Support bound probes and methods of analysis using the same

• US 20040038268A1
• Filed: 06/04/2003
• Published: 02/26/2004
• Est. Priority Date: 06/07/1989
• Status: Abandoned Application

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Fodor, Stephen P.A., Pirrung, Michael C., Stryer, Lubert, Read, J. Leighton
• Application Number:
  US10/454,566
• Publication Number:
  US 20040038268A1
• 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 2219/00315 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 2219/00621 : by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 : Covalent
• CPC Class Codes: B01J 2219/0063 : Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00637 : by coating it with another layer
• CPC Class Codes: B01J 2219/00644 : the porous medium being present in discrete locations, e.g. gel pads
• 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: C07C 229/14 : to carbon atoms of carbon skeletons containing rings
• CPC Class Codes: C07C 229/16 : to carbon atoms of hydrocarbon radicals substituted by amino or carboxyl groups, e.g. ethylenediamine-tetra-acetic acid, iminodiacetic acids
• CPC Class Codes: C07D 263/44 : Two oxygen atoms
• CPC Class Codes: C07D 317/62 : with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to atoms of the carbocyclic ring
• CPC Class Codes: C07H 19/04 : Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
• 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 1/042 : 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 1/6827 : for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6834 : Enzymatic or biochemical coupling of nucleic acids to a solid phase
• 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: C12Q 2535/131 : Allele specific probes
• CPC Class Codes: C12Q 2563/149 : Particles, e.g. beads
• CPC Class Codes: C12Q 2565/626 : being a flow cytometer
• 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 15/1433 : using image recognition
• 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: G01N 21/6452 : Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G01N 21/6458 : Fluorescence microscopy fluorescence microscopes per se G02B21/0076 and G02B21/16
• 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

Abstract

The present invention provides methods and apparatus for sequencing, fingerprinting and mapping biological macromolecules, typically biological polymers. The methods make use of a plurality of sequence specific recognition reagents which can also be used for classification of biological samples, and to characterize their sources.

Claims

1. A binary method for combinatorial synthesis of more than 10³ molecules in a total area of less than 1 cm² on a single support, comprising:

a) providing a single support structure having reaction regions, the number of reaction regions being greater than 10³/cm²;

b) directing energy at a selected first set of localized areas to activate the first set of areas for synthesis of a molecule, thereby creating a first set of activated areas;

c) contacting a monomer of the molecule with an area inclusive of the first set of activated areas of the support;

d) coupling the monomer to the first set of activated areas of the support;

e) directing energy at a selected second set of localized areas which are the same as or different from, in whole or in part, the first set of localized areas to activate the second set of areas for synthesis of a molecule, thereby creating a second set of activated areas;

f) contacting a monomer of the molecule with an area inclusive of the second set of activated areas of the support;

g) coupling the monomer to the second set of activated areas of the support; and

h) repeating steps (e), (f) and (g) until the molecules are synthesized.

2. The method of claim 1, wherein there are more than 10⁴ molecules in a total area of less than 1 cm² on a single support.

3. The method of claim 2, wherein there are more than 10⁵ molecules in a total area of less than 1 cm² on a single support.

4. The method of claim 1, wherein the method does not include the physical separation of liquids.

5. The method of claim 1, wherein the support has a surface which can be composed of the same or different material as the support and the support or the surface comprises polymers, plastics, resins, polysaccharide, silicon, silicon based materials, carbon, metals, inorganic glasses, glasses, membranes, particles, strands, precipitates, gels, sheets, tubing, spheres, containers, capillaries, pads, slices, films, plates or slides.

6. The method of claim 1, wherein the molecules are selected from the group consisting of nucleic acids, polypeptides, carbohydrates, alpha-, beta-, and omega-amino acids, polyurethanes, polyesters, polycarbonates, polyureas, polyamides, polyethyleneimines, polyarylene sulfides, polysiloxanes, polyimides, polyacetates, and mixed polymers.

7. The method of claim 1, wherein the monomers of the molecules comprise a photosensitive protecting group.

8. A method of synthesizing polymers, comprising:

providing a support;

iteratively, inactivating selected regions of the support in regions where activation is not desired;

iteratively, independently activating selected regions of the support; and

contacting the activated regions with a monomer under coupling conditions;

wherein monomers are covalently attached to the support in the activated regions on the support to form the polymers.

9. The method of claim 8, wherein more than 10⁴ polymers are synthesized on the support.

10. The method of claim 9, wherein more than 10⁵ polymers are synthesized on the support.

11. The method of claim 8, wherein the method does not include the physical separation of liquids.

12. The method of claim 8, wherein the support has a surface which can be composed of the same or different material as the support and the support or the surface comprises polymers, plastics, resins, polysaccharide, silicon, silicon based materials, carbon, metals, inorganic glasses, glasses, membranes, particles, strands, precipitates, gels, sheets, tubing, spheres, containers, capillaries, pads, slices, films, plates or slides.

13. The method of claim 8, wherein the polymers are selected from the group consisting of nucleic acids, polypeptides, carbohydrates, alpha-, beta-, and omega-amino acids, polyurethanes, polyesters, polycarbonates, polyureas, polyamides, polyethyleneimines, polyarylene sulfides, polysiloxanes, polyimides, polyacetates, and mixed polymers.

14. The method of claim 8, wherein the monomers comprise a photosensitive protecting group.

15. A method of using combinatorial chemistry methods to synthesize polymers in n^x steps, comprising:

providing a set of monomers having n members;

iteratively, coupling the monomers to a support to achieve length x in n^x steps by selectively activating areas of the support and coupling monomers to activated areas of the support, wherein the support is protected from coupling in unwanted areas by protecting groups that are removed during the activation step.

16. The method of claim 15, wherein more than 10⁴ polymers are synthesized on the support.

17. The method of claim 16, wherein more than 10⁵ polymers are synthesized on the support.

18. The method of claim 15, wherein the method does not include the physical separation of liquids.

19. The method of claim 15, wherein the support has a surface which can be composed of the same or different material as the support and the support or the surface comprises polymers, plastics, resins, polysaccharide, silicon, silicon based materials, carbon, metals, inorganic glasses, glasses, membranes, particles, strands, precipitates, gels, sheets, tubing, spheres, containers, capillaries, pads, slices, films, plates or slides.

20. The method of claim 15, wherein the polymers are selected from the group consisting of nucleic acids, polypeptides, carbohydrates, alpha-, beta-, and omega-amino acids, polyurethanes, polyesters, polycarbonates, polyureas, polyamides, polyethyleneimines, polyarylene sulfides, polysiloxanes, polyimides, polyacetates, and mixed polymers.

21. The method of claim 15, wherein the protecting groups are photosensitive protecting groups.