Combinatorial strategies for polymer synthesis

• US 7,691,330 B1
• Filed: 05/26/2000
• Issued: 04/06/2010
• Est. Priority Date: 11/22/1991
• 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., Modlin, Douglas N., Ross, Debra A., Aldwin, Lois, Fodor, Stephen P. A., Buchko, Christopher J.
• Primary Examiner(s): Ludlow; Jan M
• Application Number:
  US09/579,982
• Time in Patent Office: 3,602 Days
• Field of Search: 436/180, 436/89, 436/94, 422/100, 141/31, 738/63, 738/64, 738/648.1
• US Class Current: 422/502
• 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 2219/00364 Pipettes
• CPC Class Codes: B01J 2219/00367 capillary
• CPC Class Codes: B01J 2219/00369 in multiple or parallel arrangements
• CPC Class Codes: B01J 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00389 Feeding through valves
• CPC Class Codes: B01J 2219/00416 Vacuum
• CPC Class Codes: B01J 2219/0043 for direct application of reagents, e.g. through openings in a shutter
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00475 Sheets
• CPC Class Codes: B01J 2219/005 Beads
• 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 2219/00585 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 2219/00619 : using hydrophilic or hydrophobic regions
• 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 2219/00659 : Two-dimensional arrays
• CPC Class Codes: B01J 2219/00686 : Automatic
• CPC Class Codes: B01J 2219/00702 : Processes involving means for analysing and characterising the products
• 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: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07B 2200/11 : Compounds covalently bound to a solid support
• 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: C07K 1/045 : using devices to improve synthesis, e.g. reactors, special vessels
• CPC Class Codes: C07K 1/047 : Simultaneous synthesis of different peptide species; Peptide libraries
• 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
• CPC Class Codes: G01N 35/1072 : with provision for selective pipetting of individual channels
• CPC Class Codes: Y10S 436/809 : Multifield plates or multicontainer arrays
• CPC Class Codes: Y10T 436/143333 : Saccharide [e.g., DNA, etc.]
• CPC Class Codes: Y10T 436/25 : including sample preparation
• CPC Class Codes: Y10T 436/255 : including use of a solid sorbent, semipermeable membrane, or liquid extraction
• CPC Class Codes: Y10T 436/2575 : Volumetric liquid transfer

Abstract

A method and device for forming large arrays of polymers on a substrate (401). According to a preferred aspect of the invention, the substrate is contacted by a channel block (407) having channels (409) therein. Selected reagents are delivered through the channels, the substrate is rotated by a rotating stage (403), and the process is repeated to form arrays of polymers on the substrate. The method may be combined with light-directed methodolgies.

Claims

1. An automated apparatus for forming an array of ligands on a support having localized areas, comprising:

one or more dispensers supplied with one or more solutions of a monomer or polymer,

wherein the one or more dispensers is operative to dispense a volume of solution in a single coupling step of less than 5 nl at a distance away from a localized area,

a support having a surface and having a density of localized areas at least about 1000 localized areas per cm², and

a positioning system having a translational controller configured to repeatedly position the dispenser relative to individual localized areas on the support with the one or more dispensers dispensing the one or more solutions of the monomer or polymer for attachment at the individual localized areas until an array of at least 100 different ligands each at individual localized areas is formed.

2. The apparatus of claim 1 wherein the monomer or polymer is dissolved in the solution.

3. The apparatus of claim 1 wherein the dispenser is operative to contact the support.

4. The apparatus of claim 1 wherein the support further comprises a cover plate.

5. The apparatus of claim 1 wherein the positioning system is capable of positioning the dispenser between 5 microns and 50 microns away from the support.

6. The apparatus of claim 1 wherein the positioning system is capable of positioning the dispenser 10 microns away from the support.

7. The apparatus of claim 1 wherein the volume fits within a region on the support having a diameter of less than 300 microns.

8. The apparatus of claim 1 wherein the monomer comprises a nucleotide or an amino acid.

9. The apparatus of claim 1 wherein the polymer comprises a nucleic acid, oligonucleotide, polynucleotide, peptide, polypeptide, receptor, enzyme, antibody, catalytic polypeptide, hormone receptor, or opiate receptor.

10. The apparatus of claim 1 wherein the polymer comprises at least 2 monomers.

11. The apparatus of claim 1 wherein the polymer comprises greater than 100 monomers.

12. The apparatus of claim 1 wherein the polymer comprises at least 2, 3, 4, 5, 6, 10, 15, 20, 30, 40, 50, 75, or 100 monomers.

13. The apparatus of claim 1 wherein the support is selected from the group consisting of substantially flat substrates, substrates having raised or depressed regions, beads, gels, sheets, particles, strands, precipitates, spheres, containers, capillaries, pads, slices, films, plates, and slides.

