Articles having localized molecules disposed thereon and methods of producing same

• US 20080032301A1
• Filed: 03/29/2007
• Published: 02/07/2008
• Est. Priority Date: 03/30/2006
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Wegener, Jeffery, Peluso, Paul, Otto, Geoff, Turner, Stephen, Lyle, John, Roitman, Daniel, Xu, Yue, Korlach, Jonas, Rank, David
• Granted Patent: US 8,802,600 B2
• 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 2219/00427 using masks
• CPC Class Codes: B01J 2219/0045 using optical fibres
• 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 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00635 by reactive plasma treatment
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00639 the compounds being trapped in or bound to a porous medium
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B82Y 20/00 Nanooptics, e.g. quantum optics or photonic crystals
• 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
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2527/127 the enzyme inhibitor or activator used
• CPC Class Codes: C12Q 2565/629 being a microfluidic device
• CPC Class Codes: Y10T 29/49002 : Electrical device making

Abstract

Methods of producing substrates having selected active chemical regions by employing elements of the substrates in assisting the localization of active chemical groups in desired regions of the substrate. The methods may include optical, chemical and/or mechanical processes for the deposition, removal, activation and/or deactivation of chemical groups in selected regions of the substrate to provide selective active regions of the substrate.

Claims

1. A method of producing a substrate having selectively active regions thereon, comprising:

providing a substrate having a plurality of nanostructures defined thereon, wherein each of the nanostructures limits an ability of a first activation controlling agent to provide active chemical groups on selected portions of a surface of the substrate; and

exposing the substrate to at least the first activation controlling agent to selectively provide active chemical groups on the selected portions of the surface of the substrate.

2-30. -30. (canceled)

31. A method of preparing an analytical substrate having selected active regions thereon, comprising:

providing a substrate having an optical analysis structure disposed thereon, the optical analysis structure providing enhanced optical access to selected regions of the substrate;

providing surface functional groups capable of being activated or deactivated by a first electromagnetic radiation;

directing the first electromagnetic radiation at the substrate whereby the optical analysis structure directs the electromagnetic radiation to selectively activate or deactivate the surface functional groups in the selected regions of the substrate to provide selectively active regions of the substrate.

32. A method of providing a zero mode waveguide having an active chemical surface substantially at a bottom portion of the waveguide, comprising:

providing a zero mode waveguide disposed in a substrate;

providing functional chemical groups on surfaces of the zero mode waveguide; and

exposing first portions, but not second portions, of the surfaces of the zero mode waveguide to an activation controlling agent that selectively activates or deactivates the functional chemical groups on the first portions to provide an active chemical surface substantially at a bottom portion of the zero mode waveguide.

33. A zero mode waveguide array, comprising:

a plurality of zero mode waveguide cores disposed in a cladding layer, each core having a bottom surface; and

a chemically active surface substantially only within the cores.

34. (canceled)

35. A method of providing a substrate having selected active regions disposed thereon, comprising:

providing a substrate having an optical enhancement structure defined thereon, the optical enhancement structure being capable of directing electromagnetic radiation to provide an enhanced electromagnetic field proximal to a selected region of the substrate surface sufficient to create a trapping force proximal to the selected region;

directing electromagnetic radiation at the substrate to provide the enhanced electromagnetic field at the selected region sufficient to create a trapping force upon an active molecule proximal to the selected region; and

coupling the active molecule to the selected region.

36. A method of producing a substrate having selected active regions disposed thereon, comprising:

providing a substrate having a surface comprised of chemical functional groups, and a plurality of discrete nanoscale reaction regions defined thereon; and

patterning one or more of a chemical functional group or an activation controlling agent onto the surface in selected regions to provide active chemical functional regions substantially only in the discrete nanoscale reaction regions.

37-39. -39. (canceled)

40. A method of identifying a sequence of a nucleic acid molecule, comprising:

providing a plurality of nucleic acid polymerase/template/primer complexes within discrete observation regions on a substrate, and detecting sequential addition of nucleotides or nucleotide analogs in a template dependent manner to identify a sequence of incorporation of the nucleotides or nucleotide analogs in the plurality of observation regions;

wherein the substrate has been prepared to substantially reduce one or more of polymerase activity, polymerase presence, template presence and primer presence in regions outside of the observation regions.

41. A method of identifying a sequence of a nucleic acid molecule, comprising:

providing a plurality of nucleic acid polymerase/template/primer complexes within discrete observation regions on a substrate surface, and detecting sequential addition of nucleotides or nucleotide analogs in a template dependent manner to identify a sequence of incorporation of the nucleotides or nucleotide analogs in the plurality of observation regions;

providing an intra-observation region barrier upon the substrate surface between at least first and second discrete observation regions to substantially prevent intra-observation region diffusion of one or more reactants or products.

42-45. -45. (canceled)

46. A method of preferentially localizing desired molecules within an optical confinement disposed upon a substrate, comprising:

depositing the desired molecules over the surface of the substrate; and

selectively removing the desired molecules from the surface of the substrate that is not within the optical confinement.

47. The method of claim 46, wherein the substrate comprises an opaque layer and a transparent layer, and wherein the optical confinement comprises a zero mode waveguide disposed through the opaque layer to the transparent layer.

48. The method of claim 46, wherein selectively removing the desired molecules from the surface of the substrate that is not within the optical confinement comprises contacting the substrate with a deactivation component coupled to an exclusionary component, which exclusionary component is at least partially excluded from entering into the optical confinement.

