Optical real-time biosensor

1. A method of detection of a target molecule in a sample using an optical sensor system, the method comprising:

contacting the one or more molecular switches of an optical probe to the sample;

emitting the excitation light from the light source; and

measuring continuously, using the detector, changes of the optical signals, thereby detecting a concentration of the target molecule in the sample;

wherein the optical probe comprises:

an optical waveguide having a first end and a second end, the first end configured to receive excitation light to be propagated through the optical waveguide and to be emitted from the second end or a middle region into a surrounding medium;

one or more molecular switches attached to a facet or a sidewall of the second end or the middle region of the optical waveguide, wherein the molecular switches are configured to change conformation upon binding to a corresponding target molecule; and

one or more optical reporters, the optical reporters attached to a respective molecular switch and configured, when exposed to the excitation light, to produce an optical signal that changes upon binding of the respective molecular switch to the corresponding target molecule in the surrounding medium, wherein the optical signal is coupled back into the optical waveguide and propagated through the optical waveguide to be emitted from the first end or second end;

wherein the optical sensor system comprises:

the optical probe;

a light source configured to emit the excitation light to be coupled into the optical waveguide of the optical probe;

a detector configured to (i) receive the optical signals produced by the one or more optical reporters that are transmitted through the optical waveguide, and (ii) detect changes of the optical signals, thereby allowing for detection of a concentration of the corresponding target molecule;

wherein the sample is an in vivo tissue of a living subject and the method further comprises administering an amount of an agent to the living subject, and adjusting the amount of the agent based on the detected concentration of the target molecule in the sample.

2. The method of claim 1 , wherein the adjusting is determined by a feedback control mechanism configured to adjust the amount of the agent based on the detected concentration of the target molecule in the sample as measured by the optical sensor system.

3. The method of claim 1 , wherein the optical waveguide comprises an optical fiber.

4. The method of claim 3 , wherein the optical fiber comprises one of a single-mode optical fiber, a step-index multimode optical fiber, or a graded-index multimode optical fiber.

5. The method of claim 1 , wherein at least a first molecular switch of the one or more molecular switches is attached to the sidewall of the second end of the optical waveguide, and the respective optical reporter attached to the first molecular switch is exposed to an evanescent optical field of the excitation light adjacent the sidewall.

6. The method of claim 1 , wherein at least a first molecular switch of the one or more molecular switches is attached to the sidewall of the middle region of the optical waveguide, and the respective optical reporter attached to the first molecular switch is exposed to an evanescent optical field of the excitation light adjacent the sidewall.

7. The method of claim 6 , wherein the evanescent optical field extends to a distance less than one micron from the sidewall.

8. The method of claim 1 , wherein the one or more optical reporters comprise one or more fluorescent labels.

9. The method of claim 1 , wherein each molecular switch comprises a nucleic acid, a protein, a polymer comprising nucleic acids and proteins, or a chemically modified version thereof.

10. The method of claim 1 , wherein:

the one or more molecular switches comprise at least a first molecular switch and a second molecular switch, wherein the first molecular switch changes conformation upon binding to a first target molecule, and the second molecular switch changes conformation upon binding to a second target molecule; and

the one or more optical reporters comprise at least a first optical reporter and a second optical reporter, wherein the first optical reporter is attached to the first molecular switch and configured to produce a first optical signal in a first wavelength range upon binding to the first target molecule, and the second optical reporter is attached to the second molecular switch and configured to produce a second optical signal in a second wavelength range different from the first wavelength range upon binding to the second target molecule.

11. The method of claim 1 , wherein the excitation light is in a first wavelength range, and the optical signals produced by the one or more optical reporters are in a second wavelength range different from the first wavelength range, and the optical sensor system further comprising an optical filter coupled to the detector and configured to transmit the optical signals in the second wavelength range and block the excitation light in the first wavelength range.

