Method for isolation of independent, parallel chemical micro-reactions using a porous filter

• US 20050009022A1
• Filed: 07/08/2002
• Published: 01/13/2005
• Est. Priority Date: 07/06/2001
• Status: Abandoned Application

• Current Assignee: Hugh C. Crenshaw, Jonathan M. Rothberg, Michael P. Weiner, Said Attiya, Stephen L. Matson
• Original Assignee: Hugh C. Crenshaw, Jonathan M. Rothberg, Michael P. Weiner, Said Attiya, Stephen L. Matson
• Inventors: Attiya, Said, Matson, Stephen L., Weiner, Michael P., Rothberg, Jonathan M., Crenshaw, Hugh C.
• Application Number:
  US10/482,491
• Publication Number:
  US 20050009022A1
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 2219/00283 Reactor vessels with top opening
• CPC Class Codes: B01J 2219/00286 Reactor vessels with top and bottom openings
• CPC Class Codes: B01J 2219/00313 the reactor vessels being formed by arrays of wells in blocks
• CPC Class Codes: B01J 2219/00355 peristaltic
• CPC Class Codes: B01J 2219/00414 using suction
• CPC Class Codes: B01J 2219/00418 using pressure
• CPC Class Codes: B01J 2219/00423 using filtration, e.g. through porous frits
• CPC Class Codes: B01J 2219/00466 in a slurry
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00524 in the shape of fiber bundles
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00677 : Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00702 : Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01J 2219/00725 : Peptides
• CPC Class Codes: C12Q 1/6869 : Methods for sequencing
• 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 60/14 : for creating libraries

Abstract

The present invention relates to the field of fluid dynamics. More specifically, this invention relates to methods and apparatus for conducting densely packed, independent chemical reactions in parallel in a substantially two-dimensional array. Accordingly, this invention also focuses on the use of this array for applications such as DNA sequencing, most preferably pyrosequencing, and DNA amplification.

Claims

1. A CMRA comprising:

(a) a microreactor element comprising an array of open microchannels or open microwells, the longitudinal axes of said microchannels or microwells arranged in a substantially parallel manner; and

(b) a porous filter element in contact with the microreactor element to form a bottom to the microchannels or microwells, thereby defining a series of reaction chambers, wherein the porous filter element comprises a permselective membrane that blocks the passage of nucleic acids, proteins and beads there across, but permits the passage of low molecular weight solutes, organic solvents and water there across.

2. The CMRA of claim 1, wherein the microreactor element comprises a plate formed from a fused fiber optic bundle, wherein the microchannels extend from the top face of the plate through to the bottom face of the plate.

3. The CMRA of claim 1 further comprising an additional porous support between the microreactor element and the porous filter element.

4. The CMRA of claim 1 wherein the porous filter element comprises an ultrafilter.

5. The CMRA of claim 1 further comprising at least one mobile solid support disposed in each of a plurality of the microchannels of the microreactor element.

6. The CMRA of claim 5 wherein the mobile solid support is a bead.

7. The CMRA of claim 1 or claim 6 wherein the mobile solid support has an enzyme and/or a nucleic acid immobilized thereon.

8. A method of making the CMRA of claim 1 comprising attaching a microreactor element to a porous filter element.

19. The UMRA of claim 1 wherein the solid support is selected from the group consisting of a bead, glass surface, fiber optic or the porous membrane.

90. A method for carrying out separate parallel independent reactions in an aqueous environment, comprising:

(a) delivering a fluid containing at least one reagent to an array, using the CMRA of claim 1 or the UMRA of claim 9, wherein each of the reaction sites immersed in a substance such that when the fluid is delivered onto each reaction site, the fluid does not diffuse onto an adjacent site;

(b) washing the fluid from the array in the time period after the starting material has reacted with the reagent to form a product in each reaction site;

(c) sequentially repeating steps (a) and (b).

91. The method of claim 90 wherein the product formed in any one reaction chamber is independent of the product formed in any other reaction chamber, but is generated using one or more common reagents.

92. The method of claim 90 wherein the starting material is a nucleic acid sequence and at least one reagent in the fluid is a nucleotide or nucleotide analog.

