Label-free methods for performing assays using a colorimetric resonant reflectance optical biosensor

• US 20030068657A1
• Filed: 09/09/2002
• Published: 04/10/2003
• Est. Priority Date: 10/30/2000
• Status: Active Grant

• Current Assignee: X-Body Incorporated (Bristol-Myers Squibb Company)
• Original Assignee: Sru Biosystems Incorporated
• Inventors: Lin, Bo, Li, Peter, Cunningham, Brian T., Pien, Homer, Pepper, Jane, Qiu, Jean, Gerstenmaier, John
• Granted Patent: US 7,153,702 B2
• Time in Patent Office: Days
• US Class Current: 435/7.9
• CPC Class Codes: B01J 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00511 Walls of reactor vessels
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/0072 Organic compounds
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: B01J 2219/00743 Cells
• CPC Class Codes: B01L 2300/0636 Integrated biosensor, microarrays
• CPC Class Codes: B01L 2300/0829 Multi-well plates; Microtitration plates
• CPC Class Codes: B01L 3/5085 for multiple samples, e.g. microtitration plates
• CPC Class Codes: C40B 60/12 for screening libraries
• CPC Class Codes: G01N 21/253 for batch operation, i.e. multisample apparatus analytical automats G01N35/00
• CPC Class Codes: G01N 21/4788 Diffraction for sizing particles G01N15/0205
• CPC Class Codes: G01N 21/774 the reagent being on a grating or periodic structure
• CPC Class Codes: G01N 21/7743 the reagent-coated grating coupling light in or out of the waveguide
• CPC Class Codes: G01N 33/54373 involving physiochemical end-point determination, e.g. wave-guides, FETS, gratings
• CPC Class Codes: G02B 5/008 : Surface plasmon devices diffractive gratings with a pitch less than or comparable to the wavelength G02B5/1809; surface plasmons in integrated optics G02B6/1226; optical analysis of materials by means of surface plasmons G01N21/553
• CPC Class Codes: G02B 5/1809 : with pitch less than or comparable to the wavelength
• CPC Class Codes: Y10S 436/805 : Optical property
• CPC Class Codes: Y10S 436/809 : Multifield plates or multicontainer arrays
• CPC Class Codes: Y10S 436/81 : Tube, bottle, or dipstick

Abstract

Methods are provided for detecting biomolecular interactions. The use of labels is not required and the methods can be performed in a high-throughput manner. The invention also relates to optical devices.

Claims

1. A method of detecting cleavage of one or more entire specific binding substances from a surface of a colorimetric resonant reflectance optical biosensor, wherein one or more specific binding substances are immobilized on the surface of the biosensor at distinct locations, comprising:

a. detecting a colorimetric resonant reflectance optical biosensor peak wavelength value (PWV) of the distinct locations;

b. applying one or more cleaving molecules to the distinct locations;

c. detecting a colorimetric resonant reflectance optical PWV of the distinct locations; and

d. comparing the PWVs from step (a) with the PWVs from step (c);

wherein the cleavage of one or more entire specific binding substances is detected.

2. The method of claim 1, wherein the colorimetric resonant reflectance optical biosensor comprises an internal surface of a vessel selected from the group consisting of a microtiter well, microtiter plate, test tube, petri dish and microfluidic channel.

3. The method of claim 1, wherein the one or more specific binding substances are immobilized onto the surface of the biosensor via a nickel group, amine group, aldehyde group, acid group, alkane group, alkene group, alkyne group, aromatic group, alcohol group, ether group, ketone group, ester group, amide group, amino acid group, nitro group, nitrile group, carbohydrate group, thiol group, organic phosphate group, lipid group, phospholipid group or steroid group.

4. The method of claim 1, wherein one or more specific binding substances are arranged in an array of distinct locations on the surface of the biosensor.

5. The method of claim 1, wherein the specific binding substance is immobilized on the surface of the colorimetric resonant reflectance optical biosensor by a method selected from the group consisting of physical adsorption, chemical binding, electrochemical binding, electrostatic binding, hydrophobic binding and hydrophilic binding.

6. The method of claim 4, wherein the distinct locations define an array spot of about 50-500 microns in diameter.

7. The method of claim 1, wherein the detection comprises:

a. immobilizing one or more specific binding substances in one or more distinct locations defining an array within a well of a microtiter plate, wherein the distinct locations defining the array are located upon the surface of a colorimetric resonant reflectance optical biosensor which comprises an internal surface of the well;

b. detecting a colorimetric resonant reflectance optical PWV for one or more distinct locations within the well;

c. applying one or more cleaving molecules to the well;

d. detecting a colorimetric resonant reflectance optical PWV for one or more distinct locations within the well; and

e. comparing the PWV from step (b) with the PWV from step (d);

wherein the cleavage of one or more entire specific binding substances at the one or more distinct locations within the well is detected.

