Probe Array and Method for Producing Probe Array

• US 20090042734A1
• Filed: 03/27/2006
• Published: 02/12/2009
• Est. Priority Date: 03/25/2005
• Status: Abandoned Application

• Current Assignee: NGK Insulators Limited
• Original Assignee: NGK Insulators Limited
• Inventors: Takase, Tomokazu, Yoshida, Yasuko, Oribe, Akinobu, Yamada, Kazunari
• Application Number:
  US11/886,676
• Publication Number:
  US 20090042734A1
• Time in Patent Office: Days
• US Class Current: 506/9
• 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 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00387 Applications using probes
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00542 Alphanumeric characters
• CPC Class Codes: B01J 2219/00545 Colours
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00585 Parallel 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 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00644 the porous medium being present in discrete locations, e.g. gel pads
• 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 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01J 2219/00725 : Peptides
• CPC Class Codes: B01L 2300/0636 : Integrated biosensor, microarrays
• CPC Class Codes: B01L 2300/0819 : Microarrays; Biochips
• CPC Class Codes: B01L 2300/0822 : Slides
• CPC Class Codes: B01L 2300/0887 : Laminated structure
• CPC Class Codes: B01L 3/5085 : for multiple samples, e.g. microtitration plates
• CPC Class Codes: B01L 3/5088 : confining liquids at a location by surface tension, e.g. virtual wells on plates, wires B01L3/50857 takes precedence
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence

Abstract

An object of the present invention is to provide a probe array having partitioned array regions with uniform surface chemical properties. The probe array of the present invention includes a substrate having a plurality of partitioned array regions where many probes are immobilized and a separator attached to the substrate and including partitions partitioning the array regions. The above object can be achieved by attaching the separator including the partitions capable of partitioning instead of forming hydrophobic regions on a surface of the substrate by printing or chemical treatment.

Claims

1. A probe array comprising:

a substrate having one or more partitioned array regions where many probes are immobilized; and

a separator attached to the substrate and including partitions partitioning the array regions.

2. The probe array according to claim 1, wherein the substrate has a plurality of the array regions.

3. The probe array according to claim 1 wherein the separator is attached to a surface of a probe-immobilizing layer on the substrate, the probes being immobilized on the probe-immobilizing layer.

4. The probe array according to claim 3, wherein the separator is attached to the surface of the probe-immobilizing layer after the immobilization of the probes.

5. The probe array according to claim 1, wherein the separator has a sheet shape and is fixed to the substrate with an adhesive layer disposed therebetween.

6. The probe array according to claim 1, wherein the separator is detachably fixed to the substrate.

7. The probe array according to claim 1, wherein hydrophobic regions are disposed on at least part of the separator.

8. The probe array according to claim 7, wherein the hydrophobic regions are disposed on top surfaces of the partitions of the separator.

9. The probe array according to claim 7, wherein the hydrophobic regions have a water contact angle of 60°

or more.

10. The probe array according to claim 7, wherein the hydrophobic regions contain a material selected from the group consisting of polycarbonates, polyolefins, polyamides, polyimides, acrylic resins, and fluorides and halides thereof.

11. The probe array according to claim 1, wherein regions surrounded by the partitions of the separator partitioning the array regions constitute open cavities for interaction between the probes and samples under examination in the array regions.

12. The probe array according to claim 1, wherein the design area of the array regions defined by the partitions is 0.3 to 2,000 mm².

13. The probe array according to claim 1, wherein the substrate has 1 to 400 array regions.

14. The probe array according to claim 1, wherein the design area (Sd) of the array regions defined by the partitions is 90 mm² or less, and the percentage of effective probing area represented by the following equation (1) is 70% or more:

Percentage (%) of effective probing area=Se(mm²)/Sd(mm²)×

100 

 

(1)

wherein Se is the area of a region where the coefficient of variation of signal intensity based on probe-sample interaction is 20% or less.

15. The probe array according to claim 1, wherein the coefficient of variation of signal intensity measured by probing is 20% or less in regions other than those within the distance of 0.8 mm from the partitions in the partitioned array regions.

16. The probe array according to claim 1, wherein the partitioned array regions have a depth (d) of 10 to 240 μ

m.

17. The probe array according to claim 1, wherein the ratio (R) of the partitioned array regions which is represented by the following equation (2) is 0.02 or less:

R=d(mm)/Sd(mm²). 

 

(2)

wherein d is the depth of the array regions and Sd is the design area of the array regions.

18. The probe array according to claim 1, wherein the separator is configured so that the partitions can have different heights.

19. The probe array according to claim 18, wherein the separator is configured so that the partitions can have different heights within the range of 10 to 1,000 μ

m.

20. The probe array according to claim 1, wherein the separator is configured so that the height of the partitions can be reduced by removing at least part of the partitions.

21. The probe array according to claim 18, wherein the partitions of the separator have a height of 60 μ

m or more when a reaction is caused by supplying samples under examination to the probes and have a height of less than 60 μ

m when a signal from a reaction product is detected after the reaction.

22. The probe array according to claim 18, wherein the area of the array regions is 0.3 mm² or more.

23. The probe array according to claim 18, wherein the separator has a laminated structure.

24. The probe array according to claim 18, wherein the separator includes a vulnerable portion where the partitions can be at least partially removed.

