotropy of the reference source to determine whether a FRET interaction is occurring.

19. The method of claim 15, further comprising using the anisotropy of the reference source as a reference to determine a change in the anisotropy of the first wavelength or the second wavelength.

20. The method of claim 15, wherein the anisotropies of the first and second wavelengths and the reference source are measured simultaneously.

21. The method of claim 15, wherein the anisotropies of the first and second wavelengths and reference source are measured sequentially in a time frame that is short with respect to a systematic measured change in signal readout.

22. The method of claim 15, wherein the reference source is a spot of a fluorescent dye that has been printed or deposited on a substrate used for measurement.

23. The method of claim 15, wherein the reference source is a fluorescent dye impregnated or incorporated into a substrate or bead material used for measurement.

24. A method for detecting whether a FRET interaction is occurring between a first chemical entity in association with a donor fluorophore and a second chemical entity in association with an acceptor fluorophore, the method comprising:

exposing at least one of the fluorophores to radiation at an excitation wavelength for the donor fluorophore;

measuring a polarization anisotropy of a fluorescent signal at an emission wavelength for the donor fluorophore and at an emission wavelength for the acceptor fluorophore; and

comparing the measured anisotropies to determine whether a FRET interaction is occurring between the first and second chemical entities.

25. The method of claim 24, where both the donor and the acceptor fluorophore has a high intrinsic anisotropy.

26. The method of claim 24, wherein using the anisotropy at the donor fluorophore'"'"'s emission wavelength serves as an internal reference to determine or quantify a change in the anisotropy of the acceptor fluorophore'"'"'s emission wavelength.

27. The method of claim 24, wherein the anisotropies of the donor fluorophore and acceptor fluorophore are measured simultaneously.

28. The method of claim 24, wherein the anisotropies of the first and second wavelengths are measured sequentially in a time frame that is short with respect to a systematic measured change in signal readout.

29. The method of claim 24, wherein a FRET interaction is determined to occur when the measured anisotropy at the emission wavelength of the acceptor fluorophore changes relative to the measured anisotropy at the emission wavelength of the donor fluorophore.

30. The method of claim 24, wherein the first and second chemical entities are included in a target region for FRET analysis, the target region including one or more of microbeads, spots, spot on spot, spot on a slide combined with a bead, samples or objects confined in a capillary tube, samples or objects confined in a microfluidic channel, aggregates or colonies of cells confined in a liquid region such as a well or droplet, and aggregates or colonies of cells immobilized on a surface or surface layer.

31. The method of claim 24, wherein the donor fluorophore is a Cyan Fluorescent Protein and the acceptor fluorophore is a Yellow Fluorescent Protein.

32. The method of claim 24, wherein the donor fluorophore is a Green Fluorescent Protein and the acceptor fluorophore is a Red Fluorescent Protein.

33. The method of claim 24, wherein at least one of the first and second chemical entities comprises a streptavidin.

34. The method of claim 24, wherein one of the first and second chemical entities is a small molecule that becomes sterically hindered upon binding to the other of the first and second chemical entities.

35. The method of claim 24, wherein the donor fluorophore and the acceptor fluorophore are the same.

36. A method for detecting whether a FRET interaction is occurring between a first chemical entity in association with a donor fluorophore and a second chemical entity in association with an acceptor fluorophore, the method comprising:

exposing a region containing the fluorophores to radiation at an excitation wavelength for the donor fluorophore;

measuring a polarization anisotropy of a fluorescent signal at an emission wavelength for the acceptor fluorophore;

measuring a polarization anisotropy at the wavelength of a reference signal in the regions containing the fluorophores; and

comparing the measured anisotropies to determine whether a FRET interaction is occurring between the first and second chemical entities.

37. The method of claim 36, wherein the reference signal comprises radiation other than fluorescence of the donor fluorophore.