8. The method of claim 1, wherein the specific binding substance is selected from the group consisting of nucleic acids, peptides, protein solutions, peptide solutions, single or double stranded DNA solutions, RNA solutions, RNA-DNA hybrid solutions, solutions containing compounds from a combinatorial chemical library, antigen, polyclonal antibody, monoclonal antibody, single chain antibody (scFv), F(ab) fragment, F(ab′

)₂ fragment, Fv fragment, small organic molecule, cell, virus, bacteria, polymer and biological sample.

9. The method of claim 1, wherein a peak wavelength value (PWV) is a relative measure of the binding substance that is bound to the biosensor.

10. The method of claim 1, wherein the cleaving molecule is selected from the group consisting of proteases, lipases, nucleases, lyases, peptidases, hydrolases, ligases, kinases and phosphatases.

11. A method of detecting inhibition activity of one or more molecules against enzyme or binding partners that effect or bind molecules which cleave specific binding substances, wherein the specific binding substances are immobilized on a surface of a colorimetric resonant reflectance optical biosensor comprising:

a. detecting a colorimetric resonant reflectance optical PWV of a distinct location;

b. applying one or more molecules suspected of having inhibition activity to the distinct location;

c. applying one or more enzymes or binding partners to the distinct location;

d. detecting the colorimetric resonant reflectance optical PWV of the distinct location;

e. comparing the PWV from step (a) with the PWV from step (d); and

wherein inhibition activity of one or more molecules against the enzymes or binding partners which effect or bind one or more specific binding substances is detected.

12. The method of claim 11, wherein the colorimetric resonant reflectance optical biosensor comprises an internal surface of a vessel selected from the group consisting of a microtiter well, microtiter plate, test tube, petri dish and microfluidic channel.

13. The method of claim 11, wherein the one or more specific binding substances are selected from the group consisting of nucleic acids, peptides, protein solutions, peptide solutions, single or double stranded DNA solutions, RNA solutions, RNA-DNA hybrid solutions, solutions containing compounds from a combinatorial chemical library, antigen, polyclonal antibody, monoclonal antibody, single chain antibody (scFv), F(ab) fragment, F(ab′

)₂ fragment, Fv fragment, small organic molecule, cell, virus, bacteria, polymer and biological sample.

14. The method of claim 11, wherein the one or more binding substances are immobilized onto the surface of the biosensor via a nickel group, amine group, aldehyde group, acid group, alkane group, alkene group, alkyne group, aromatic group, alcohol group, ether group, ketone group, ester group, amide group, amino acid group, nitro group, nitrile group, carbohydrate group, thiol group, organic phosphate group, lipid group, phospholipid group and steroid group.

15. The method of claim 11, wherein one or more specific binding substances are arranged in an array of distinct locations on the surface of the biosensor.

16. The method of claim 11, wherein the specific binding substance is immobilized on the surface of the colorimetric resonant reflectance optical biosensor by a method selected from the group consisting of physical adsorption, chemical binding, electrochemical binding, electrostatic binding, hydrophobic binding and hydrophilic binding.

17. The method of claim 15, wherein a distinct location defines an array spot of about 50-500 microns in diameter.

18. The method of claim 11, wherein the detection comprises:

a. immobilizing one or more specific binding substances in one or more distinct locations defining an array within a well of a microtiter plate, wherein the distinct locations defining an array are located upon the surface of a colorimetric resonant reflectance optical biosensor which comprises an internal surface of the well;

b. detecting a colorimetric resonant reflectance optical PWV for the one or more distinct locations within the well;

c. applying one or more molecules suspected of having inhibition activity to the well;

d. applying one or more enzyme or binding partners to the well;

e. detecting a colorimetric resonant reflectance optical PWV for the one or more distinct locations within the well; and

f. comparing the PWV from step (b) with the PWV from step (e); and

wherein the inhibition activity of one or more molecules against enzyme or binding partners molecules which effect or bind one or more specific binding substances at each distinct location within a well is detected.

19. The method of claim 13, wherein the polymer is selected from the group of long chain molecules with multiple active sites per molecule consisting of hydrogel, dextran, poly-amino acids and derivatives thereof, including poly-1-lysine, poly-d-lysine, poly-phe-lysine and poly-glu-lysine.

20. The method of claim 11, wherein the enzyme is selected from the group consisting of proteases, lipases, nucleases, lyases, peptidases, hydrolases, ligases, kinases and phosphatases.

21. A method of detecting a change in a cell growth pattern comprising:

a. growing cells on a colorimetric resonant reflectance optical biosensor;

b. detecting a colorimetric resonant reflectance optical PWV;

c. applying a test reagent to the cells;

d. detecting the colorimetric resonant reflectance optical PWV; and

e. comparing the PWV of step (b) to the PWV of step (d);

wherein a difference between the colorimetric resonant reflectance optical PWV of step (b) in relation to the colorimetric resonant reflectance optical PWV of step (d) indicates a change in a cell growth pattern.

22. The method of claim 21 wherein the change in cell growth pattern is selected from the group consisting of cell morphology, cell adhesion, cell migration, cell proliferation and cell death.

23. The method of claim 21 wherein the colorimetric resonant reflectance optical biosensor comprises an internal surface of a vessel selected from the group consisting of a microtiter well, microtiter plate, test tube, petri dish and microfluidic channel.

