Stage and platform for building a biochip and biochip

• US 7,736,888 B2
• Filed: 01/17/2003
• Issued: 06/15/2010
• Est. Priority Date: 12/12/2000
• Status: Active Grant

• Current Assignee: Autogenomics
• Original Assignee: Autogenomics
• Inventors: Mahant, Vijay K., Kureshy, Fareed
• Primary Examiner(s): CROW, ROBERT THOMAS
• Application Number:
  US10/346,879
• Publication Number:
  US 20040005697A1
• Time in Patent Office: 2,706 Days
• Field of Search: 435/6, 435/283.1, 435/287.1, 435/287.2
• US Class Current: 435/283.1
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• 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 2219/00731 Saccharides
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 40/12 Libraries containing saccharides or polysaccharides, or derivatives thereof
• CPC Class Codes: G01N 33/542 with steric inhibition or signal modification, e.g. fluorescent quenching
• CPC Class Codes: G01N 33/54366 Apparatus specially adapted for solid-phase testing

Abstract

A biochip, a platform which composes the biochip, and a stage which composes the platform. The biochip is for detecting analytes in a test sample. The platform comprises a stage. The stage of the invention includes a carrier.

Claims

1. A biochip comprising:

a carrier, optionally with a hydrophilic surface;

at least one light-blocking matrix layer comprising at least one of a gelatin, a polyvinyl alcohol, a polyvinyl pyrrolidone, an agarose, and a polyacrylamide, and further comprising a light-blocking agent, wherein the at least one light-blocking matrix layer is coupled to the carrier and the optional hydrophilic surface and is effective to render the carrier optically inactive;

a coupling matrix layer coupled to the light-blocking matrix layer, and a cross-linking agent suspended within the coupling matrix layer, wherein the cross-linking agent is optionally covalently coupled to the coupling matrix layer;

a plurality of distinct nucleic acids, each of the plurality of nucleic acids having a capture portion that non-covalently binds to the cross-linking agent, and wherein the distinct nucleic acids are non-covalently bound to the cross-linking agent in the coupling matrix layer at respective distinct and predetermined positions on the coupling matrix layer;

an optional modification matrix layer coupled to the coupling matrix layer, wherein the modification matrix layer provides at least one of a chromatographic function, a light absorbing function, a penetration delay function, and an assay function; and

wherein the light-blocking matrix layer is disposed between the carrier and the coupling matrix layer, and wherein the coupling matrix layer is disposed above the light blocking matrix layer and below the optional modification matrix layer.

2. The biochip of claim 1 wherein at least one of the light-blocking matrix layer, the coupling matrix layer, and the modification matrix layer comprises agarose at a concentration of about 1% by weight to about 5% by weight.

3. The biochip of claim 2 wherein the chromatographic function is selected from the group consisting of size exclusion chromatography, affinity chromatography, and ion exchange chromatography.

4. The biochip of claim 2 wherein the light absorbing function is selected from the group consisting of filtering of an incident light and filtering of an emitted light.

5. The biochip of claim 2 wherein the assay function is selected from the group consisting of providing a substrate for an enzymatic assay, providing a co-substrate for an enzymatic assay, providing an enzyme for an enzymatic assay, and providing a chromogenic or luminogenic substrate for an enzymatic assay.

6. The biochip of claim 2 further comprising a base matrix layer that is disposed between the hydrophilic surface and the light-blocking matrix layer.

7. The biochip of claim 2 wherein the light blocking agent is iron oxide and wherein the cross-linking agent is avidin or streptavidin.