25. The probe array according to claim 24, wherein the separator is a laminate and the vulnerable portion is an interface between any layers of the laminate.

26. The probe array according to claim 1, wherein the separator includes overhanging portions protruding from at least part of the tops of the partitions to above the array regions.

27. The probe array according to claim 26, wherein the overhanging portions are disposed around the entire peripheries of the array regions.

28. The probe array according to claim 26, wherein the overhanging portions include segments protruding from the partitions to above the array regions with hydrophobic regions disposed in at least regions of the segments where the segments can come in contact with solutions under examination.

29. The probe array according to claim 26, wherein the height of lowermost ends of the overhanging portions is 40 to 990 μ

m.

30. The probe array according to claim 26, wherein the overhanging portions protrude within such a distance as not to reach the probes immobilized in the array regions.

31. The probe array according to claim 26, wherein regions defined by inner peripheral surfaces of the overhanging portions are regions where the probes are immobilized in the array regions.

32. The probe array according to claim 26, wherein parts including the overhanging portions can be integrated with and/or removed from the rest of the partitions.

33. The probe array according to claim 32, wherein the entire overhanging portions can be integrated with and/or removed from the rest of the partitions.

34. The probe array according to claim 1, wherein the separator constitutes at least part of the height of the partitions partitioning the array regions.

35. The probe array according to claim 1, wherein the substrate constitutes at least part of the height of the partitions partitioning the array regions.

36. The probe array according to claim 1, further comprising a discrimination layer having a color and/or image that allows discrimination of the array regions.

37. The probe array according to claim 36, wherein the discrimination layer is disposed on the substrate side of the separator.

38. The probe array according to claim 36, wherein the separator includes the discrimination layer.

39. The probe array according to claim 36, wherein the discrimination layer is formed by printing.

40. The probe array according to claim 36, wherein the discrimination layer has a color that allows discrimination of the array regions.

41. The probe array according to claim 36, wherein the discrimination layer has one or more marks selected from letters, numbers, symbols, and graphics to allow identification of the array regions.

42. The probe array according to claim 1, wherein the probes are nucleic acid probes.

43. The probe array according to claim 1, wherein the probes are protein probes.

53. A separator comprising partitions for partitioning one or more array regions where many probes are immobilized on a substrate, wherein the separator is used for the probe array according to claim 1.

58. A method for hybridizing nucleic acid, comprising a step of supplying solutions containing nucleic acid samples under examination into the array regions of the probe array according to claim 42 to hybridize the samples under examination with the probes.

59. The hybridization method according to claim 58, wherein

the probe array has open cavities for hybridization in the array regions;

and

the hybridization step is performed under humidified conditions by supplying the solutions under examination into the open cavities.

60. A reaction method using a probe array, the method comprising a step of supplying solutions under examination into the array regions of the probe array according to claim 43 to cause a reaction with the probes.

44. A separator comprising partitions for partitioning one or more array regions where many probes are immobilized on a substrate.

45. The separator according to claim 44, wherein the substrate has a plurality of the array regions.

46. The separator according to claim 44, wherein hydrophobic regions are disposed on top surfaces of the partitions of the separator.

47. The separator according to claim 44, wherein the separator is configured so that the partitions can have different heights.

48. The separator according to claim 44, further comprising overhanging portions protruding from at least part of the tops of the partitions to above the array regions.

49. The separator according to claim 44, further comprising a discrimination layer having a color and/or image that allows discrimination of the array regions.

50. The separator according to claim 49, wherein the discrimination layer is disposed on the substrate side.

51. The separator according to claim 49, wherein the discrimination layer is formed by printing.

52. The separator according to claim 44, wherein the separator has a laminated structure.

54. A probe array having one or more array regions where many probes are immobilized, the array regions being partitioned by the separator according to claim 44.

55. The probe array according to claim 54, wherein the probe array has a plurality of the array regions.

56. A method for producing a probe array, the method comprising:

a step of immobilizing many probes in one or more array regions on a substrate; and

a step of partitioning the many probes into the array regions by attaching a separator to a surface of the substrate where the probes are immobilized, the separator including partitions capable of partitioning the surface of the substrate.

57. The production method according to claim 56, wherein a plurality of the array regions is formed.

61. A reaction method using a probe array, the method comprising:

a reaction step of causing a reaction by supplying solutions under examination into one or more array regions, partitioned by partitions having a first height, where many probes are immobilized on a substrate of the probe array; and

a subsequent step of cleaning or detection of a reaction product after the reaction step, the subsequent step being performed without the partitions present or with the height of the partitions reduced to a second height lower than the first height.

62. The reaction method according to claim 61, further comprising a step, prior to the reaction step, of forming the partitions having the first height on the substrate after the probes are immobilized on the substrate.

63. The reaction method according to claim 61, wherein

the partitions having the first height in the reaction step include overhanging portions protruding from at least part of the tops of the partitions to above the array regions;

and

the height of the partitions is reduced to the second height by removing the overhanging portions in the subsequent step.

64. The reaction method according to claim 61, wherein the partitions are formed by attaching a separator capable of partitioning the array regions to a surface of the substrate.

65. The reaction method according to claim 64, wherein the separator is a laminate.