Method of shielding biosynthesis reactions from the ambient environment on an array

• US 6,890,723 B2
• Filed: 01/09/2002
• Issued: 05/10/2005
• Est. Priority Date: 10/22/1999
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Perbost, Michel G. M., Lefkowitz, Steven M.
• Primary Examiner(s): Ponnaluri, Padmashri
• Assistant Examiner(s): TRAN, MY CHAU T
• Application Number:
  US10/043,590
• Publication Number:
  US 20020086327A1
• Time in Patent Office: 1,217 Days
• Field of Search: 435/3, 435/4, 435/287.1, 435/287.2, 435/DIG.49, 435/7.1, 436/518
• US Class Current: 506/13
• 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 2219/00497 Features relating to the solid phase supports
• 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 2219/00599 Solution-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 2219/00617 by chemical means
• 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 2219/00698 Measurement and control of process parameters
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 50/08 Liquid phase synthesis, i.e. wherein all library building blocks are in liquid phase or in solution during library creation; Particular methods of cleavage from the liquid support
• CPC Class Codes: C40B 60/14 for creating libraries

Abstract

A method of fabricating an array of biopolymers provides a shield for biochemical reactions and biochemical reactants and is particularly useful for those reactions and reactants that are susceptible to reaction with a component of the ambient environment during the fabrication of the array. The method is applicable to the conventional fabrication and synthesis methods used to fabricate a biopolymer array, such as in situ synthesis of biopolymers on an array and the attachment of pre-synthesized biopolymers on to an array. The method comprises applying a non-miscible fluid (NMF) to the array surface where the biopolymers are being synthesized or attached. The NMF is inert and insoluble with the biochemical reactants and other ancillary materials in solution used in conventional synthesis or attachment of biopolymers. The NMF provides a shield between the ambient atmosphere and the biopolymer synthesis materials or the deprotected pre-synthesized biopolymer at the surface of the array during the synthesis or attachment processes. The NMF may be applied as droplets over each feature location on the surface or may be applied by flooding the surface of the array to fully cover the features. Biomonomer or biopolymer solutions are deposited into or through the NMF to the feature locations on the surface of the array where the synthesis or attachment reactions are to take place using conventional deposition equipment to eject the solutions into the NMF. The NMF provides a shield for activated biomonomers that are susceptible to reaction with a component in the ambient environment, such as moisture in the air. Moreover, the NMF provides a shield for pre-synthesized biopolymers that are susceptible to evaporation when deprotected for attachment to the array surface. The method provides a means by which the potential reactivity of the activated biomonomer or deprotected biopolymer with an ambient atmosphere component can be kept low. As a result, biopolymer arrays can be more accurately fabricated.

Claims

1. A method of fabricating a biopolymer array from pre-synthesized biopolymers, wherein the array has a surface that is prepared for linking with the pre-synthesized biopolymers, and wherein the pre-synthesized biopolymers are in solution for linking to the prepared surface, the method comprising the steps of:

adding a non-miscible fluid (NMF) to the array surface, the NMF being inert, immiscible and insoluble in aqueous solution; and

depositing the biopolymer solution on the array surface and linking the biopolymer to the surface.

2. The method of claim 1 wherein the biopolymer solution is deposited on the array surface through the NMF.

3. The method of claim 1 wherein the biopolymers are deprotected and in an aqueous solution, the method additionally comprising removing the NMF and unlinked biopolymer solution from the surface.

4. The method of claim 1, wherein the step of adding the NMF comprises the step of applying a quantity of NMF to completely cover the array surface;

and wherein the step of depositing comprises the step of loading the biopolymer solution into a pulsejet of a deposition system and ejecting the solution as droplets through the NMF to the array surface for linkage.

5. The method of claim 4 wherein the biopolymer in the loaded solution is deprotected.

6. The method of claim 1, wherein the step of adding the NMF comprises the step of applying a quantity of NMF sufficient to cover each one of a plurality of feature locations where the biopolymer will be linked on the array surface;

and wherein the step of depositing comprises the step of loading a deprotected biopolymer solution into a pulsejet of a deposition system and ejecting the solution as droplets into the NMF at the feature location for linkage.

7. The method of claim 1, wherein the step of adding the NMF comprises the step of immersing the prepared array surface into a quantity of NMF;

and wherein the step of depositing comprises the step of loading a deprotected biopolymer solution into a pulsejet of a deposition system and ejecting the solution as droplets through the NMF to the array surface for linkage.

10. The method of claim 1, wherein linking the biopolymer to the surface is facilitated by the added NMF.

11. The method of claim 1, wherein the added NMF facilitates linking the biopolymer to the surface by blocking evaporation of the biopolymer solution while the solution is on the surface.

12. The method of claim 1, wherein the NMF has a density that is different from a density of the biopolymer solution.

13. The method of claim 1, wherein the NMF has a viscosity that is different than a viscosity of the biopolymer solution.

14. The method of claim 1, wherein the NMF has one or both of a density and a viscosity different from that of the biopolymer solution,, and wherein the biopolymer solution is deposited on the array surface through the NMF.

15. The method of claim 1, wherein the NMF is selected from heptane, octane, nonane, decane, undecane, dodecane, tridecane, tetradecane, pentadecane, hexadecane, heptadecane, cyeloheptane, cyclooctane, cyclononane, and cyclodecane.

8. A method of shielding biosynthesis reactions and sensitive biosynthesis reactants from the ambient environment comprising the steps of:

(a) applying a non-miscible fluid (NMF) to one or more sites where the biosynthesis reactions take place, the NMF being inert and insoluble with respect to the biosynthesis reactions and the biosynthesis reactants, the NMF covering the one or more sites; and

(b) depositing one or more of the sensitive biosynthesis reactants through the NMF on the one or more sites.

9. The method of claim 8, wherein the applied NMF blocks evaporation of the biopolymer reactants from the one or more sites.

16. A method of fabricating a biopolymer array from pre-synthesized biopolymers, wherein the array has a surface that is prepared for linking with the pre-synthesized biopolymers, and wherein the pre-synthesized biopolymers are in aqueous solution for linking to the prepared surface, the method comprising the steps of:

adding a non-miscible fluid (NMF) to the array surface, the NMF being inert, immiscible and insoluble in aqueous solution; and

depositing the biopolymer solution on the array surface and linking the biopolymer to the surface,

wherein the NMF covers the deposited biopolymer solution during linkage.

17. The method of claim 16, wherein the added NMF facilitates linking the biopolymer to the surface comprising blocking evaporation of the biopolymer solution while on the array surface.

18. The method of claim 16, wherein the biopolymers are deprotected in the aqueous solution, and wherein the method additionally comprises removing the NMP and unlinked biopolymer solution from the surface.

19. The method of claim 16, wherein the NMF is a hydrocarbon selected from heptane, octane, nonane, decane, undecane, dodecane, tridecane, tetradecane, pentadecane, hexadecane, heptadecane, cycloheptane, cyclooctane, cyclononane, and cyclodecane.