Method and apparatus for chemical and biochemical reactions using photo-generated reagents

• US 6,426,184 B1
• Filed: 02/10/1999
• Issued: 07/30/2002
• Est. Priority Date: 02/11/1998
• Status: Expired due to Term

• Current Assignee: University of Houston (University of Houston System), University of Houston Law Center (University of Houston System), Board of Regents of the University of Michigan (University of Michigan)
• Original Assignee: Board of Regents of the University of Michigan (University of Michigan)
• Inventors: Gao, Xiaolian, Gulari, Erdogan, Zhou, Xiaochuan
• Primary Examiner(s): CELSA, BENNETT M
• Application Number:
  US09/248,093
• Publication Number:
  US 20020081582A1
• Time in Patent Office: 1,266 Days
• Field of Search: 435/6, 435/7.1, 422/134, 422/129, 530/333-337
• 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 2219/00434 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. Specifically, the method and apparatus of the present invention have applications in parallel synthesis of molecular sequence arrays on solid surfaces.

Claims

1. A method of attaching monomers at specific reaction sites on a substrate, said specific reaction sites containing one or more non-photolabile protected initiating moieties, the method comprising:

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

b) isolating said specific reaction sites;

c) irradiating a selected number of the isolated reaction sites to produce, in situ, at least one photo-generated reagent without the formation of a polymeric coating layer, thereby directly deprotecting the initiating moieties at the irradiated reaction sites so as to create deprotected initiating moieties; and

d) contacting said substrate with a first monomer, said first monomer comprising an unprotected reactive site and a protected reactive site, under conditions such that said unprotected reactive site of said monomer couples with said deprotected initiating moieties so as to create an attached first monomer.

2. The method of claim 1, wherein said initiating moieties of step (a) comprise linker molecules, each of said linker molecules comprising a reactive functional group protected by an acid-labile protecting group.

3. The method of claim 2, wherein said reactive functional group of said linker molecules comprises a hydroxyl group.

4. The method of claim 1, wherein said first monomer is selected from the group consisting of nucleophosphoramidites, nucleophosphonates and analogs thereof.

5. The method of claim 1, wherein said attached first monomer of step (d) comprises a nucleotide monomer with a protected group.

6. The method of claim 5, wherein said protected group is protected by an acid-labile group.

7. The method of claim 5, further comprising the step of deprotecting said protected group so as to create a deprotected attached nucleotide monomer.

8. The method of claim 7, further comprising the step of contacting said deprotected attached nucleotide monomer with a second monomer, said second monomer comprising an unprotected reactive site and a protected reactive group, under conditions such that said unprotected reactive site of said second monomer couples with said deprotected attached nucleotide monomer so as to create an attached second monomer, said attached first and second monomers comprises a multimer.

9. The method of claim 8, wherein said multimer comprises DNA.

10. The method of claim 1, wherein said attachment of said monomers occurs with a yield of 98% or greater.

11. The method of claim 1, wherein said initiating moieties of step (a) comprise oligomers to which a monomer can be attached.