49. The method of claim 48, wherein the deactivation component comprises an enzyme.

50. The method of claim 49, wherein the enzyme is selected from the group consisting of a protease, a nuclease, and a carbohydrase.

51. The method of claim 50, wherein the enzyme is a site-specific protease.

52. The method of claim 48, wherein the exclusionary component is a large particle or a macromolecule.

53. The method of claim 52, wherein the exclusionary component comprises a bead.

54. The method of claim 52, wherein the exclusionary component comprises a rigid or semi-rigid elongated polymer.

55. The method of claim 52, wherein the exclusionary component comprises a double-stranded nucleic acid molecule.

56. The method of claim 48, wherein the deactivation component is a protease and the exclusionary component is a double-stranded DNA molecule.

57. The method of claim 46, wherein the desired molecules are enzymes.

58. The method of claim 46, wherein the desired molecules comprise binding moieties.

59. The method of claim 58, wherein the desired molecules are biotin molecules.

60. A method of localizing a molecule within an optical confinement disposed on a substrate, comprising:

providing a light activated coupling group on the surface of the substrate, including within the optical confinement;

directing activating radiation at the substrate, wherein the optical confinement permits activation radiation to be incident only within the optical confinement; and

coupling the molecule to the light activated coupling group.

61. A method of selectively immobilizing a molecule of interest on a substrate, comprising:

providing a substrate having a first surface component and a second surface component where the first and second surface component have different surface characteristics; and

selectively coupling the molecule of interest to the first surface component, based upon a difference between the surface characteristics of the first surface component and the surface characteristics of the second surface component.

62. The method of claim 61, wherein the first surface component comprises SiO₂ and the second surface component comprises a metal or metal oxide.

63. The method of claim 61, wherein the differing surface characteristics comprise surface charge.

64. The method of claim 63, wherein the first surface component has a negative surface charge and the second surface component has a positive surface charge.

65. The method of claim 61, wherein the substrate comprises a layer of the second surface component on a layer of the first surface component, and wherein the substrate comprises a zero mode waveguide disposed through the second surface component layer to the first surface component layer.

66. The method of claim 61, wherein the molecule of interest associates preferentially to the first surface component.

67. The method of claim 61, wherein the substrate is contacted with a first composition that selectively associates with the first surface component based upon the difference between the surface characteristics of the first and second surface components.

68. The method of claim 67, wherein the first composition comprises a first coupling group, and wherein selectively coupling the molecule of interest to the first surface component comprises coupling the molecule of interest to the first coupling group.

69. The method of claim 68, wherein the first coupling group comprises biotin.

70. The method of claim 67, wherein the first composition comprises a silane.

71. The method of claim 70, wherein the first composition comprises a biotin-PEG-silane.

72. The method of claim 67, wherein the first composition comprises a phospholipid.

73. The method of claim 67, wherein the first composition comprises poly(L-lysine)-poly(ethylene glycol) or poly(L-lysine)-poly(ethylene glycol)-biotin.

74. The method of claim 61, comprising contacting the substrate with a second composition that selectively associates with the second surface component based upon the difference between the surface characteristics of the first and second surface components.

75. The method of claim 74, wherein the second composition comprises a polyelectrolyte.

76. The method of claim 74, wherein the second composition comprises a polyelectrolyte-PEG copolymer.

77. The method of claim 74, comprising depositing a polyelectrolyte multilayer on the second surface component.

78. The method of claim 74, wherein the second composition comprises a compound comprising one or more phosphonic acid groups.

79. The method of claim 78, wherein the second composition is polyvinylphosphonic acid.

80. The method of claim 78, wherein the second composition is selected from the group consisting of:

81. The method of claim 78, wherein the second composition is selected from the group consisting of:

2-carboxyethyl phosphonic acid;

amino tri(methylene phosphonic acid);

1-hydroxyethylidene-1,1-diphosphonic acid;

hexamethylenediaminetetra (methylenephosphonic acid);

diethylenetriamine penta(methylene phosphonic acid);

ethylenediamine tetra(methylene phosphonic acid);

bis(hexamethylene triamine penta(methylenephosphonic acid));

2-phosphonobutane-1,2,4-tricarboxylic acid; and

monoethanolamine diphosphonate.

82. The method of claim 74, wherein the second composition comprises a compound comprising one or more phosphate groups.

83. The method of claim 74, wherein the second composition comprises an alkyl phosphate or an alkyl phosphonate.

84. The method of claim 74, wherein the second composition is selected from the group consisting of:

octyl phosphonic acid, decyl phosphonic acid, dodecyl phosphonic acid, hexadecyl phosphonic acid, octadecyl phosphonic acid, docosyl phosphonic acid, hydroxy-dodecyl phosphonic acid, hydroxy-undecenyl-phosphonic acid, decanediylbis(phosphonic acid), dodecylphosphate, and hydroxy-dodecylphosphate.

85. The method of claim 74, wherein the second composition comprises a second coupling group.

86. The method of claim 61, wherein selectively coupling the molecule of interest to the first surface component comprises contacting the substrate with a first composition that selectively associates with the first surface component and coupling the molecule of interest to the first composition;

the method further comprising contacting the substrate with a second composition that selectively associates with the second surface component.

87. A method of selectively depositing a molecule of interest on selected regions of a substrate, comprising:

providing a substrate having first and second components, the first component comprising a conductive material and the second component comprising an insulator; and

applying an electrical potential to the first component so as to increase or decrease association of a molecule of interest with a surface of the first component.