Method and apparatus for conducting an array of chemical reactions on a support surface

• US 6,210,894 B1
• Filed: 05/18/1999
• Issued: 04/03/2001
• Est. Priority Date: 09/04/1991
• Status: Expired due to Fees

• Current Assignee: Metrigenix Incorporated
• Original Assignee: Protogene Laboratories, Inc.
• Inventors: Brennan, Thomas M.
• Primary Examiner(s): Houtteman, Scott W.
• Application Number:
  US09/314,456
• Time in Patent Office: 686 Days
• Field of Search: 435/6, 536/23.1
• US Class Current: 435/6.11
• 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 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00527 Sheets
• 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 2219/0061 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 2219/00619 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 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• 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 2219/00675 In-situ synthesis on the substrate
• 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: C03C 17/30 : with silicon-containing compounds
• CPC Class Codes: C07B 2200/11 : Compounds covalently bound to a solid support
• CPC Class Codes: C07B 61/00 : Other general methods
• 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: 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: 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 50/14 : Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: C40B 80/00 : Linkers or spacers specially adapted for combinatorial chemistry or libraries, e.g. traceless linkers or safety-catch linkers
• CPC Class Codes: Y02P 20/582 : Recycling of unreacted starting or intermediate materials

Abstract

The invention provides apparatus and methods for making arrays of functionalized binding sites on a support surface. The invention further provides apparatus and methods for sequencing oligonucleotides and for identifying the amino acid sequence of peptides that bind to biologically active macromolecules, by specifically binding biologically active macromolecules to arrays of peptides or peptide mimetics.

Claims

1. A method for conducting chemical reactions between a solution of a chemical reactant and an array of functionalized binding sites on a support surface comprising adding the solution of chemical reactant to the functionalized binding site in an amount where the solution of chemical reactant at each binding site is separate from the solution of chemical reactant at other binding sites by surface tension.

10. The method according to claim 1, 2, 3, or 4, wherein said support surface has 10-10⁴ functionalized binding sites per cm².

11. The method according to claim 10, wherein each functionalized binding site is about 50-2000 microns diameter.

12. The method according to claim 1, 2, 3, or 4, wherein said support surface is glass.

13. The method according to claim 1, 2, 3, or 4, wherein said support surface is a derivatized polymer selected from the group consisting of nylon, polyethylene, polypropylene, polystyrene and polytetrafluorethylene.

14. The method of claim 1 wherein the area of the support surface of the functionalized binding site has a higher surface tension relative to the support surface surrounding each functionalized binding site.

15. The method of claim 1 wherein the volume of the chemical reactant solution is 50 picoliter to 2 microliter.

16. The method of claim 1 wherein the chemical reaction between the chemical reactant and functionalized binding site forms covalent bonds.

17. The method of claim 1 wherein chemical reactant reacts with the functionalized binding site by non-covalent binding interactions.

2. A method of making nucleic acid array plates comprising:

a) coating a support surface with a positive or negative photoresist substance which is subsequently exposed to light and developed to create a pattern of a first exposed region and a photoresist coated region on the support;

b) reacting said first exposed region with a reagent to form a stable hydrophobic matrix on said first exposed region;

c) removing the remaining photoresist coat on said photoresisted coated region so as to form a second exposed region; and

d) adding at least a first nucleic acid coupling reagent to at least one area of said second exposed region on the nucleic acid array plate.

5. The method according to claim 2, 3, or 4, wherein said support surface comprising a covalently linked layer of inert siloxane.

6. The method according to claim 5, wherein said inert siloxane is tridecafluro-1,1,2,2-tetrahydrooctyl siloxane.

8. The method of making array plates according to claim 2 or 3, wherein said first nucleic acid reagent comprises a first nucleotide.

9. The method of making array plates according to claim 8, further comprising adding additional nucleotides to said first nucleotide.

18. The method of claim 2 or 3 where said nucleic acid coupling reagent is a phosphoramidite.

19. The method of claim 2 or 3 where said nucleic acid coupling reagent is an H-phosphonate.

3. A method of making nucleic acid array plates comprising:

a) coating a support surface with a positive or negative photoresist substance which is subsequently exposed to light and developed to create a pattern of a first exposed surface and a photoresist coated surface on the support;

b) reacting said first exposed surface with a reagent to form a stable hydrophobic matrix on said first exposed surface;

c) removing the photoresist coat on said photoresisted coated surface so as to form a second exposed surface;

d) reacting said second exposed surface with a second reagent so as to convert said second exposed surface to functionalized hydrophilic binding sites; and

e) adding at least a first nucleic acid coupling reagent to at least one of said functionalized hydrophilic binding sites.

7. The method according to claim 3 or 4, wherein said functional hydrophilic binding sites comprise siloxane compounds selected from the group consisting of hydroxyalkyl siloxane, dihydroxyalkyl siloxanes, and aminoalkyl siloxanes.

4. A method of making nucleic acid array plates comprising the step of forming a pattern of functionalized hydrophilic binding sites on a support surface, wherein said functionalized hydrophilic binding sites are chemically reactive to bind nucleic acids in an aqueous solution deposited thereon, and wherein said functionalized hydrophilic binding sites are more polar than their surrounding surface to cause separation of said aqueous solution at one binding site from aqueous solutions at adjacent binding sites.