93. The method of claim 90 wherein the fluid additionally comprises a polymerase capable of reacting the nucleic acid sequence and the nucleotide or nucleotide analog.

94. The method of claim 90 additionally comprising repeating steps (a) and (b) sequentially.

95. The method of claim 90 wherein the substance is mineral oil.

96. The method of claim 90 wherein the reaction sites are defined by concentration polarization.

9. A UMRA comprising a porous filter element against which molecules are concentrated by concentration polarization wherein discrete reaction chambers are formed in discrete locations on the surface of or within the porous filter element by depositing reactant molecules at discrete sites on or within the porous filter element.

10. The UMRA of claim 9 wherein the reaction chambers are formed by depositing mobile solid supports having said reactant molecules immobilized thereon, on the surface of, or within, the porous element.

11. The UMRA of claim 9 wherein the porous filter element comprises an ultrafilter.

12. The UMRA of claim 9 wherein the mobile solid support is a bead.

13. The UMRA of claim 10 or claim 12 wherein the mobile solid support has an enzyme and/or a nucleic acid immobilized thereon.

14. A UMRA comprising:

(a) a porous membrane with discrete reaction sites formed by depositing mobile solid supports having said reactant molecules thereon, on the surface of, or within the porous membrane;

(b) a nucleic acid template immobilized to a solid support; and

(c) optionally, at least one immobilized enzyme.

15. The UMRA of claim 14 wherein the mobile solid support is a bead.

16. The UMRA of claim 14 wherein the porous membrane is nylon membrane.

17. The UMRA of claim 14 wherein the porous membrane is made of a woven fiber.

18. The UMRA of claim 14 wherein the porous membrane pore size at least 0.02 μ

m.

20. The UMRA of claim 14 wherein the immobilized enzyme is immobilized to a bead or the porous membrane.

21. The UMRA of claim 14 wherein the immobilized enzyme is selected from the group consisting of ATP sulfurylase, luciferase, hypoxanthine phosphoribosyltransferase, xanthine oxidase, uricase or peroxidase.

22. An array comprising:

(a) a first porous membrane with a plurality of discrete reaction sites disposed thereon, and/or within, wherein each reaction site has immobilized template adhered to the surface; and

(b) a second porous membrane with at least one enzyme located on the surface of, and/or within, the membrane, wherein the second porous membrane is in direct contact with the first porous membrane.

23. The array of claim 22 wherein the first or second membrane is a nylon membrane.

24. The array of claim 22 wherein the porous membrane is made of a woven fiber.

25. The array of claim 22 wherein the each reaction site is defined by the pores of the porous membrane.

26. The array of claim 22 wherein the first and second porous membranes have a pore size of at least 0.2 μ

m.

27. The array of claim 22 wherein the template is immobilized to a bead or to the porous membrane.

28. The array of claim 22 wherein the enzyme is selected from the group consisting of ATP sulfurylase, luciferase, hypoxanthine phosphoribosyltransferase, xanthine oxidase, uricase or peroxidase.

29. A CMRA comprising an array of open microchannels or microwells attached to a porous filter or membrane.

30. The CMRA of claim 29 further comprising a mechanical support, wherein the mechanical support separates the microchannels from the porous membrane.

31. The CMRA of claim 30 wherein the mechanical support is selected from the group consisting of plastic mesh, wire screening or molded or machined spacers.

32. The CMRA of claim 29 wherein the porous membrane is a nylon membrane.

33. The CMRA of claim 29 wherein the porous membrane is made of a woven fiber.

34. The CMRA of claim 29 wherein the membrane pore size is at least 0.02 μ

m.

35. The CMRA of claim 29 wherein the microchannels are formed by concentration polarization.

36. An apparatus for determining the nucleic acid sequence in a template nucleic acid polymer, comprising:

(a) a CMRA or UMRA;

(b) nucleic acid delivery means for introducing template nucleic acid polymers to the discrete reaction sites;

(c) nucleic acid delivery means to deliver reagents to the reaction sites to create a polymerization environment in which the nucleic acid polymers will act as template polymers for the synthesis of complementary nucleic acid polymers when nucleotides are added;

(d) convective flow delivery means to immobilize reagents to the porous membrane;

(e) detection means for detecting the formation of inorganic pyrophosphate enzymatically; and

(f) data processing means to determine the identity of each nucleotide in the complementary polymers and thus the sequence of the template polymers.

