Device for chemical and biochemical reactions using photo-generated reagents

• US 7,491,680 B2
• Filed: 09/11/2002
• Issued: 02/17/2009
• Est. Priority Date: 02/11/1998
• Status: Expired due to Fees

• Current Assignee: University of Houston Law Center (University of Houston System), Board of Regents of the University of Michigan (University of Michigan)
• Original Assignee: University of Houston (University of Houston System), Board of Regents of the University of Michigan (University of Michigan)
• Inventors: Gao, Xiaolian, Zhou, Xiaochuan, Gulari, Erdogan
• Primary Examiner(s): Schultz; J D
• Assistant Examiner(s): Lundgren; Jeffrey S.
• Application Number:
  US10/241,411
• Publication Number:
  US 20030138363A1
• Time in Patent Office: 2,351 Days
• Field of Search: 435/4, 435/7.2, 435/287.1, 435/287.2, 435/DIG.46, 435/DIG.49, 530/334, 436/523, 436/524
• US Class Current: 506/27
• 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 2219/00434 Liquid crystal masks
• CPC Class Codes: B01J 2219/00439 using micromirror arrays
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 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 2219/00605 the compounds being directly bound or immobilised to solid supports
• 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 2219/00617 by chemical means
• 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 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00659 Two-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 2219/00711 : Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01J 2219/00725 : Peptides
• 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: 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: C07K 1/045 : using devices to improve synthesis, e.g. reactors, special vessels
• CPC Class Codes: C07K 1/047 : Simultaneous synthesis of different peptide species; Peptide libraries
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 40/12 : Libraries containing saccharides or polysaccharides, or derivatives thereof
• CPC Class Codes: C40B 50/14 : Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: G03F 7/00 : Photomechanical, e.g. photolithographic, production of textured or patterned surfaces, e.g. printing surfaces; Materials therefor, e.g. comprising photoresists; Apparatus specially adapted therefor using photoresist structures for special production processes, see the relevant places, e.g. B44C, H01L, e.g. H01L21/00, H05K

Abstract

This invention provides method and apparatus for performing chemical and biochemical reactions in solution using in situ generated photo-products as reagent or co-reagent. In some embodiments, the present invention provides methods and devices for generating one or more selected multimers at specific reaction sites on a substrate comprising contacting the substrate with a liquid solution comprising photo-reagent precursors, isolating the reaction sites, selectively irradiating the reaction sites with a digital micromirror device, and contacting the substrate with monomers. The method and apparatus of the present invention have applications in parallel synthesis of molecular sequence arrays on solid surfaces.

Claims

1. A method for synthesizing one or more selected multimers at specific reaction sites on a substrate, the specific reaction sites containing one or more protected initiation moieties, the method comprising:

(a) contacting the substrate with a liquid solution comprising one or more photo-reagent precursors, said precursors selected from the group consisting of acid precursors and base precursors, such that the liquid solution is in contact with the initiation moieties;

(b) fluidly isolating the specific reaction sites;

(c) irradiating a selected number of the isolated reaction sites, without use of a photolithographic mask, with an optical system comprising a light source and a computer-controlled spatial optical modulator comprising a digital micromirror device to produce at least one photo-generated reagent that directly deprotects the initiation moieties at the irradiated reaction sites so as to create deprotected initiation moieties;

(d) contacting the substrate with one or more monomers, the monomers comprising an unprotected reactive site and a protected reactive site, under conditions such that the unprotected reactive site of the monomers couple with the deprotected initiation moieties so as to create new initiation moieties with attached monomers; and

(e) repeating steps (a)-(d) until the selected multimers are synthesized.

2. The method of claim 1, wherein the selected multimers are DNA.

3. The method of claim 2, wherein the DNA is selected from the group consisting of nucleotide phosphoramidites and analogs thereof.

4. The method of claim 1, wherein the selected multimers are oligonucleotides.

5. The method of claim 1, wherein the selected multimers are RNA.

6. The method of claim 1, wherein the selected multimers are DNA/RNA hybrids.

7. The method of claim 1, wherein the selected multimers are peptides.

8. The method of claim 1, wherein the selected multimers are oligosaccharides.

9. The method of claim 1, wherein the selected multimers are carbohydrates.

10. The method of claim 1, wherein the initiation moieties comprise linker molecules, each of the linker molecules comprising a reactive functional group protected by an acid-labile protecting group.

11. The method of claim 10, wherein the reactive functional group of the linker molecules comprises a hydroxyl group.

12. The method of claim 1, wherein the protected reactive site in step (d) is protected by an acid-labile group.

13. The method of claim 1, wherein the protected reactive site in step (d) is protected by an base-labile group.

14. The method of claim 1, wherein the coupling of the monomers with the deprotected initiation moieties in step (d) occurs with a yield of 98% or greater.

25. The method of claim 1, wherein said method for synthesizing is utilized to manufacture an array of multimers.

26. The method of claim 25, wherein said array of multimers is utilized for determining nucleotide sequence.

27. The method of claim 25, wherein said array of multimers is utilized for probing interactions of nucleic acids.

28. The method of claim 25, wherein said array of multimers is utilized for identifying gene mutations.

29. The method of claim 25, wherein said array of multimers is utilized for monitoring gene expression.

30. The method of claim 25, wherein said array of multimers is utilized for detecting pathogens.

15. A method for synthesizing, in solution, one or more selected multimers at specific reaction sites on a substrate, the specific reaction sites containing one or more protected initiation moieties, the method comprising:

(a) contacting the substrate with a liquid solution comprising one or more photo-generated reagents, wherein said photogenerated reagents are generated, without use of a photolithographic mask, using an optical system comprising a light source and a computer-controlled spatial optical modulator comprising a digital micromirror device to irradiate specific, fluidly isolated reaction sites, such that the liquid solution is in contact with a selected number of initiation moieties, thereby directly deprotecting the initiation moieties so as to create deprotected initiation moieties;

(b) contacting the substrate with one or more monomers, the monomers comprising an unprotected reactive site and a protected reactive site, under conditions such that the unprotected reactive site of the monomers couple with the deprotected initiation moieties so as to create new initiation moieties with attached monomers; and

(c) repeating steps (a)-(b) until the selected multimers are synthesized.

16. The method of claim 15, wherein the selected multimers are DNA.

17. The method of claim 16, wherein the DNA is selected from the group consisting of nucleotide phosphoramidites and analogs thereof.

18. The method of claim 15, wherein the selected multimers are oligonucleotides.

19. The method of claim 15, wherein the selected multimers are RNA.

20. The method of claim 15, wherein the selected multimers are DNA/RNA hybrids.

21. The method of claim 15, wherein the selected multimers are peptides.

22. The method of claim 15, wherein the selected multimers are oligosaccharides.

23. The method of claim 15, wherein the selected multimers are carbohydrates.

24. The method of claim 15, wherein the coupling of the monomers with the deprotected initiation moieties in step (b) occurs with a yield of 98% or greater.