14. The apparatus of claim 1 wherein the support comprises a gel.

15. The apparatus of claim 1 wherein the support comprises biological materials, nonbiological materials, organic materials or inorganic materials.

16. The apparatus of claim 1 wherein the support is a disc, square, or circle.

17. The apparatus of claim 1 wherein the localized area is smaller than 1 mm².

18. The apparatus of claim 1 wherein the localized area is smaller than 0.5 mm².

19. The apparatus of claim 1 wherein the localized area is smaller than 10,000 μ

m².

20. The apparatus of claim 1 wherein the localized area is smaller than 100 μ

m².

21. The apparatus of claim 1 wherein the array includes ligands that are at least 5% pure in their respective localized areas.

22. The apparatus of claim 1 wherein the array includes ligands that are at least between 10% and 20% pure in their respective localized areas.

23. The apparatus of claim 1 wherein the array includes ligands that are at least between 80% and 90% pure in their respective localized areas.

24. The apparatus of claim 1 wherein the array includes ligands that are at least greater than 95% pure in their respective localized areas.

25. The apparatus of claim 1 wherein the array includes at least 1000 different ligands at different localized areas.

26. The apparatus of claim 1 wherein the array includes at least 10,000 different ligands at different localized areas.

27. The apparatus of claim 1 wherein the array includes at least 100,000 different ligands at different localized areas.

28. The apparatus of claim 1 wherein the array includes at least 1,000,000 different ligands at different localized areas.

29. The apparatus of claim 1, wherein the array includes at least 1000 different ligands occupying localized areas within 1 cm² of the surface of the support.

30. The apparatus of claim 1, wherein the support comprises glass, derivatized glass, borosilicate glass, quartz, a polymeric material, polystyrene, polycarbonate, silicon or a gel.

31. The apparatus of claim 1, wherein the solution of the monomer or polymer comprises an aqueous solution.

32. The apparatus of claim 1 wherein the apparatus includes a plurality of dispensers.

33. The apparatus of claim 1, wherein the support bears at least two reference points for positioning the dispenser over at least one of said localized areas for release of said volume of solution.

34. The apparatus of claim 33, wherein the reference points comprise global reference points for positioning the dispenser over a local region of the surface of the support, and local reference points within the local region for positioning the dispenser over a localized area within the local region.

35. The apparatus of claim 33, wherein the dispenser further comprises a camera for identifying the reference points.

36. The apparatus of claim 33 further comprising a device for sensing changes in capacitance to identify the reference points.

37. The apparatus of claim 33 further comprising a device for sensing changes in light intensity to identify the reference points.

38. The apparatus of claim 33 further comprising a device for sensing changes in resistivity to identify the reference points.

39. The apparatus of claim 33 further comprising a device for sensing changes in optical properties to identify the reference points.

40. The apparatus of claim 33 further comprising a device for sensing changes in magnetic properties to identify the reference points.

41. The apparatus of claim 32 wherein the plurality of dispensers comprises a manifold of delivery lines.

42. The apparatus of claim 32 wherein the plurality of dispensers comprises an array of pipettes.

43. The apparatus of claim 32 wherein the plurality of dispensers comprises a series of tubes.

44. The apparatus of claim 32 wherein the plurality of dispensers includes control valves.

45. The apparatus of claim 1 wherein the support includes linker molecules.

46. The apparatus of claim 1 wherein the dispenser is moveable relative to the support.

47. The apparatus of claim 1 wherein the support is moveable relative to the dispenser.

48. The apparatus of claim 1 wherein the one or more localized areas are spaced less than 3 mm apart.

49. The apparatus of claim 1 wherein the one or more localized areas are spaced less than between 5 microns and 100 microns apart.

50. The apparatus of claim 1 wherein the one or more localized areas has an angular relation between each localized area of about 1 degree.

51. The apparatus of claim 1 wherein the one or more localized areas has an angular relation between each localized area of about 0.1 degree.

52. The apparatus of claim 1 wherein the support comprises at least 100 localized areas.

53. The apparatus of claim 1 wherein the support comprises at least 1000 localized areas.

54. The apparatus of claim 1 wherein the support comprises at least 10,000 localized areas.

55. The apparatus of claim 1 wherein the support comprises at least 10,000 localized areas per cm² of surface of substrate.

56. The apparatus of claim 1 wherein the support comprises a strand including one or more of glass, derivatized glass, quartz, or a polymeric material.

57. The apparatus of claim 1 wherein the dispenser comprises a dispenser tip and a sheath encircling the dispenser tip and rigidly extending a fixed distance beyond the dispenser tip.