8. A biochip comprising:

a carrier with a first and second surface;

a base matrix layer comprising at least one of a gelatin, a polyvinyl alcohol, a polyvinyl pyrrolidone, an agarose, and a polyacrylamide, wherein the base matrix layer is coupled to the first surface;

a light-blocking matrix layer coupled to the base matrix layer and comprising at least one of a gelatin, a polyvinyl alcohol, a polyvinyl pyrrolidone, an agarose, and a polyacrylamide, and further comprising a light-blocking agent, wherein the light-blocking matrix layer is coupled to the base matrix layer and is effective to render the carrier optically inactive;

a coupling matrix layer coupled to the light-blocking matrix layer, and a cross-linking agent suspended within the coupling matrix layer, wherein the cross-linking agent is optionally covalently coupled to the coupling matrix layer;

a plurality of distinct nucleic acids, each of the plurality of distinct nucleic acids having a capture portion that binds non-covalently to the cross-linking agent, and wherein the nucleic acids are bound to the cross-linking agent in the coupling matrix layer in respective distinct and predetermined positions on the coupling matrix layer;

wherein the light-blocking matrix layer is disposed between the carrier and the coupling matrix layer;

wherein at least one of the base layer, the light-blocking matrix layer, and the coupling matrix layer includes an additive selected from the group consisting of a buffer, a detergent, a humectant, and a light-blocking agent; and

wherein the plurality of distinct nucleic acids are coupled to the coupling matrix layer such that they form a plurality of nucleic acid spots having respective diameters of between 20 and 1000 micrometer.

9. The biochip of claim 8 wherein at least one of the base matrix layer, the light-blocking matrix layer, and the coupling matrix layer comprise agarose at a concentration of about 1% by weight to about 5% by weight.

10. The biochip of claim 9 wherein the buffer is an amphoteric buffer, and wherein the light blocking agent is an iron oxide.

11. The biochip of claim 9 wherein the coupling matrix layer comprises aldehyde-activated agarose at a concentration of about 1% by weight to about 5% by weight.

12. The biochip of claim 11 wherein the cross-linking agent is avidin, streptavidin, or an antibody, and wherein the cross-linking agent is covalently coupled to the coupling matrix layer.

13. The biochip of claim 12 wherein the capture portion comprises a biotin.

14. The biochip of claim 9 wherein the carrier is a flexible and optically pure polymer film with a thickness of about 100 micrometers and further includes a gelatin coating as the hydrophilic coating.

15. The biochip of claim 9 wherein the additive is present in an amount effective to control surface irregularity of the coupling matrix layer, thereby allowing optical detection using a confocal microscope of a plurality of signals from a plurality of analytes bound to the plurality of nucleic acids without recalibration of the confocal microscope.

16. The biochip of claim 9 wherein the light-blocking agent is present at a concentration to increase a signal-to-noise ratio when an optical detection of a signal from the biochip is employed.

17. A biochip comprising:

a carrier with a first and second surface;

at least one light-blocking matrix layer comprising at least one of a gelatin, a polyvinyl alcohol, a polyvinyl pyrrolidone, an agarose, and a polyacrylamide, and further comprising a light-blocking agent, wherein the at least one light-blocking matrix layer is coupled to the carrier and is effective to render the carrier optically inactive;

a coupling matrix layer coupled to the light-blocking matrix layer, and a cross-linking agent suspended within the coupling matrix layer, wherein the cross-linking agent is optionally covalently coupled to the coupling matrix layer;

wherein the light-blocking matrix layer is disposed between the carrier and the coupling matrix layer;

a plurality of distinct nucleic acids, each of the plurality of nucleic acids having a capture portion that binds non-covalently to the cross-linking agent, and wherein the distinct nucleic acids are bound to the cross-linking agent in the coupling matrix layer in respective distinct and predetermined positions; and

wherein the plurality of nucleic acids are coupled to the coupling matrix layer such that they form a plurality of nucleic acid spots having respective diameters of between 20 and 1000 micrometer.

18. The biochip of claim 17 wherein at least one of the light-blocking matrix layer and the coupling matrix layer comprise agarose at a concentration of about 1% by weight to about 5% by weight, and wherein the light-blocking agent is present at a concentration to increase a signal-to-noise ratio when an optical detection of a signal from the biochip is employed.

19. The biochip of claim 18 wherein the carrier is a flexible and optically pure polymer film with a thickness of about 100 micrometers and further includes a gelatin, a polyvinyl alcohol, or a polyvinyl pyrrolidone coating as a hydrophilic coating.

20. The biochip of claim 18 further comprising a base matrix layer that is disposed between the carrier and the light-blocking matrix layer.