12. The method of claim 1 , wherein the excitation light is in a first wavelength range, wherein the optical signals produced by the one or more optical reporters are in a second wavelength range different from the first wavelength range, and the detector comprises an optical spectrometer.

13. The method of claim 1 , wherein the optical probe further comprises a tube surrounding the second end of the optical waveguide, the tube being configured to protect the second end of the optical waveguide when inserted into the sample.

14. The method of claim 1 , wherein the system comprises at least a first optical probe and a second optical probe, wherein

the first optical probe comprises:

a first optical waveguide having a first end and a second end, the first end configured to receive excitation light to be propagated through the first optical waveguide and to be emitted from the first end or the second end into a surrounding medium;

one or more first molecular switches attached to a facet or a sidewall of the second end or a middle region of the optical waveguide, wherein the first molecular switches are configured to change conformation upon binding to a corresponding first target molecule; and

one or more first optical reporters, the first optical reporters attached to a respective molecular switch and configured, when exposed to the excitation light, to produce a first optical signal change upon binding of the respective molecular switch to the corresponding first target molecule in the surrounding medium, wherein the first optical signal is coupled back into the optical waveguide via the second end and propagated through the optical waveguide to be emitted from the first end or the second end; and

the second optical probe comprises:

a second optical waveguide having a first end and a second end, the first end configured to receive excitation light to be propagated through the second optical waveguide and to be emitted from the first end or the second end into a surrounding medium;

one or more second molecular switches attached to a facet or a sidewall of the second end or a middle region of the second optical waveguide, wherein the second molecular switches are configured to change conformation upon binding to a corresponding second target molecule; and

one or more second optical reporters, the second optical reporters attached to a respective molecular switch and configured, when exposed to the excitation light, to produce a second optical signal change upon binding of the respective molecular switch to the corresponding second target molecule in the surrounding medium, wherein the second optical signal is coupled back into the optical waveguide via the second end and propagated through the second optical waveguide to be emitted from the first end or the second end.

15. A method of detection of a target molecule in a sample using an optical sensor system, the method comprising:

contacting the one or more molecular switches of an optical probe to the sample;

emitting the excitation light from the light source; and

measuring, using the detector, changes of the optical signals, thereby detecting a concentration of the target molecule in the sample;

wherein the optical sensor system comprises:

the optical probe;

a light source configured to emit the excitation light to be coupled into the optical waveguide of the optical probe;

a detector configured to (i) receive the optical signals produced by the one or more optical reporters that are transmitted through the optical waveguide, and (ii) detect changes of the optical signals, thereby allowing for detection of a concentration of the corresponding target molecule; and

wherein the optical probe comprises:

an optical waveguide having a first end and a second end, the first end configured to receive excitation light to be propagated through the optical waveguide and to be emitted from the second end or a middle region into a surrounding medium;

one or more molecular switches attached to a facet or a sidewall of the second end or the middle region of the optical waveguide, wherein the molecular switches are configured to change conformation upon binding to a corresponding target molecule; and

one or more optical reporters, the optical reporters attached to a respective molecular switch and configured, when exposed to the excitation light, to produce an optical signal that changes upon binding of the respective molecular switch to the corresponding target molecule in the surrounding medium, wherein the optical signal is coupled back into the optical waveguide and propagated through the optical waveguide to be emitted from the first end or second end;

wherein the optical reporters comprise a donor fluorophore and an acceptor fluorophore,

wherein the measuring comprises measuring a first optical signal at the emission wavelength of the donor fluorophore and a second optical signal at the emission wavelength of the acceptor fluorophore, and

wherein the first optical signal and the second optical signal are at different levels when the molecular switch is not bound to the target molecule compared to when the molecular switch is bound to the target molecule.

16. The method of claim 15 , wherein,

(a) when the molecular switch is bound to the target molecule, the donor fluorophore and the acceptor are in proximity of each other to produce a FRET signal; or

(b) when the molecular switch is not bound to the target molecule, the donor fluorophore and the acceptor are in proximity of each other to produce a FRET signal.