58. The apparatus of claim 1 wherein the surface of the support comprises a hydrophilic or hydrophobic substance.

59. The apparatus of claim 1 wherein the surface of the support comprises a photoresist.

60. The apparatus of claim 1 wherein the surface of the support is pretreated.

61. The apparatus of claim 1 wherein the dispenser comprises a pipette.

62. The apparatus of claim 1 wherein the dispenser comprises a capillary tube.

63. The apparatus of claim 1 wherein the dispenser comprises an osmotic pump.

64. The apparatus of claim 1 wherein the dispenser comprises a cell sorter.

65. The apparatus of claim 1, wherein the array includes at least 10,000 different polymers occupying localized areas within 1 cm² of the surface of the support.

66. The apparatus of claim 1 wherein the dispenser and the substrate have a common frame of reference.

67. The apparatus of claim 1 wherein the dispenser is coupled to a translational mechanism.

68. The apparatus of claim 67 wherein the translational mechanism moves at a rate of 3 to 10 stops per second.

69. The apparatus of claim 68 wherein the translational mechanism is accurate within 1 μ

m.

70. The apparatus of claim 67 wherein the translational mechanism includes a closed loop position feedback mechanism.

71. The apparatus of claim 67 wherein the translational mechanism operates with insignificant backlash.

72. The apparatus of claim 67 wherein the translational mechanism is an electro-mechanical mechanism.

73. The apparatus of claim 72 wherein the electro-mechanical mechanism has a greater than 1 μ

m repeatability relative to reaction region diameter travel distance.

74. The apparatus of claim 1 wherein the dispenser is operative to repeatedly perform single coupling steps wherein each coupling step dispenses droplets no greater than 5 nl to the same or a different localized area.

75. The apparatus of claim 33 including a laser for locating a reference point.

76. An automated apparatus for forming an array of ligands on a support having localized areas, comprising:

an array of dispensing units supplied with one or more solutions of a monomer or polymer,

wherein the dispensing units are operative to dispense droplets in a single coupling step of no greater than 5 nl at a distance away from a localized area,

a support having a surface and having a density of localized areas at least about 1000 localized areas per cm², and

a positioning system including a translational controller capable of repeatedly positioning the dispensing units relative to individual localized areas on the support with the dispensing units dispensing the one or more solutions of the monomer or polymer for attachment at the individual localized areas until an array of at least 100 different ligands each at individual localized areas is formed.

77. The apparatus of claim 76 wherein the monomer or polymer is dissolved in the solution.

78. The apparatus of claim 76 wherein the dispenser is operative to contact the support.

79. The apparatus of claim 76 wherein the droplet fits within a region on the support having a diameter of less than 300 microns.

80. The apparatus of claim 76 wherein the monomer comprises a nucleotide or an amino acid.

81. The apparatus of claim 76 wherein the polymer comprises a nucleic acid, oligonucleotide, polynucleotide, peptide, polypeptide, receptor, enzyme, antibody, catalytic polypeptide, hormone receptor, or opiate receptor.

82. The apparatus of claim 76 wherein the polymer comprises at least 2 monomers.

83. The apparatus of claim 76 wherein the polymer comprises greater than 100 monomers.

84. The apparatus of claim 76 wherein the polymer comprises 2, 3, 4, 5, 6, 10, 15, 20, 30, 40, 50, 75, or 100 monomers.

85. The apparatus of claim 76 wherein the support is selected from the group consisting of substantially flat substrates, substrates having raised or depressed regions, beads, gels, sheets, particles, strands, precipitates, spheres, containers, capillaries, pads, slices, films, plates, and slides.

86. The apparatus of claim 76 wherein the support comprises a gel.

87. The apparatus of claim 76 wherein the support comprises biological materials, nonbiological materials, organic materials or inorganic materials.

88. The apparatus of claim 76 wherein the support is a disc, square, or circle.

89. The apparatus of claim 76 wherein the localized area is smaller than 1 mm².

90. The apparatus of claim 76 wherein the localized area is smaller than 0.5 mm².

91. The apparatus of claim 76 wherein the localized area is smaller than 10,000 μ

m².

92. The apparatus of claim 76 wherein the localized area is smaller than 100 μ

m².

93. The apparatus of claim 76 wherein the array of substances includes at least 100 different polymers at different localized areas.

94. The apparatus of claim 76 wherein the array of ligands includes at least 1000 different polymers at different localized areas.

95. The apparatus of claim 76 wherein the array of ligands includes at least 10,000 different polymers at different localized areas.

96. The apparatus of claim 77 wherein the array of ligands includes at least 100,000 different polymers at different localized areas.

97. The apparatus of claim 78 wherein the array of ligands includes at least 1,000,000 different polymers at different localized areas.

98. The apparatus of claim 76, wherein the array of ligands includes at least 1000 different polymers occupying localized areas within 1 cm² of the surface of the support.

99. The apparatus of claim 76, wherein the support comprises glass, derivatized glass, borosilicate glass, quartz, a polymeric material, polystyrene, polycarbonate, silicon or a gel.

