Method and apparatus for hybridization

• US 6,551,817 B2
• Filed: 01/14/2002
• Issued: 04/22/2003
• 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: Winkler, James L., Goss, Virginia W., Besemer, Donald M.
• Primary Examiner(s): Siew, Jeffrey
• Application Number:
  US10/046,623
• Publication Number:
  US 20020058331A1
• Time in Patent Office: 463 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: 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. A apparatus for hybridization, comprising:

a cavity including a probe array with different probes comprising biological polymers immobilized on a surface; and

an inlet and an outlet arranged in communication with said cavity for introducing and removing fluids from said cavity, said cavity, said inlet and outlet being constructed and arranged to provide bubble formation during hybridization of a target to said probes of said probe array and thereby increasing a hybridization rate of said target to said probes.

2. The apparatus of claim 1 constructed to receive a chip comprising said probe array.

3. The apparatus of claim 1 or 2 comprising a channel fluidly coupling said cavity to said inlet or said outlet.

4. The apparatus of claim 1 or 2 wherein said inlet includes a septum.

5. The apparatus of claim 1 or 2 wherein said outlet includes a septum.

6. The apparatus of claim 1 or 2 wherein said outlet is constructed and arranged to enable escape of bubbles from said cavity after said hybridization.

7. The apparatus of claim 1 or 2, wherein said biological polymers include nucleic acids.

8. The apparatus of claim 7, wherein said nucleic acids are attached to said surface through a linker group.

9. The apparatus of claim 7, wherein said nucleic acids are from 4 to 20 nucleotides in length.

10. The apparatus of claim 1 or 2, wherein each of said polymers is separately located within an area of about 1 μ

m² to about 1000 μ

m².

11. The apparatus of claim 10 wherein said nucleic acids have a density exceeding 400 different nucleic acids per cm².

12. The apparatus of claim 1 or 2 wherein said biological polymers include proteins or polypeptides.

13. The apparatus of claim 1 or 2, wherein said biological polymers include at least one type selected from a group consisting of:

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

14. The apparatus of claim 1 including an optically transparent substrate having said surface including said immobilized probe array.

15. The apparatus of claim 1, 2 or 14 including an agitator for agitating fluid inside said cavity during hybridization.

28. The apparatus of claim 14, wherein said substrate includes flat glass.

29. The apparatus of claim 14, wherein said substrate includes SiO₂.

30. The apparatus of claim 14, wherein said substrate is fixedly attached with respect to said cavity.

31. The apparatus of claim 14, wherein said substrate is fixedly attached with respect to said cavity using an adhesive.

32. The apparatus of claim 14, wherein said substrate is formed by separating a wafer into a plurality of substrates.

16. An apparatus for hybridizing polymers to targets, comprising:

a probe array having a plurality of different biological polymers on a surface;

a package for housing the probe array; and

a cavity defined by said package, said cavity being constructed for receiving fluid and being constructed to freely move bubbles in contact with said probe array for agitating the fluid with respect to said probe array.

17. The apparatus of claim 16 further comprising septa for introduction or removal of the fluid.

18. The apparatus of claim 16, wherein said biological polymers include at least one type selected from a group consisting of:

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

19. The apparatus of claim 16, wherein each of said polymers is separately located within an area of about 1 μ

m² to about 1000 μ

m².

20. The apparatus of claim 16, wherein said nucleic acids have a density exceeding 400 different nucleic acids per cm².

21. The apparatus of claim 16, wherein said biological polymers are selected from the group consisting of nucleic acids and proteins.

33. The apparatus of claim 16 wherein said probe array is associated with an optically transparent substrate.

34. The apparatus of claim 33, wherein said substrate includes flat glass.

35. The apparatus of claim 33, wherein said substrate includes SiO₂.

36. The apparatus of claim 33, wherein said substrate is fixedly attached with respect to said cavity.

37. The apparatus of claim 33, wherein said substrate is fixedly attached with respect to said cavity using an adhesive.

38. The apparatus of claim 33, wherein said substrate is formed by separating a wafer into a plurality of substrates.

22. A method of evaluating probe arrays comprising the acts of:

providing a package for housing a probe array having a plurality of different biological polymers immobilized with respect to a substrate, said package defining a cavity constructed for receiving fluid;

delivering the fluid including targets inside said cavity for hybridization; and

achieving bubble formation during hybridization and thereby increasing a hybridization rate of said targets to the polymers of said probe array.

23. The method of claim 22, wherein said package includes an inlet and an outlet comprising a re-enterable seals, and said act of delivering said fluid includes:

piercing said seal of said inlet;

piercing said seal of said outlet; and

flowing said fluid from said inlet into said cavity and out through said outlet.

24. The method of claim 22 further comprising the act of agitating said target molecules to facilitate reaction between the polymers of the probe array and the targets.

25. The method of claim 22 further comprising the act of identifying at least one location where at least one said targets is located on said probe array.

26. The method as recited in claim 25, wherein said identifying act comprises placing said package in a detection system.

27. The method as recited in claim 25, 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.