Random array of micro-spheres for the analysis of nucleic acids

• US 7,011,945 B2
• Filed: 12/21/2001
• Issued: 03/14/2006
• Est. Priority Date: 12/21/2001
• Status: Expired due to Fees

• Current Assignee: CareStream Health Incorporated
• Original Assignee: Eastman Kodak Company
• Inventors: Chari, Krishnan, Vizard, Douglas L., Qiao, Tiecheng A.
• Primary Examiner(s): FORMAN, BETTY J
• Application Number:
  US10/036,828
• Publication Number:
  US 20030143542A1
• Time in Patent Office: 1,544 Days
• Field of Search: 435/6, 435/174, 435/283.1, 435/287.1, 435/288.7, 536/23.1, 536/24.3, 536/26.6
• US Class Current: 435/6.11
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00466 in a slurry
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00545 Colours
• CPC Class Codes: B01J 2219/00547 Bar codes
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Abstract

A method of identifying nucleic acid samples comprising: providing a mircoarray including a substrate coated with a composition including a population of micro-spheres dispersed in a fluid containing a gelling agent or a precursor to a gelling agent and immobilized at random positions on the substrate, at least one sub-population of said population micro-spheres containing an optical barcode generated from at least one colorant associated with the micro-spheres and including a nucleic acid probe sequence; contacting said array with a target nucleic acid sequence; and detecting the color barcode of said sub-population of micro-spheres due to the interaction of said probe nucleic acid sequence and said target nucleic acid sequence.

Claims

1. A method of identifying biological samples comprising:

providing a microarray including a substrate having no preselected sites for association with micro-spheres wherein providing comprises coating said substrate with a composition including a population of micro-spheres dispersed in a fluid containing gelatin and immobilizing said micro-spheres in a single layer of single micro-spheres at random positions and at a uniform density on the substrate, at least one sub-population of said population of micro-spheres containing an optical barcode generated from at least one colorant associated with the micro-spheres and wherein said microspheres have a biological probe attached thereto;

contacting said microarray with a biological target sample;

detecting the optical barcode of said sub-population of micro-spheres due to the interaction of said biological probe and said biological target sample; and

identifying said biological sample.

2. The method of claim 1 wherein said microarray population of micro-spheres includes a plurality of sub-populations of micro-spheres, wherein each said sub-population of micro-spheres obtains a unique optical barcode and has a unique biological probe.

3. The method of claim 1 wherein said optical barcode is generated by two or more colorants.

4. The method of claim 1 wherein said optical barcode is generated by a mixture of red (R), green (G), and blue (B) colorants.

5. The method of claim 1 wherein said at least one sub-population of micro-spheres has a luminescent property to produce a luminescent image and wherein said detecting includes:

(a) whole frame imaging capture of the luminescent image resulting from said interaction of said biological probe and said biological target sample to produce a first image;

(b) whole frame imaging capture of said microarray under bright field illumination to obtain the micro-sphere optical barcode to produce a second image; and

(c) processing said first and second images to obtain identification of said biological target sample.

6. The method of claim 5 wherein said processing uses a pattern recognition algorithm to obtain said identification.

7. The method of claim 1 wherein said at least one sub-population of micro-spheres has a fluorescent property and wherein said detecting includes:

(a) whole frame imaging capture of the fluorescent image resulting from said interaction of said probe and said target to produce a first image;

(b) whole frame imaging capture of said microarray under bright field illumination to obtain the micro-sphere optical barcode to produce a second image; and

(c) processing said first and second images to obtain identification of said sample.

8. The method of claim 1 wherein said substrate is characterized by an absence of specific sites capable of interacting physically or chemically with the micro-spheres.

9. The method of claim 1 wherein said micro-spheres bear surface active sites which contain said probe.

10. The method of claim 1 wherein said micro-spheres have a mean diameter between 1 and 50 microns.

11. The method of claim 1 wherein said micro-spheres have a mean diameter between 3 and 30 microns.

12. The method of claim 1 wherein said micro-spheres have a mean diameter between 5 and 20 microns.

13. The method of claim 1 wherein said micro-spheres in the composition are immobilized on the substrate in a concentration between 100 and 1 million micro-spheres per cm².

14. The method of claim 1 wherein said micro-spheres in the composition are immobilized on the substrate in a concentration between 1000 and 200,000 micro-spheres per cm².

15. The method of claim 1 wherein said micro-spheres in the composition are immobilized on the substrate in a concentration between 10,000 and 100,000 micro-spheres per cm².

16. The method of claim 1 wherein said micro-spheres comprise a synthetic or natural polymeric material.

17. The method of claim 16 wherein said polymeric material is an amorphous polymer.

18. The method of claim 17 wherein said amorphous polymer is polystyrene.

19. The method of claim 1 wherein said micro-spheres contain a polymeric material and less than 30 weight percent of a crosslinking agent.

20. The method of claim 1 wherein said micro-spheres are prepared by emulsion polymerization or limited coalescence.

21. A method of identifying biological samples comprising:

providing a microarray wherein providing comprises coating a substrate with a composition including a population of micro-spheres dispersed in a fluid containing gelatin and immobilizing a single layer of single micro-spheres at random positions at a uniform density on the substrate wherein the substrate has no preselected sites for association with micro-spheres, at least one sub-population of said population of micro-spheres containing an optical barcode generated from at least one colorant associated with the micro-spheres, said colorant having one of a luminescent or fluorescent property and wherein said micro-spheres have a biological probe sequence attached thereto;

contacting said microarray with a biological target sample; and

detecting the optical barcode of said sub-population of micro-spheres due to the interaction of said probe and said target by;

(a) whole frame imaging of the luminescent or fluorescent image resulting from said interaction to produce a first image;

(b) whole frame imaging capture of said microarray under bright field illumination to obtain the micro-sphere optical barcode to produce a second image; and

(c) processing said first and second images to obtain identification of said biological sample.

22. The method of claim 21 wherein said processing uses a pattern recognition algorithm to obtain said identification.

23. The method of claim 21 wherein said microarray population of micro-spheres includes a plurality of sub-populations of micro-spheres, wherein each said sub-population of micro-spheres contains a unique optical barcode and has a unique probe.

24. The method of claim 21 wherein said optical barcode is generated by two or more colorants.

25. The method of claim 21 wherein said optical barcode is generated by a mixture of red (R), green (G), and blue (B) colorants.