Hybridization device and method

• US 6,733,977 B2
• Filed: 08/28/2002
• Issued: 05/11/2004
• Est. Priority Date: 06/08/1994
• Status: Expired due to Fees

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Goss, Virginia W., Besemer, Donald M., Winkler, James L.
• Primary Examiner(s): Siew, Jeffrey
• Application Number:
  US10/229,759
• Publication Number:
  US 20030003499A1
• Time in Patent Office: 622 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: 506/9
• CPC Class Codes: B01F 33/252 using bubbles as loose mixing element
• CPC Class Codes: B01F 33/30 Micromixers
• CPC Class Codes: B01F 33/40 Mixers using gas or liquid agitation, e.g. with air supply tubes
• CPC Class Codes: B01F 33/45 Magnetic mixers; Mixers with magnetically driven stirrers
• CPC Class Codes: B01F 33/452 using independent floating stirring elements
• 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 2219/00353 Pumps
• CPC Class Codes: B01J 2219/00371 comprising electrodes
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00531 essentially square
• CPC Class Codes: B01J 2219/00536 in the shape of disks
• CPC Class Codes: B01J 2219/0054 Means for coding or tagging the apparatus or the reagents
• CPC Class Codes: B01J 2219/00547 Bar codes
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 : DNA chips
• CPC Class Codes: B01J 2219/0061 : The surface being organic
• CPC Class Codes: B01J 2219/00612 : the surface being inorganic
• CPC Class Codes: B01J 2219/00621 : by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 : Covalent
• CPC Class Codes: B01J 2219/00637 : by coating it with another layer
• CPC Class Codes: B01J 2219/00641 : the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00659 : Two-dimensional arrays
• CPC Class Codes: B01J 2219/00662 : Two-dimensional arrays within two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 : using computers
• CPC Class Codes: B01J 2219/00695 : Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00711 : Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01J 2219/00725 : Peptides
• CPC Class Codes: B01J 2219/00731 : Saccharides
• CPC Class Codes: B01L 2200/025 : Align devices or objects to ensure defined positions relative to each other
• CPC Class Codes: B01L 2200/027 : for microfluidic devices
• CPC Class Codes: B01L 2200/0689 : Sealing
• CPC Class Codes: B01L 2200/12 : Specific details about manufacturing devices
• CPC Class Codes: B01L 2200/147 : Employing temperature sensors
• CPC Class Codes: B01L 2300/0636 : Integrated biosensor, microarrays
• CPC Class Codes: B01L 2300/0816 : Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0819 : Microarrays; Biochips
• CPC Class Codes: B01L 2300/0825 : Test strips
• CPC Class Codes: B01L 2300/0877 : Flow chambers
• CPC Class Codes: B01L 2300/1805 : Conductive heating, heat from thermostatted solids is conducted to receptacles, e.g. heating plates, blocks
• CPC Class Codes: B01L 2400/0439 : ultrasonic vibrations, vibrating piezo elements
• CPC Class Codes: B01L 2400/0442 : thermal energy, e.g. vaporisation, bubble jet
• CPC Class Codes: B01L 2400/0487 : fluid pressure, pneumatics
• CPC Class Codes: B01L 2400/0611 : duck bill valves
• CPC Class Codes: B01L 2400/065 : sliding valves
• CPC Class Codes: B01L 3/5027 : by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: B01L 3/502707 : characterised by the manufacture of the container or its components by shaping or joining plastic parts B29C59/00, B29C65/00; by laminating B32B37/00; manufacture of microstructural devices in general B81C
• CPC Class Codes: B01L 3/502715 : characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B01L 9/52 : Supports specially adapted for flat sample carriers, e.g. for plates, slides, chips
• CPC Class Codes: B01L 9/527 : for microfluidic devices, e.g. used for lab-on-a-chip
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07H 21/00 : Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• 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: C40B 60/14 : for creating libraries
• CPC Class Codes: C40B 70/00 : Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
• CPC Class Codes: G01N 2035/00158 : Elements containing microarrays, i.e. "biochip"
• CPC Class Codes: H01L 21/67144 : Apparatus for mounting on conductive members, e.g. leadframes or conductors on insulating substrates
• CPC Class Codes: Y10T 436/25 : including sample preparation

Abstract

A body 300 having a cavity 310 for mounting a substrate 120 fabricated with probe sequences at known locations according to the methods disclosed in U.S. Pat. No. 5,143,854 and PCT WO 92/10092 or others, is provided. The cavity includes inlets 350 and 360 for introducing selected fluids into the cavity to contact the probes. Accordingly, a commercially feasible device for use in high throughput assay systems is provided.

