Methods for in situ generation of nucleic acid molecules

• US 20060078927A1
• Filed: 09/23/2005
• Published: 04/13/2006
• Est. Priority Date: 03/29/2004
• Status: Abandoned Application

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Peck, Bill J., Leproust, Eric M.
• Application Number:
  US11/234,701
• Publication Number:
  US 20060078927A1
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 2219/00547 Bar codes
• CPC Class Codes: B01J 2219/00576 fluorophore
• 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 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00657 One-dimensional arrays
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00662 Two-dimensional arrays within two-dimensional arrays
• CPC Class Codes: B01J 2219/00664 Three-dimensional arrays
• CPC Class Codes: B01J 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00691 using robots
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01J 2219/00725 : Peptides
• CPC Class Codes: B01J 2219/00729 : Peptide nucleic acids [PNA]
• CPC Class Codes: B01J 2219/00731 : Saccharides
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/68 : involving nucleic acids

Abstract

Methods of producing nucleic acid molecules using an in situ nucleic acid synthesis protocol are provided. The method can comprise contacting a substrate comprising an attached blocked nucleoside monomer or polymer with a deblocking fluid to remove the blocking group, thereby generating an unblocked attached nucleoside monomer or polymer; displacing the deblocking fluid from the substrate surface comprising the attached unblocked nucleoside monomer or polymer with a purging fluid; and reacting the attached unblocked nucleoside monomer or polymer with another blocked nucleoside monomer. Nucleic acid molecules produced by the methods are also provided and can be attached to or released from the substrate (e.g., provided in solution or in a lyophilized form).

Claims

1. A method for synthesizing a nucleic acid molecule on a substrate, comprising:

contacting a substrate comprising an attached blocked nucleoside monomer or polymer with a deblocking fluid to remove the blocking group, thereby generating an unblocked attached nucleoside monomer or polymer;

displacing the deblocking fluid from the substrate surface comprising the attached unblocked nucleoside monomer or polymer with a purging fluid;

reacting the attached unblocked nucleoside monomer or polymer with another blocked nucleoside monomer.

2. The method of claim 1, wherein a blocked nucleoside monomer is attached to the substrate by contacting the substrate with a fluid comprising a blocked nucleoside monomer at a location on the substrate that comprises hydroxyl functional groups.

3. The method of claim 1, wherein steps of the method are repeated a plurality of times.

4. The method of claim 1, wherein the nucleic acid molecule synthesized is greater than 60 nucleotides.

5. The method of claim 1, wherein the nucleic acid molecule synthesized is greater than 100 nucleotides.

6. The method of claim 1, wherein the substrate comprises a non-porous surface.

7. The method of claim 1, wherein the substrate comprises a surface of a planar support.

8. The method of claim 1, wherein the substrate is a bead.

9. The method of claim 1, wherein the displacing step causes minimal mixing of deblocking and purging fluids.

10. The method of claim 1, wherein the substrate comprises a surface of a support containable within a flow cell.

11. The method of claim 1, wherein the purging fluid has a density that is different from the blocking fluid.

12. The method of claim 1, wherein the purging fluid and the deblocking fluid have a density difference of at least about 0.01.

13. The method according to claim 1, wherein the purging fluid has a density that is higher than the density of the deblocking fluid.

14. The method according to claim 1, wherein the purging fluid has a density that is lower than the density of the deblocking fluid.

15. The method according to claim 1, wherein the purging fluid is an organic fluid.

16. The method according to claim 1, wherein the purging fluid comprises an oxidizing agent.

17. The method according to claim 1, wherein the purging fluid comprises a wash fluid.

18. The method according to claim 17, wherein the wash fluid is an organic fluid.

19. The method according to claim 17, wherein the wash fluid is acetonitrile.

20. The method according to claim 1, wherein deblocking fluid is displaced from the surface with a purging fluid by flowing the purging fluid across the surface in a manner sufficient to produce a stratified fluid interface that moves across the surface.

21. The method according to claim 1, wherein the purging fluid is flowed across the surface at a rate ranging from about 1 cm/s to about 20 cm/s.

22. The method of claim 1, wherein the purging fluid limits the efficiency of deblocking by the deblocking fluid.

23. The method of claim 2, wherein the hydroxyl functional groups are provided by 5′

-OH groups of nucleoside monomers or polymers attached to the substrate.

24. The method of claim 1, wherein the step of displacing occurs in a flow cell.

25. The method of claim 2, wherein the blocked nucleoside monomer is deposited at the location by pulse jetting.

26. The method of claim 1, wherein the blocking group comprises an acid labile blocking group and wherein the deblocking fluid comprises an acid.

27. The method of claim 1, wherein the substrate is contained within a chamber of a flow cell when contacted with deblocking fluid and wherein the chamber comprises at least one fluid inlet and at least one fluid outlet.

28. The method of claim 27, wherein the flow cell is oriented in an at least partially vertical position.

29. The method of claim 17, wherein a pressure gradient is used to produce the stratified interface.

30. The method of claim 1, wherein the deblocking fluid comprises an organic solvent that has a vapor pressure that is less than about 13 Kpa at 0°

C. and 1 ATM.

31. The method of claim 1, further comprising contacting the substrate comprising the attached blocked nucleoside monomer or polymer with an oxidation fluid prior to contacting with the deblocking fluid.

32. The method of claim 1, further comprising releasing the nucleic acid from the array.

38. The method of claim 8, wherein the bead is non-porous.

39. The method of claim 24, wherein the flow cell is configured as a column.

40. The method of claim 39, wherein the support comprises a non-porous bead.

41. A substrate comprising a nucleic acid molecule at a location on the substrate made by the method of claim 1.

42. The substrate of claim 41, wherein the nucleic acid molecule comprises a cleavable site for releasing the nucleic acid molecule from the substrate.

43. The substrate of claim 41, further comprising a plurality of nucleic acid molecules at the location, wherein at least about 50% of the nucleic acid molecules are at least 60 nucleotides in length and wherein at least about one the nucleotides is susceptible to a depurination reaction.

44. The substrate of claim 43, wherein at least about 50% of the nucleic acid molecules are at least about 100 nucleotides in length.

45. A plurality of nucleic acid molecules released from a location on a substrate made by the method of claim 1.

46. The plurality of nucleic acid molecules of claim 42, wherein at least 50% of the nucleic acid molecules are at least about 60 nucleotides in length and wherein at least one of the nucleotides is susceptible to a depurination reaction.

33. A method of producing a substrate of at least two oligonucleotides bonded to different locations on a surface of the substrate, comprising:

contacting blocked nucleoside monomers to at least a first location and a second different location of a substrate surface displaying functional groups under conditions sufficient for the blocked nucleoside monomers to bond to the surface in first and second locations to produce a substrate surface displaying bound blocked monomers;

contacting the surface displaying bound blocked monomers with a deblocking fluid to remove the blocking group, thereby generating unblocked nucleoside monomers at the first and second locations;

displacing the deblocking fluid from the surface comprising the bound unblocked monomers at the first and second locations with a purging fluid;

reacting the attached unblocked nucleoside monomers at the first and second locations with another blocked nucleoside monomer.

34. The method of claim 33, wherein the at least two oligonucleotides comprise the same sequence composition.

35. The method of claim 33, wherein the at least two oligonucleotides comprise different sequence compositions.

36. The method of claim 33, further comprising contacting the bonded blocked monomers with an oxidation fluid prior to contacting the surface with the deblocking solution.

37. The method of claim 33, further comprising releasing the at least two oligonucleotides from the substrate.