37. The apparatus of claim 36 wherein the porous membrane is a nylon membrane.

38. The apparatus of claim 36 wherein the nylon membrane is made of a woven fiber.

39. The apparatus of claim 36 wherein the pore size is at least 0.02 μ

m.

40. The apparatus of claim 36 wherein the discrete reaction sites are formed by concentration polarization.

41. The apparatus of claim 36 wherein the convective flow delivery means is a syringe or a peristaltic pump.

42. The apparatus of claim 36 wherein the template nucleic acid is attached to a solid support.

43. The apparatus of claim 42 wherein the solid support is selected from the group consisting of a bead, glass surface, fiber optic or porous membrane.

44. The apparatus of claim 36 wherein the enzyme detecting inorganic pyrophosphate is selected from the group consisting of ATP sulfurylase, luciferase, hypoxanthine phosphoribosyltransferase, xanthine oxidase, uricase or peroxidase.

45. The apparatus of claim 36 wherein the detection means is a CCD camera.

46. The apparatus of claim 36 wherein the data processing means is a computer.

47. An apparatus for processing a plurality of analytes, the apparatus comprising:

(a) a CMRA or an UMRA;

(b) fluid means for delivering processing reagents from one or more reservoirs to the flow chamber so that the analytes disposed therein are exposed to the reagents; and

(c) detection means for detecting a sequence of optical signals from each of the reaction sites, each optical signal of the sequence being indicative of an interaction between a processing reagent and the analyte disposed in the reaction site, wherein the detection means is in communication with the reaction site.

48. The apparatus of claim 47 wherein the porous membrane is a nylon membrane.

49. The apparatus of claim 47 wherein the pore size is at least 0.02 μ

m.

50. The apparatus of claim 47 wherein the template nucleic acid is attached to a solid support.

51. The apparatus of claim 50 wherein the solid support is selected from the group consisting of a bead, glass surface, fiber optic or porous membrane.

52. The apparatus of claim 47 wherein the convective flow delivery means is a peristaltic pump.

53. The apparatus of claim 47 wherein the enzyme detecting inorganic pyrophosphate is selected from the group consisting of ATP sulfurylase, luciferase, hypoxanthine phosphoribosyltransferase, xanthine oxidase, uricase or peroxidase.

54. The apparatus of claim 47 wherein the detection means is a CCD camera.

55. The apparatus of claim 47 wherein the data processing means is a computer.

58. The apparatus of claim 53 wherein the pore size is at least 0.02 μ

m.

59. The apparatus of claim 53 wherein the template nucleic acid is attached to a solid support.

60. The apparatus of claim 59 wherein the solid support is selected from the group consisting of a bead, glass surface, fiber optic or porous membrane.

61. The apparatus of claim 53 wherein the convective flow delivery means is a peristaltic pump.

62. The apparatus of claim 53 wherein the enzyme detecting inorganic pyrophosphate is selected from the group consisting of ATP sulfurylase, luciferase, hypoxanthine phosphoribosyltransferase, xanthine oxidase, uricase or peroxidase.

63. The apparatus of claim 53 wherein the detection means is a CCD camera.

64. The apparatus of claim 53 wherein the data processing means is a computer.

56. An apparatus for determining the base sequence of a plurality of nucleotides on an array, the apparatus comprising:

(a) a CMRA or UMRA;

(b) reagent delivery means for adding an activated nucleotide 5′

-triphosphate precursor of one known nitrogenous base to a reaction mixture to each reaction site, each reaction mixture comprising a template-directed nucleotide polymerase and a single-stranded polynucleotide template hybridized to a complementary oligonucleotide primer strand at least one nucleotide residue shorter than the templates to form at least one unpaired nucleotide residue in each template at the 3′