24. The method of claim 23, wherein one or more different types of cells are grown on a microtiter plate, and wherein one or more types of cells are grown in a well of the microtiter plate.

25. A method of detecting the binding of molecules released from cells grown in a semi-permeable internal sleeve held in contact with a colorimetric resonant reflectance optical biosensor comprising:

a. detecting a colorimetric resonant reflectance optical PWV of a distinct location of the biosensor;

b. growing cells in the semi-permeable internal sleeve held in contact with the colorimetric resonant reflectance optical biosensor at the distinct location;

c. detecting the colorimetric resonant reflectance optical PWV of the distinct location;

d. comparing the PWV of step (a) to the PWV of step (c);

wherein binding of the molecules released from cells grown in the semi-permeable internal sleeve held in contact with the colorimetric resonant reflectance optical biosensor to the one or more specific binding substances is detected.

26. The method of claim 25, wherein the colorimetric resonant reflectance optical biosensor comprises an internal surface of a vessel selected from the group consisting of a microtiter well, microtiter plate, test tube, petri dish and microfluidic channel.

27. The method of claim 25, wherein the semi-permeable internal sleeve is a removable porous or non-removable porous insert that is held in contact or in close proximity with the surface of a biosensor, wherein the sleeve is permeable to molecules secreted from the cells cultured on its surface and wherein the sleeve is impermeable to whole cells.

28. The method of claim 25, wherein the one or more binding substances is immobilized onto the surface of the biosensor via a nickel group, amine group, aldehyde group, acid group, alkane group, alkene group, alkyne group, aromatic group, alcohol group, ether group, ketone group, ester group, amide group, amino acid group, nitro group, nitrile group, carbohydrate group, thiol group, organic phosphate group, lipid group, phospholipid group and steroid group.

29. The method of claim 25, wherein one or more specific binding substances are arranged in an array of distinct locations on the surface of the biosensor.

30. The method of claim 25, wherein the specific binding substance is immobilized on the surface of the colorimetric resonant reflectance optical biosensor by a method selected from the group consisting of physical adsorption, chemical binding, electrochemical binding, electrostatic binding, hydrophobic binding and hydrophilic binding.

31. The method of claim 29, wherein the distinct locations define an array spot of about 50-500 microns in diameter.

32. The method of claim 25, wherein the detection comprises:

a. immobilizing one or more binding substances in one or more distinct locations defining an array within a well of a microtiter plate, wherein a colorimetric resonant reflectance optical biosensor comprises an internal surface of the well;

b. detecting a colorimetric resonant reflectance optical PWV for the one or more distinct locations defining an array within the well;

c. growing cells in a semi-permeable internal sleeve held in contact with the well;

d. detecting the colorimetric resonant reflectance optical PWV for the one or more distinct locations within the well; and

e. comparing the PWV of step (b) to the PWV of step (d);

wherein the difference between the colorimetric resonant reflectance optical PWV of step (d) in relation to the colorimetric resonant reflectance optical PWV of step (b) indicates the relative binding of one or more molecules secreted from the cells growing on the semi-permeable internal sleeve within a well to the one or more specific binding substances immobilized at distinct locations within the well on the surface of a colorimetric resonant reflectance optical biosensor.

33. The method of claim 25, wherein specific binding substance is selected from the group consisting of nucleic acids, peptides, protein solutions, peptide solutions, single or double stranded DNA solutions, RNA solutions, RNA-DNA hybrid solutions, solutions containing compounds from a combinatorial chemical library, antigen, polyclonal antibody, monoclonal antibody, single chain antibody (scFv), F(ab) fragment, F(ab′

)₂ fragment, Fv fragment, small organic molecule, cell, virus, bacteria, polymer or biological sample.

34. The method of claim 33, wherein the biological sample is selected from the group consisting of blood, plasma, serum, gastrointestinal secretions, homogenates of tissues or tumors, synovial fluid, feces, saliva, sputum, cyst fluid, amniotic fluid, cerebrospinal fluid, peritoneal fluid, lung lavage fluid, semen, lymphatic fluid, tears and prostatic fluid;

35. The method of claim 33, wherein the polymer is selected from the group of long chain molecules with multiple active sites per molecule consisting of hydrogel, dextran, poly-amino acids and derivatives thereof, including poly-1-lysine, poly-d-lysine, poly-phe-lysine and poly-glu-lysine.

36. The method of claim 25, wherein an increase in the colorimetric resonant reflectance optical PWV detected in step (d) in relation to the colorimetric resonant reflectance optical PWV of step (b) is a relative measure of the proportion of molecules released from cells grown in the semi-permeable internal sleeve that bind to the specific binding substances immobilized on the biosensor surface.

37. The method of claim 25, wherein the difference between the resonant optical biosensor PWV of step (d) in relation to the resonant optical biosensor PWV of step (b) is a relative measure of the molecules released from cells grown in a semi-permeable internal sleeve that are bound to the specific binding substances.