Biopolymer arrays and their fabrication

• US 6,306,599 B1
• Filed: 07/16/1999
• Issued: 10/23/2001
• Est. Priority Date: 07/16/1999
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Perbost, Michel G. M.
• Primary Examiner(s): Fredman, Jeffrey
• Assistant Examiner(s): Chakrabarti, Arun K.
• Application Number:
  US09/356,249
• Time in Patent Office: 830 Days
• Field of Search: 435/6, 536/22.1, 536/25.34, 536/27
• 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 2219/00527 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 2219/00617 by chemical means
• 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 2219/00707 separated from the reactor apparatus
• CPC Class Codes: B01J 2219/00722 Nucleotides
• 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: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 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

A method of fabricating an addressable array of biopolymers on a substrate using a biomonomer with a first linking group which must be activated for linking to a substrate bound moiety, and apparatus and computer program products for executing the method. The method includes forming on a region of the substrate carrying the substrate bound moiety, a solid activator composition. A biomonomer containing fluid composition is deposited on the region so that the solid activator activates the first linking group and the biomonomer links to the substrate bound moiety. The foregoing steps may be repeated, wherein a biomonomer deposited and linked to the substrate bound moiety in one cycle is the substrate bound moiety for the next cycle, so as to form the biopolymer.

Claims

1. A method of fabricating an addressable array of biopolymers on a substrate using a biomonomer with a first linking group which must be activated for linking to a substrate bound moiety, comprising, at each of multiple different regions of the substrate:

(a) forming on a region of the substrate carrying the substrate bound moiety, a solid activator composition;

(b) depositing a biomonomer containing fluid composition on the region so that the solid activator activates the first linking group and the biomonomer links to the substrate bound moiety; and

(c) repeating steps (a) and (b), wherein a biomonomer deposited and linked to the substrate bound moiety in one cycle is the substrate bound moiety for the next cycle, so as to form the biopolymer;

so as to form the addressable array;

wherein the biomonomer fluid composition deposited at a region covers an area greater than that covered by the solid activator composition at the same region.

2. A method according to claim 1 wherein step (a), the solid activator composition is formed prior to depositing the biomonomer containing fluid, by depositing a composition of solid activator as a fluid composition, and allowing fluid to evaporate.

3. A method according to claim 2 wherein the biomonomer fluid composition deposited at a region covers an area greater than that covered by the activator fluid composition at the same region.

4. A method according to claim 2 wherein the fluid composition has less than 20% by weight of solid activator content.

5. A method according to claim 2 wherein the biopolymers are polynucleotides and the biomonomer is a nucleoside monomer.

6. A method according to claim 5 wherein the polynucleotide is a DNA.

7. A method according to claim 1 wherein the activated biomonomer reacts with a component in an ambient atmosphere.

8. A method according to claim 5 wherein the biomonomer is a phosphoramidite.

9. A method according to claim 1 wherein different biomonomers are deposited in different cycles.

10. A method according to claim 1 wherein the same biomonomers are deposited in different cycles.

11. A method according to claim 2 wherein the biomonomer fluid composition includes a fluid different from that of the activator fluid composition.

12. A method of evaluating for the presence of a target polynucleotide in a sample, using an addressable array fabricated in accordance with the method of claim 1, the method comprising:

(a) exposing the sample to the array, such that target polynucleotide which may be present will bind to one or more predetermined regions of the array; and

(b) observing a binding pattern on the array and evaluating the presence of the target polynucleotide based on the observed binding pattern.

13. A method of fabricating an addressable array of biopolymers on a substrate using biomonomers each with a first linking group which must be activated for linking to a substrate bound moiety, and a deposition system with a head having multiple pulse jets each of which can dispense droplets of a fluid onto a substrate, each jet including a chamber with an orifice, and including an ejector which, when activated, causes a droplet to be ejected from the orifice, the method comprising:

(a) depositing onto a region of the substrate carrying the substrate bound moiety, a fluid comprising of a solid activator;

(b) allowing fluid of the composition to evaporate to form the solid activator on the region;

(c) then depositing from a pulse jet onto the region, a droplet of a biomonomer containing fluid composition so that the solid activator activates the first linking group and the biomonomer links to the substrate bound moiety; and

(d) repeating steps (a) through (c) at each of multiple regions of the substrate, wherein at each region a biomonomer deposited and linked to the substrate bound moiety in one cycle is the substrate bound moiety for the next cycle, so as to form the addressable array of biopolymers;

wherein a droplet of biomonomer fluid composition deposited at a region will cover an area greater than that covered by a preceding droplet of activator fluid composition at the same region.

14. A method according to claim 13 wherein the fluid composition of solid activator is deposited as a droplet from a pulse jet.

15. A method according to claim 13 wherein the fluid composition of solid activator is applied as a continuous layer over multiple regions.

16. A method according to claim 14 wherein the fluid of the solid activator fluid composition has a boiling point of less than 100°

C.

17. A method according to claim 13 wherein the biomonomer containing fluid composition uses a fluid different from that of the fluid composition of solid activator.

18. A method according to claim 17 wherein the fluid of the solid activator fluid composition has a boiling point of less than 100°

C., while the fluid of the biomonomer containing fluid composition has a boiling point of greater than 100°

C.

19. A method according to claim 13 wherein the activator fluid composition has less than 20% by weight solid activator content.

20. A method according to claim 13 wherein the biopolymers are polynucleotides and the biomonomer is a nucleoside monomer.

21. A method according to claim 13 wherein the polynucleotide is a DNA.

22. A method according to claim 13 wherein the activated biomonomer reacts with a component in an ambient atmosphere.

23. A method according to claim 13 wherein the biomonomer is a phosphoramidite.

24. A method according to claim 13 wherein, for each of the multiple regions, different biomonomers are deposited in different cycles.

25. A method of evaluating for the presence of a target polynucleotide in a sample, using an addressable array fabricated in accordance with the method of claim 13, the method comprising:

(a) exposing the sample to the array, such that target polynucleotide which may be present will bind to one or more predetermined regions of the array; and

(b) observing a binding pattern on the array and evaluating the presence of the target polynucleotide based on the observed binding pattern.