Method of conducting a plurality of reactions

• US 6,121,048 A
• Filed: 10/18/1994
• Issued: 09/19/2000
• Est. Priority Date: 10/18/1994
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Zaffaroni, Alejandro C., Modlin, Douglas N., Buchko, Christopher J.
• Primary Examiner(s): ALEXANDER, LYLE
• Application Number:
  US08/327,512
• Time in Patent Office: 2,163 Days
• Field of Search: 422/62, 422/63, 422/64, 436/43, 436/45, 436/91, 436/94, 436/165
• US Class Current: 506/14
• 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 2219/00367 capillary
• CPC Class Codes: B01J 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00536 in the shape of disks
• 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 2219/0061 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 2219/00635 by reactive plasma treatment
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/0072 Organic compounds
• CPC Class Codes: B01L 2300/0893 having a very large number of wells, microfabricated wells
• CPC Class Codes: B01L 3/5085 for multiple samples, e.g. microtitration plates
• CPC Class Codes: C40B 60/14 for creating libraries
• CPC Class Codes: G01N 2035/1039 : Micropipettes, e.g. microcapillary tubes
• CPC Class Codes: Y10T 436/111666 : Utilizing a centrifuge or compartmented rotor
• CPC Class Codes: Y10T 436/143333 : Saccharide [e.g., DNA, etc.]
• CPC Class Codes: Y10T 436/2575 : Volumetric liquid transfer

Abstract

An apparatus and method is provided for preparing and using a very large and diverse array of compounds on a substrate having rapidly accessible locations. The substrate contains cells in which the compounds of the array are located. Surrounding the cells is a non-wetable surface that prevents the solution in one cell from moving to adjacent cells. The compounds are delivered to the individual cells of the array by a micropipette attached to an X-Y translation stage.

Claims

1. A method for conducting a plurality of reactions on a substrate comprising at least one surface, said at least one surface comprising a plurality of cells at known locations, the location of each cell being encoded by information readable with an optical, electrical, magnetic or electromagnetic sensor, said method comprising:

(a) selecting a first set of one or more cells on said at least one surface of said substrate;

(b) decoding the locations of said first set of one or more cells by said sensor and delivering a first reactant to each cell of said first set of one or more cells;

(c) selecting a second set of one or more cells on said at least one surface of said substrate;

(d) decoding the locations of said second set of one or more cells by said sensor and delivering a second reactant to each cell of said second set of one or more cells; and

(e) reacting said first reactant in each cell of said first set of one or more cells and said second reactant in each cell of said second set of one or more cells such that covalent bonds are formed with said surface, wherein the first reactant is prevented from contacting the second set of one or more cells and the second reactant is prevented from contacting the first set of one or more cells.

2. The method of claim 1 where said delivering the first reactant to each cell of the first set of one or more cells comprises:

(a) identifying a reference mark on said at least one surface of the substrate;

(b) moving a dispenser of said reactants a fixed distance and direction from said reference mark such that the dispenser is positioned approximately above a first cell of the first set of one or more cells;

(c) delivering the first reactant to the first cell; and

(d) repeating (b) and (c) for each remaining cell of the first set of one or more cells.

3. The method of claim 1 wherein the first and second reactants are receptors.

4. The method of claim 1 wherein said substrate is a rotatable disk, and said delivering a first reactant to each cell of said first set of one or more cells comprises:

(a) moving a dispenser of said first reactant to the radial position of a first cell from said first set of one or more cells;

(b) rotating of said substrate with respect to the dispenser such that the dispenser is positioned approximately above said first cell;

(c) delivering said first reactant to said first cell;

(d) repeating (a), (b), and (c) for each remaining cell of said first set of one or more cells.

5. The method of claim 1 wherein the first and second reactants are delivered to the cells from a micropipette.

6. The method of claim 1 wherein the first and second reactants are delivered in charged droplets from capillaries having electrodes attached thereto.

7. The method of claim 1 wherein the substrate has surface regions surrounding the plurality of cells, the surface regions having a hydrophobic surface.

8. The method of claim 1, wherein said substrate is a rotatable disk, and said delivering a second reactant to each cell of said second set of one or more cells comprises:

(a) moving a dispenser of said second reactant to the radial position of a first cell from said second set of one or more cells;

(b) rotating said substrate with respect to the dispenser such that the dispenser is positioned approximately above said first cell;

(c) delivering said second reactant to said first cell; and

(d) repeating (a), (b), and (c) for each remaining cell of said second set of one or more cells.

