Immobilized molecular synthesis of systematically substituted compounds

• US 5,527,681 A
• Filed: 11/05/1992
• Issued: 06/18/1996
• Est. Priority Date: 06/07/1989
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymax Incorporated
• Inventors: Holmes, Christopher P.
• Primary Examiner(s): Spiegel, Carol A.
• Application Number:
  US07/972,007
• Time in Patent Office: 1,321 Days
• Field of Search: 435/6, 435/7.92, 435/5, 435/973-974, 436/518, 436/527-532, 436/809, 530/333-337, 427/2, 427/2.11, 536/25.3, 536/25.31, 536/25.32
• US Class Current: 506/16
• 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 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00434 Liquid crystal masks
• CPC Class Codes: B01J 2219/00436 Maskless processes
• CPC Class Codes: B01J 2219/00459 Beads
• CPC Class Codes: B01J 2219/00468 by manipulation of individual beads
• CPC Class Codes: B01J 2219/00475 Sheets
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00531 essentially square
• 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 2219/00626 : Covalent
• CPC Class Codes: B01J 2219/00637 : by coating it with another layer
• CPC Class Codes: B01J 2219/00648 : by the use of solid beads
• CPC Class Codes: B01J 2219/00659 : Two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 : using computers
• CPC Class Codes: B01J 2219/00695 : Synthesis control routines, e.g. using computer programs
• 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: B82Y 10/00 : Nanotechnology for information processing, storage or transmission, e.g. quantum computing or single electron logic
• 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 19/10 : with the saccharide radical esterified by phosphoric or polyphosphoric acids
• 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 1/04 : on carriers C07K1/003, C07K1/006 take precedence
• CPC Class Codes: C07K 1/042 : characterised by the nature of the carrier
• 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: C07K 17/06 : attached to the carrier via a bridging agent
• CPC Class Codes: C07K 17/14 : Peptides being immobilised on, or in, an inorganic carrier
• CPC Class Codes: C07K 7/06 : having 5 to 11 amino acids
• CPC Class Codes: C12Q 1/6809 : Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6816 : characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6874 : involving nucleic acid arrays, e.g. sequencing by hybridisation
• 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 60/14 : for creating libraries
• CPC Class Codes: G01N 21/6428 : Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• 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
• CPC Class Codes: G03F 7/265 : Selective reaction with inorganic or organometallic reagents after image-wise exposure, e.g. silylation
• CPC Class Codes: G03F 7/38 : Treatment before imagewise removal, e.g. prebaking G03F7/265 takes precedence
• CPC Class Codes: G11C 13/0014 : comprising cells based on organic memory material
• CPC Class Codes: G11C 13/0019 : comprising bio-molecules
• CPC Class Codes: Y02P 20/55 : Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups
• CPC Class Codes: Y10S 435/973 : Simultaneous determination of more than one analyte
• CPC Class Codes: Y10S 435/974 : Aids related test
• CPC Class Codes: Y10S 436/809 : Multifield plates or multicontainer arrays

Abstract

A synthetic strategy for the creation of large scale chemical diversity is claimed. Solid-phase chemistry, photolabile protecting groups, and photolithography are used to achieve light-directed spatially-addressable parallel chemical synthesis of an array of polymers that are based on a target polymer. The array includes systematically substituted versions of the target polymer.

Claims

1. A method of synthesizing an array of oligonucleotides on a surface of a substrate, the method comprising the steps of:

identifying a target oligonucleotide having a nucleic acid monomer sequence complementary to a receptor oligonucleotide of interest;

synthesizing an array of oligonucleotides on said surface of said substrate by the steps of activating predefined regions of said substrate and covalently coupling selected nucleic acid monomers to said substrate to form an array of oligonucleotides, said array of oligonucleotides comprising more than one group of oligonucleotides, wherein each of said more than one group consists of a sequence of nucleic acid monomers that is the same as the nucleic acid monomer sequence of said target oligonucleotide, except that each of said more than one group has a different single position in said nucleic acid monomer sequence of said target oligonucleotide substituted with each member of a basis set of nucleic acid monomers; and

determining which oligonucleotide sequence in each of said groups of oligonucleotides specifically binds to said receptor oligonucleotide of interest.

2. The method as recited in claim 1 wherein said determining step comprises the steps of:

contacting said array with said receptor oligonucleotide of interest;

determining which oligonucleotide sequence in each of said groups of oligonucleotides in said array are complementary to said receptor oligonucleotide of interest by identifying where said receptor oligonucleotide of interest has bound said array.

3. The method as recited in claim 1 wherein said synthesizing step comprises synthesizing said more than one group of oligonucleotides by the steps of:

performing a first series of activation and coupling steps in which each activation and coupling step in said first series of activation and coupling steps activates and couples nucleic acid monomers in said nucleic acid monomer sequence of said target oligonucleotide in a selected region of said substrate, each selected region comprising a portion of a region activated in a previous step of said first series of activation and coupling steps; and

performing a second series of activation and coupling steps to couple each member of the basis set of nucleic acid monomers to a different portion of the oligonucleotides formed in each step of said first series of activation and coupling steps.

4. The method as recited in claim 1 wherein said activating steps comprise the step of irradiating said substrate.

5. The method as recited in claim 3 wherein said activation steps comprise the step of irradiating said substrate.

6. The method as recited in claim 3, wherein said synthesizing step, further comprises the steps of performing a third series of activation and coupling steps in which each of said activation and coupling steps couples nucleic acid monomers in said nucleic acid monomer sequence of said target oligonucleotide to said oligonucleotides synthesized in said first and second series of activation and coupling steps.

7. The method as recited in claim 5 wherein the substrate is planar, and:

said first series of irradiating steps uses a first mask having at least first and second transparent regions spanning a vertical portion of said substrate; and

said second series of irradiating steps uses a mask having a horizontally oriented transparent region spanning portions of said substrate corresponding to said first and second transparent regions.