Manufacture of arrays with varying deposition parameters

• US 7,078,505 B2
• Filed: 06/06/2002
• Issued: 07/18/2006
• Est. Priority Date: 06/06/2002
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Maranowski, Michelle M., Mobed-Miremadi, Maryam, Peck, Bill J., Leproust, Eric M., Caren, Michael P., Bass, Jay K., Kanemoto, Roy H.
• Primary Examiner(s): Forman, B J
• Application Number:
  US10/165,783
• Publication Number:
  US 20030228422A1
• Time in Patent Office: 1,503 Days
• Field of Search: 435/6, 435/174, 435/283.1, 435/287.2, 536/23.1, 536/25.3
• US Class Current: 536/23.1
• CPC Class Codes: B01J 2219/00286 Reactor vessels with top and bottom openings
• CPC Class Codes: B01J 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00529 DNA chips
• 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 2219/00608 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 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00695 Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00698 Measurement and control of process parameters
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 3/0241 Drop counters; Drop formers making arrays for combinatorial libraries B01J19/0046; automation of dispensing for analysis G01N35/10
• CPC Class Codes: C03C 17/002 for flat glass, e.g. float glass
• CPC Class Codes: C03C 17/32 with synthetic or natural resins C03C17/30 takes precedence
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 for creating libraries

Abstract

Methods are disclosed for synthesizing a plurality of compounds on the surface of supports. The synthesis comprises a series of cycles of steps in which reagents for conducting the synthesis are deposited on the surface of the support to form the chemical compounds. At least one physical parameter of the deposition varies between cycles The method comprises conducting the synthesis in at least two sets of cycles, arbitrarily designated as a first set and a second set. Each cycle comprises at least one step of depositing reagents on a surface by means of droplet dispensing elements that traverse the surface of the support. At least one, and desirably all, of the following deposition parameters are employed as indicated: The number of times of repetition for a step of depositing reagents in at least one cycle of the second set is less than the number of times of repetition for a corresponding step in at least one cycle of the first set. The rate of deposition in at least one cycle of the second set is slower than or equal to the rate of deposition in at least one cycle of the first set. The rate of traversal of the dispensing elements over the surface of the support in at least one cycle of the second set is greater than such rate of traversal in at least one cycle of the first set.

Claims

1. A method for synthesizing an array of polymer features on the surface of a support, said method comprising (a) initiating multiple cycles of drop deposition of reagents onto the surface of the support from drop dispensing elements, which elements optionally traverse the surface of the support, wherein each cycle comprises at least one step of deposition of monomers or polymer subunits and at least one step of deposition of an activation agent, (b) varying at least one physical parameter of the drop deposition between cycles and (c) completing said multiple cycles to form said array of polymer features wherein the at least one physical parameter is number of drops to each desired polymer feature location, rate of drop deposition, or rate of traversal.

2. A method according to claim 1 wherein, in subsequent cycles of said method, the number of drops decreases, the rate of deposition decreases, or the rate of traversal increases.

3. A method for synthesizing a plurality of biopolymers on a surface of a support wherein said synthesis comprises steps in which reagents for conducting said synthesis are deposited on the surface of the support to form said biopolymers, said method comprising conducting said synthesis in at least two sets of cycles, a first set and a second set, each cycle comprising at least one step of depositing monomers or polymer subunits on a surface and at least one step of depositing an activation agent on the surface by means of droplet dispensing elements that traverse the surface of said support, wherein said first set and said second set are repeated to form said biopolymers and wherein:

(a) the number of times of repetition for a step in at least one cycle of said second set is less than the number of times of repetition for a corresponding step in at least one cycle of said first set, and/or

(b) the rate of deposition in at least one cycle of said second set is less than the rate of deposition in at least one cycle of said first set, and/or

(c) the rate of traversal in at least one cycle of said second set is greater than the rate of traversal in at least one cycle of said first set.

4. A method according to claim 3 wherein the number of times of repetition for a step in at least one cycle of said second set is less than 3.

5. A method according to claim 3 wherein the number of times of repetition for a step in a corresponding cycle of said first set is greater than 3.

6. A method according to claim 3 wherein the rate of deposition in a cycle of said method in said first set is at least 5000 times per second.

7. A method according to claim 3 wherein the rate of deposition in a cycle of said method in said second set is less than 0.75 times the rate in a cycle in the first set.

8. A method according to claim 3 wherein the rate of traversal of said droplet-dispensing elements in a cycle of said method in said first set is at least 120 millimeters per second.

9. A method according to claim 3 wherein the rate of traversal of said droplet-dispensing elements in a cycle of said method in said second set is at least 1.5 times the speed in a cycle in said first set.

10. A method according to claim 3 wherein said biopolymers are polynucleotides or polypeptides.

11. A method according to claim 10 wherein said biopolymers are polynucleotides and said polymer subunits are phosphoramidite reagents.

12. A method according to claim 3 wherein said reagents comprise a first reagent and a third reagent and said first reagent and said third reagent are biomonomers or biopolymer subunits activated for reaction on said surface.