9. The method of claim 1 wherein the first and second reactants are monomers.

10. The method of claim 9 wherein the monomers are selected from the group consisting of amino acids, nucleotides and saccharides.

11. A method for conducting a plurality of reactions on a substrate comprising at least one surface, said at least one surface comprising a plurality of cells at known locations, the method comprising:

(a) selecting a first set of one or more cells and a second set of one or more cells on said at least one surface of said substrate;

(b) delivering a solution of a first reactant to the first set of one or more cells and delivering a solution of a second reactant to the second set of one or more cells; and

(c) conducting reactions of the first reactant in the first set of one or more cells and of the second reactant in the second set of one or more cells such that covalent bonds are formed with said surface;

wherein regions of the substrate surrounding the first set of one or more cells are covered with a layer of protecting groups that are non-wetting with respect to the solutions of the first and second reactants.

12. The method of claim 11 wherein delivering a solution of a first reactant to the first set of one or more cells comprises:

(a) identifying a reference mark on said at least one surface of the substrate;

(b) moving a dispenser of said first reactant a fixed distance and direction from said reference mark such that the dispenser is positioned approximately above a first cell of the first set of one or more cells;

(c) delivering said reactant to said first cell; and

(d) repeating (a) and (b) for each remaining cell of the first set of one or more cells.

13. The method of claim 11 wherein the protecting groups are selected from the group consisting of alkyl silanes.

14. The method of claim 11, wherein said delivering a solution of a second reactant to the second set of one or more cells comprises:

(a) identifying a reference mark on said at least one surface of the substrate;

(b) moving a dispenser of said first reactant a fixed distance and direction from said reference mark such that the dispenser is positioned approximately above a first cell of the second set of one or more cells;

(c) delivering said reactant to said first cell; and

(d) repeating (a) and (b) for each remaining cell of the second set of one ore more cells.

15. A method for conducting a plurality of reactions on a substrate, said method comprising:

(a) providing a substrate comprising at least one surface, said at least one surface comprising a plurality of cells at known locations, wherein each cell of the plurality of cells comprises an area for conducting a reaction and the location of each cell on said at least one surface of the substrate is encoded by information readable with an optical, electrical, magnetic or electromagnetic sensor;

(a) selecting a first set of one or more cells on the surface on the substrate;

(b) locating each cell of the first set of one or more cells by the sensor and delivering a first reactant to each cell of the first set of one or more cells;

(c) selecting a second set of one or more cells on the surface of the substrate;

(d) locating each cell of the second set of one or more cells by the sensor and delivering a second reactant to each cell of the second set of one or more cells; and

(e) reacting the first reactant in each cell of the first set of one or more cells and the second reactant in each cell of the second set of one or more cells such that covalent bonds are formed with said surface, wherein the first reactant is prevented from contacting the second set of one or more cells and the second reactant is prevented from contacting the first set of one or more cells.

16. The method of claim 15, wherein the spacing between each cell of the first and second sets of one or more cells is 10 μ

m² or less.

17. The method of claim 15, wherein the area of each cell of the first and second sets of one or more cells is less than about 1 mm².

18. The method of claim 17, wherein the area of each cell of the first and second sets of one or more cells is between about 100 μ

m² and about 1 mm².

19. A method for conducting a plurality of reactions on a substrate comprising:

(a) providing a substrate comprising a magnetic or optical storage medium and a plurality of cells at known locations thereon, the location of each cell being encoded by information readable with an optical, electrical, magnetic or electromagnetic sensor;

(b) selecting a first set of one or more cells on the substrate;

(c) locating each cell of the first set of one or more cells by the sensor and delivering a first reactant to each cell of the first set of one or more cells;

(d) selecting a second set of one or more cells on the substrate;

(e) locating each cell of the second set of one or more cells by the sensor and delivering a second reactant to each cell of the second set of one or more cells; and

(f) reacting the first reactant in each cell of the first set of one or more cells and the second reactant in each cell of the second set of one or more cells such that covalent bonds are formed with said surface, wherein the first reactant is prevented from contacting the second set of one or more cells and the second reactant is prevented from contacting the first set of one or more cells.

20. The method of claim 19, wherein the substrate is an optical or magnetic storage disk.