-end of the primer strand, under reaction conditions which allow incorporation of the activated nucleoside 5′

-triphosphate precursor onto the 3′

-end of the primer strands, provided the nitrogenous base of the activated nucleoside 5′

-triphosphate precursor is complementary to the nitrogenous base of the unpaired nucleotide residue of the templates;

(c) detection means for detecting whether or not the nucleoside 5′

-triphosphate precursor was incorporated into the primer strands in which incorporation of the nucleoside 5′

-triphosphate precursor indicates that the unpaired nucleotide residue of the template has a nitrogenous base composition that is complementary to that of the incorporated nucleoside 5′

-triphosphate precursor; and

(d) means for sequentially repeating steps (b) and (c), wherein each sequential repetition adds and detects the incorporation of one type of activated nucleoside 5′

-triphosphate precursor of known nitrogenous base composition; and

(e) data processing means for determining the base sequence of the unpaired nucleotide residues of the template in each reaction chamber from the sequence of incorporation of said nucleoside precursors.

57. The apparatus of claim 56 wherein the porous membrane is a nylon membrane.

65. An apparatus for determining the nucleic acid sequence in a template nucleic acid polymer, comprising:

(a) a CMRA or UMRA;

(b) nucleic acid delivery means for introducing a template nucleic acid polymers onto the reaction sites;

(c) nucleic acid delivery means to deliver reagents to the reaction chambers to create polymerization environment in which the nucleic acid polymers will act as a template polymers for the synthesis of complementary nucleic acid polymers when nucleotides are added;

(d) reagent delivery means for successively providing to the polymerization environment a series of feedstocks, each feedstock comprising a nucleotide selected from among the nucleotides from which the complementary nucleic acid polymer will be formed, such that if the nucleotide in the feedstock is complementary to the next nucleotide in the template polymer to be sequenced said nucleotide will be incorporated into the complementary polymer and inorganic pyrophosphate will be released;

(e) detection means for detecting the formation of inorganic pyrophosphate enzymatically; and

(f) data processing means to determine the identity of each nucleotide in the complementary polymers and thus the sequence of the template polymers.

66. The apparatus of claim 65 wherein the porous membrane is a nylon membrane.

67. The apparatus of claim 65 wherein the pore size is at least 0.02 μ

m.

68. The apparatus of claim 65 wherein the template nucleic acid is attached to a solid support.

69. The apparatus of claim 68 wherein the solid Support is selected from the group consisting of a bead, glass surface, fiber optic or porous membrane.

70. The apparatus of claim 65 wherein the convective flow delivery means is a peristaltic pump.

71. The apparatus of claim 65 wherein the enzyme detecting inorganic pyrophosphate is selected from the group consisting of ATP sulfurylase, luciferase, hypoxanthine phosphoribosyltransferase, xanthine oxidase, uricase or peroxidase.

72. The apparatus of claim 65 wherein the detection means is a CCD camera.

73. The apparatus of claim 65 wherein the data processing means is a computer.

74. A system for sequencing a nucleic acid comprising the following components:

(a) a CMRA or UMRA;

(b) at least one enzyme immobilized on a solid support;

(c) means for flowing reagents over said porous membrane;

(d) means for detection; and

(e) means for determining the sequence of the nucleic acid.

75. The system of claim 74 wherein the porous membrane is a nylon membrane.

76. The system of claim 74 wherein the porous membrane has a pore size is at least 0.02 μ

m.

77. The system of claim 74 wherein the reaction sites are formed by concentration polarization.

78. The system of claim 74 wherein the immobilized enzyme is selected from the group consisting of ATP sulfurylase, luciferase, hypoxanthine phosphoribosyltransferase, xanthine oxidase, uricase or peroxidase.

79. The system of claim 74 wherein the solid support is selected from the group consisting of a bead, glass surface, fiber optic or porous membrane.