13. A method according to claim 12 wherein said reagents comprise a second reagent and a fourth reagent and said second reagent and said fourth reagent are an activation agent.

14. A method according to claim 12 wherein said activation agent is a tetrazole.

15. A method according to claim 3 wherein a number of steps in a cycle of said first set is 1 to about 25.

16. A method according to claim 3 wherein a number of steps in a cycle of said second set is 1 to about 25.

17. A method for synthesizing a plurality of biopolymers on a surface of a support wherein said synthesis comprises steps in which reagents for conducting said synthesis are deposited on the surface of the support to form said biopolymers by droplet dispensing elements, said method comprising:

(a) a first set of cycles wherein each cycle of said method comprises the following steps, which are repeated X number of times;

(i) dispensing to a surface of a support a first reagent for forming biopolymers wherein said first reagent is a biomonomer or biopolymer subunit and is dispensed at predetermined locations by means of a plurality of droplet dispensing elements, all of which dispense said first reagent N number of times at a rate of A times per second, wherein said first reagent may be the same as, or different from, said first reagent of a previous step of said cycle, and

(ii) dispensing to said surface a second reagent for forming said biopolymers wherein said second reagent is dispensed at predetermined locations by means of a plurality of droplet dispensing elements, all of which dispense said second reagent N′

number of times at a rate of A′

times per second,

wherein said second reagent may be the same as, or different from, said second reagent of a previous step of said cycle and wherein said droplet dispensing elements traverse the surface of said support at a rate of traversal T, wherein N and N′ and

A and A′

may be the same or different,

(b) a second set of cycles wherein each cycle of said method comprises the following steps, which are repeated Y number of times;

(i) dispensing to said surface a third reagent for forming said biopolymers wherein said third reagent is a biomonomer or biopolymeric subunit dispensed by means of a plurality of droplet dispensing elements, all of which dispense said third reagent M number of times at a rate of B times per second wherein in at least one cycle of the sets of cycles M is less than N and B is less than or equal to A, wherein said third reagent may be the same as, or different from, said third reagent of a previous step of said cycle, and

(ii) dispensing to said surface a fourth reagent for forming said biopolymers wherein said fourth reagent is dispensed by means of a plurality of droplet dispensing elements, all of which dispense said fourth reagent M′

number of times at a rate of B′

times per second wherein M and M′ and

B and B′

may be the same or different and wherein in at least one cycle of the sets of cycles M′

is less than N′ and

B′

is less than or equal to A′ and

wherein said fourth reagent may be the same as, or different from, said fourth reagent of a previous step of said cycle and wherein said droplet dispensing elements traverse the surface of said support at a rate of traversal U that in at least one cycle is greater than T, and

(c) repeating said first set of cycles of said method and said second set of cycles of said method to form said plurality of biopolymers.

18. A method according to claim 17 wherein said biopolymers are polynucleotides or polypeptides.

19. A method according to claim 17 wherein said first reagent and said third reagent are nucleotide monomers or polynucleotide subunits activated for reaction on said surface.

20. A method according to claim 19 wherein said nucleotide monomers or polynucleotide subunits are phosphoramidite reagents.

21. A method according to claim 17 wherein said second reagent and said fourth reagent are an activation agent.

22. A method according to claim 21 wherein said activation agent is tetrazole.

23. A method according to claim 17 wherein X is 1 to about 25.

24. A method according to claim 17 wherein Y is 1 to about 25.

25. A method according to claim 17 wherein N is about 3 to about 50.

26. A method according to claim 17 wherein M is about 1 to about 30.

27. A method according to claim 17 wherein A is about 5,000 to about 40,000 times per second.

28. A method according to claim 17 wherein B is less than 0.75 times A.

29. A method according to claim 17 wherein T is about 120 millimeters per second to about 2 meters per second.

30. A method according to claim 17 wherein U is at least 1.5 times T.

31. A method according to claim 17 wherein said dispensing elements are nozzles.

32. A method according to claim 17 wherein said first cycle and said second cycle each comprise at least one wash step, which may or may not involve said droplet dispensing elements.

33. A method according to claim 17 for synthesizing an array of polynucleotides on the surface of a support.

34. A method according to claim 33 wherein said first cycle and said second cycle comprise at least one step of applying an oxidizing agent to said surface, which may or may not involve said droplet dispensing elements.

35. A method according to claim 17 for the synthesis of polynucleotides on said surface further comprising the steps of subjecting said surface to an oxidizing agent and subjecting said surface to an agent for removing a protecting group, each of which steps may or may not involve said droplet dispensing elements.

36. A method according to claim 17 wherein said biopolymers are synthesized on said surface in multiple arrays and said support is subsequently diced into individual arrays of biopolymers on a support.

37. A method according to claim 17 further comprising exposing the array to a sample and reading the array.

38. A method comprising forwarding data representing a result obtained from a reading of the array by a method of claim 37.

39. A method according to claim 38 wherein the data is transmitted to a remote location.

40. A method comprising receiving data representing a result of a reading an array by a method of claim 37.