100. The apparatus of claim 76, wherein the solution comprises an aqueous solution.

101. The apparatus of claim 76, wherein the support bears at least two reference points for positioning the dispenser over at least one of said localized areas for release of said droplet.

102. The apparatus of claim 101, wherein the reference points comprise global reference points for positioning the dispenser over a local region of the surface of the support, and local reference points within the local region for positioning the dispenser over a localized area within the local region.

103. The apparatus of claim 101, wherein the dispenser further comprises a camera for identifying the reference points.

104. The apparatus of claim 101 further comprising a device for sensing changes in capacitance to identify the reference points.

105. The apparatus of claim 101 further comprising a device for sensing changes in light intensity to identify the reference points.

106. The apparatus of claim 101 further comprising a device for sensing changes in resistivity to identify the reference points.

107. The apparatus of claim 101 further comprising a device for sensing changes in optical properties to identify the reference points.

108. The apparatus of claim 101 further comprising a device for sensing changes in magnetic properties to identify the reference points.

109. The apparatus of claim 76 wherein the array of dispensing units comprises a manifold of delivery lines.

110. The apparatus of claim 76 wherein the array of dispensing units comprises an array of pipettes.

111. The apparatus of claim 76 wherein the array of dispensing units comprises a series of tubes.

112. The apparatus of claim 76 wherein the array of dispensing units is moveable relative to the support.

113. The apparatus of claim 76 wherein the support is moveable relative to the array of dispensing units.

114. The apparatus of claim 76 wherein the one or more localized areas are spaced less than 3 mm apart.

115. The apparatus of claim 76 wherein the one or more localized areas are spaced less than between 5 microns and 100 microns apart.

116. The apparatus of claim 76 wherein the one or more localized areas has an angular relation between each localized area of about 1 degree.

117. The apparatus of claim 76 wherein the one or more localized areas has an angular relation between each localized area of about 0.1 degree.

118. The apparatus of claim 76 wherein the support comprises at least 100 localized areas.

119. The apparatus of claim 76 wherein the support comprises at least 1000 localized areas.

120. The apparatus of claim 76 wherein the support comprises at least 10,000 localized areas.

121. The apparatus of claim 76 wherein the support comprises at least 10,000 localized areas per cm² of surface of substrate.

122. The apparatus of claim 76 wherein the support comprises a strand including one or more of glass, derivatized glass, quartz, or a polymeric material.

123. The apparatus of claim 76 wherein the surface of the support comprises a hydrophilic or hydrophobic substance.

124. The apparatus of claim 76 wherein the surface of the support comprises a photoresist.

125. The apparatus of claim 76 wherein the surface of the support is pretreated.

126. The apparatus of claim 76, wherein the array of substances includes at least 10,000 different polymers occupying localized areas within 1 cm² of the surface of the support.

127. The apparatus of claim 76 including a laser for locating a reference point.

128. An automated apparatus for forming an array of polypeptides or polynucleotides on a support having localized areas, comprising:

one or more dispensers supplied with plural solutions of polypeptides or polynucleotides,

wherein the one or more dispensers is operative to dispense a volume of the plural solutions in a single coupling step of less than 5 nl at a distance away from a localized area,

a support having a density of localized areas at least about 1000 localized areas per cm², and

a positioning system including a translation controller configured to repeatedly position the one or more dispensers relative to individual localized areas on the support with the one or more dispensers dispensing the plural solutions of the polypeptides or polynucleotides for attachment at the individual localized areas until an array of at least 1000 different ligands each at individual localized areas is formed.

129. The apparatus of claim 128 wherein the dispenser is operative to contact the support.

130. The apparatus of claim 128 wherein the positioning system is capable of positioning the dispenser between 5 microns and 50 microns away from the support.

131. The apparatus of claim 128 wherein the volume fits within a region on the support having a diameter of less than 300 microns.

132. The apparatus of claim 128 wherein the polypeptide or polynucleotide comprises at least 2, 3, 4, 5, 6, 10, 15, 20, 30, 40, 50, 75, or 100 monomers.

133. The apparatus of claim 128 wherein the support is selected from the group consisting of substantially flat substrates, substrates having raised or depressed regions, beads, gels, sheets, particles, strands, precipitates, spheres, containers, capillaries, pads, slices, films, plates, and slides.

134. The apparatus of claim 128 wherein the support comprises a gel.

135. The apparatus of claim 128 wherein the localized area is smaller than 0.5 mm².

136. The apparatus of claim 128 wherein the localized area is smaller than 10,000 μ

m².

137. The apparatus of claim 128 wherein the apparatus includes a plurality of dispensers.

138. The apparatus of claim 137 wherein the plurality of dispensers comprises a manifold of delivery lines.

139. The apparatus of claim 137 wherein the plurality of dispensers comprises an array of pipettes.

140. The apparatus of claim 137 wherein the plurality of dispensers comprises a series of tubes.