Linear microarrays

• US 6,514,751 B2
• Filed: 08/20/2001
• Issued: 02/04/2003
• Est. Priority Date: 10/02/1998
• Status: Expired due to Fees

• Current Assignee: Incyte Corporation
• Original Assignee: Incyte Corporation
• Inventors: Park, Sang Chul, Johann, Timothy W.
• Primary Examiner(s): Siew, Jeffrey
• Application Number:
  US09/933,570
• Publication Number:
  US 20020072065A1
• Time in Patent Office: 533 Days
• Field of Search: 435/6, 435/7.1, 435/91.1, 435/91.2, 435/287.2, 536/22.1, 536/23.1, 536/24-- 2
• US Class Current: 435/287.2
• 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 2219/00286 Reactor vessels with top and bottom openings
• CPC Class Codes: B01J 2219/00367 capillary
• CPC Class Codes: B01J 2219/0038 Drawing
• CPC Class Codes: B01J 2219/00468 by manipulation of individual beads
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00509 Microcolumns
• CPC Class Codes: B01J 2219/0052 in the shape of elongated tubes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00657 One-dimensional arrays
• CPC Class Codes: B01J 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 for creating libraries

Abstract

The present invention provides a method and a composition for detecting the levels of a plurality of biomolecular probes in a sample. In particular, the invention relates to a hybridization composition for detecting the presence or levels of different polynucleotide sequences in a sample.

Claims

1. A device for detecting a plurality of biomolecular probes in a sample, said device comprising a vessel comprising:

(a) a casing having an inner surface and input and output openings,

(b) a nonporous substrate having an outer surface and contained within said casing,

(c) a liquid sample comprising biomolecular probes and contained within said casing,

wherein the substrate outer surface contains a plurality of regions arranged in a defined manner and each of said regions has a different one of a plurality of immobilized specific binding targets which specifically bind a corresponding one of the plurality of the biomolecular probes, and said substrate outer surface is in close proximity with the inner surface of said casing so as to minimize the ratio of the liquid sample volume contained within said casing to the substrate outer surface area, yet permit flow of the liquid sample from the input opening, between the substrate outer surface and the casing inner surface, and to the output opening,

wherein the vessel is one of a plurality of vessels arranged in a two-dimensional arrangement.

2. The device of claim 1, wherein the vessel is one of a plurality of vessels arranged in a three-dimensional arrangement.

3. The device of claim 1, wherein the vessel is one of a plurality of vessels arranged in parallel.

4. The device of claim 1, wherein the vessel is one of a plurality of vessels arranged in parallel, in a three-dimensional arrangement.

5. The device of claim 1, wherein the immobilized binding targets and corresponding biomolecular probes comprise polynucleotides which specifically bind by hybridization.

6. The device of claim 1, wherein the ratio of the liquid sample volume contained within the casing to the substrate outer surface area is less than about 1×

10<sup>−

3</sup> m.

7. The device of claim 1, wherein the ratio of the liquid sample volume contained within the casing to the substrate outer surface area is less than about 1×

10<sup>−

5</sup> m.

8. The device of claim 1, wherein the ratio of the liquid sample volume contained within the casing to the substrate outer surface area is less than about 1×

10<sup>−

9</sup> m.

9. The device of claim 1, wherein the substrate is elongate and has a length and the regions are arranged with a linear density of greater than 1×

10³ regions per centimeter of the length.

10. The device of claim 1, wherein the substrate is elongate and has a length and the regions are arranged with a linear density of greater than 1×

10⁶ regions per centimeter of the length.

11. The device of claim 1, wherein the substrate is selected from the group consisting of an elongate rod less than 10 um in diameter and a plurality of beads, each bead less than 10 um in diameter.

21. A method for detecting biomolecular probes in a sample, said method comprising the step of using a device according to claim 1 to detect specific binding of the biomolecular probes to the immobilized targets.

12. A device for detecting a plurality of biomolecular probes in a sample, said device comprising a vessel comprising:

(a) a casing having an inner surface and input and output openings,

(b) a nonporous substrate having an outer surface and contained within said casing,

(c) a liquid sample comprising biomolecular probes and contained within said casing,

wherein the substrate outer surface contains a plurality of regions arranged in a defined manner and each of said regions has a different one of a plurality of immobilized specific binding targets which specifically bind a corresponding one of the plurality of the biomolecular probes, and said substrate outer surface is in close proximity with the inner surface of said casing so as to minimize the ratio of the liquid sample volume contained within said casing to the substrate outer surface area, yet permit flow of the liquid sample from the input opening, between the substrate outer surface and the casing inner surface, and to the output opening,

wherein the device is adapted for differential gene expression analysis, wherein the immobilized binding targets and corresponding biomolecular probes comprise polynucleotides which specifically bind by hybridization, and wherein the probes comprise two sets, wherein the probes of each set are derived from a different sample source and comprise a different label.

13. The device of claim 12, wherein the probes of each set comprise a different fluorescent label with distinguishable emission spectra.

14. The device of claim 12, wherein the probes of the two sets comprise Cy3 and Cy5 fluorophores, respectively.

15. The device of claim 12, wherein the ratio of the liquid sample volume contained within the casing to the substrate outer surface area is less than about 1×

10<sup>−

3</sup> m.

16. The device of claim 12, wherein the ratio of the liquid sample volume contained within the casing to the substrate outer surface area is less than about 1×

10<sup>−

5</sup> m.

17. The device of claim 12, wherein the ratio of the liquid sample volume contained within the casing to the substrate outer surface area is less than about 1×

10<sup>−

9</sup> m.

18. The device of claim 12, wherein the substrate is elongate and has a length and the regions are arranged with a linear density of greater than 1×

10³ regions per centimeter of the length.

19. The device of claim 13, wherein the substrate is elongate and has a length and the regions are arranged with a linear density of greater than 1×

10⁶ regions per centimeter of the length.

20. The device of claim 13, wherein the substrate is selected from the group consisting of an elongate rod less than 10 um in diameter and a plurality of beads, each bead less than 10 um in diameter.

22. A method for detecting biomolecular probes in a sample, said method comprising the step of using a device according to claim 12 to detect specific binding of the biomolecular probes to the immobilized targets.