Claims

1. An apparatus for hybridization of probe arrays, comprising:

a substrate comprising a first surface and a second surface, said first surface comprising said probe array of biological polymers disposed thereon, said probe array comprising greater than 100 different probes at known locations on said first surface; and

a housing comprising a mounting surface and a fluid cavity;

said fluid cavity comprising an inlet port constructed to permit fluid flow into said cavity through said inlet port, wherein said first surface of said substrate is sealably mounted with respect to said mounting surface thereby sealably covering said cavity and whereby said probe array is located inside said cavity.

2. The apparatus of claim 1 further including a gasket for sealing said fluid cavity.

3. The apparatus of claim 1 further including a septa located at said inlet port arranged for providing a reenterable seal.

4. The apparatus of claim 1, wherein said substrate is light transparent.

5. The apparatus of claim 4, wherein said light transparent substrate includes glass.

6. The apparatus of claim 4, wherein said light transparent substrate includes SiO₂.

7. The apparatus of claim 1, wherein said substrate is suitable for optical scanning by an optical scanner.

8. The apparatus of claim 1, wherein said substrate is suitable for optical scanning by an optical scanner employing an excitation source and a detector constructed and arranged detection of fluorescent radiation emitted from said probe array.

9. The apparatus of claim 1, wherein said substrate is inseparably mounted with respect to said housing.

10. The apparatus of claim 1, wherein said housing is made of plastic.

11. The apparatus of claim 1, wherein said biological polymers include nucleic acids.

12. The apparatus of claim 11, wherein said nucleic acids are attached to said surface through a linker group.

13. The apparatus of claim 11, wherein said nucleic acids are from 4 to 20 nucleotides in length.

14. The apparatus of claim 1, wherein each of said polymers is separately located within an area of about 1 μ

m² to about 1000 μ

m².

15. The apparatus of claim 14 wherein said nucleic acids have a density exceeding 400 different nucleic acids per cm².

16. The apparatus of claim 1, wherein said biological polymers include proteins or polypeptides.

17. The apparatus of claim 1, wherein said biological polymers include one of the following:

agonists and antagonists for cell membrane receptor, toxins, venoms, viral epitopes, hormones, hormone receptors, enzymes, enzyme substrates, cofactors, drugs, lectins, sugars, oligosaccharides or monoclonal antibodies.

18. A method of hybridizing probe arrays comprising the acts of:

providing a substrate comprising a first surface and a second surface, said first surface comprising said probe array of biological polymers disposed thereon, said probe array comprising greater than 100 different probes at known locations on said first surface;

sealably mounting said substrate to a housing comprising a mounting surface and a fluid cavity;

said fluid cavity comprising an inlet port constructed to permit fluid flow into said cavity through said inlet port, wherein said sealably mounting act provides said probe array located inside said cavity; and

introducing said fluid inside said cavity to hybridize said probe array of biological polymers.

19. The method of claim 18, wherein said housing includes an inlet comprising a re-enterable seals, and said act of introducing said fluid includes:

piercing said seal of said inlet; and

flowing said fluid from said inlet into said cavity.

20. The method of claim 19 further including the act of agitating said target molecules to facilitate reaction between the polymers of the probe array and targets located in said fluid.

21. The method of claim 18, wherein said act of sealably mounting includes inseparably mounting said substrate to said mounting surface of said housing.

22. The method of claim 18 further including a gasket for sealing said fluid cavity.

23. The method of claim 18 further including a septa located at said inlet port arranged for providing a reenterable seal.

24. The method of claim 18, wherein said substrate is light transparent.

25. The method of claim 24, wherein said light transparent substrate includes glass.

26. The method of claim 24, wherein said light transparent substrate includes SiO₂.

27. The method of claim 18, wherein said substrate is suitable for optical scanning by an optical scanner.

28. The method of claim 18 further comprising the act of identifying at least one location where at least one said targets is located on said probe array.

29. The method as recited in claim 28, wherein said identifying act comprises placing said package in a detection system.

30. The method as recited in claim 28, wherein said identifying act comprises placing said package in a scanning system, and wherein said scanning system is capable of imaging labeled targets on said probe array.