80. The system of claim 74 wherein the means for detection is a CCD camera.

81. The system of claim 74 wherein the means for determining a sequence is by pyrophosphate sequencing.

82. A system for sequencing a nucleic acid comprising the following components:

(a) a CMRA or UMRA

(b) at least one enzyme immobilized on a solid support;

(c) means for flowing reagents over said porous membrane;

(d) means for enzymatic detection; and

(e) means for determining the sequence of the nucleic acid.

83. The system of claim 82 wherein the porous membrane is a nylon membrane.

84. The system of claim 82 wherein the porous membrane has a pore size is at least 0.02 μ

m.

85. The system of claim 82 wherein the reaction sites are formed by concentration polarization.

86. The system of claim 82 wherein the immobilized enzyme is selected from the group consisting of ATP sulfurylase, luciferase, hypoxanthine phosphoribosyltransferase, xanthine oxidase, uricase or peroxidase.

87. The system of claim 82 wherein the solid support is selected from the group consisting of a bead, glass surface, fiber optic or porous membrane.

88. The system of claim 82 wherein the means for detection is a CCD camera.

89. The system of claim 82 wherein the means for determining a sequence is by pyrophosphate sequencing.

97. A method of determining the base sequence of nucleotides in an array format, the method comprising the steps of:

(a) adding an activated nucleoside 5′

-triphopsphate precursor of one known nitrogenous base composition to a plurality of reaction sites localized on a CMRA or UMRA, wherein the reaction site is comprised of a template-directed nucleotide polymerase and a heterogenous population of single stranded templates hybridized to complementary oligonucleotide primer strands at least one nucleotide residue shorter than the templates to form at least one unpaired nucleotide residue in each template at the 3′

end of the primer strand under reaction conditions which allow incorporation of the activated nucleoside 5′

-triphosphate precursor onto the 3′

end of the primer strand under reaction conditions which allow incorporation of the activated nucleoside 5′

-triphosphate precursor onto the 3′

end of the primer strands, provided the nitrogenous base of the activated nucleoside 5′

-triphosphate precursor is complementary to the nitrogenous base of the unpaired nucleotide residue of the templates;

(b) detecting whether or not the nucleoside 5′

-triphosphate precursor was incorporated into the primer strands in which incorporation of the nucleoside 5′

-triphosphate precursor indicates that the unpaired nucleotide residue of the template has a nitrogenous base composition that is complementary to that of the incorporated nucleoside 5′

-triphosphate precursor; and

(c) sequentially repeating steps (a) and (b), wherein each sequential repetition adds and detects the incorporation of one type of activated nucleoside 5′

-triphosphate precursor of known nitrogenous base composition;

(d) determining the base sequence of the unpaired nucleotide residues of the template from the sequence of incorporation of said nucleoside precursors.

98. The method of claim 97 wherein the detection of the incorporation of the activated precursor is accomplished enzymatically.

99. The method of claim 98 wherein the enzyme is selected from the group consisting of ATP sulfurylase, luciferase, hypoxanthine phosphoribosyltransferase, xanthine oxidase, uricase or peroxidase.

100. The method of claim 97 wherein the enzyme is immobilized to a solid support.

101. The method of claim 97 wherein the solid support is selected from the group comprising a bead, glass surface, fiber optic or porous membrane.

102. A method of determining the base sequence of a plurality of nucleotides on an array, said method comprising:

(a) providing a plurality of sample DNA'"'"'s, each disposed within a plurality of reaction sites on a CMRA or UMRA;

(b) detecting the light level emitted from a plurality of reaction sites on respective proportional of an optically sensitive device;

(c) converting the light impinging upon each of said portions of said optically sensitive device into an electrical signal which is distinguishable from the signals from all of said other regions;

(d) determining a light intensity for each of said discrete regions from the corresponding electrical signal;

(e) recording the variations of said electrical signals with time.

103. The method of claim 102 wherein the porous membrane is a nylon membrane.

104. The method of claim 102 wherein the pore size is at least 0.2 μ

m.

105. The method of claim 102 wherein the detection is performed enzymatically.

106. The method of claim 105 wherein the enzyme is selected from the group consisting of ATP sulfurylase, luciferase, hypoxanthine phosphoribosyltransferase, xanthine oxidase, uricase or peroxidase.