System for determining receptor-ligand binding affinity

• US 6,491,871 B1
• Filed: 12/09/1997
• Issued: 12/10/2002
• Est. Priority Date: 06/07/1989
• Status: Expired due to Fees

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Winkler, James L., Fodor, Stephen P.A.
• Primary Examiner(s): SNAY, JEFFREY R
• Application Number:
  US08/999,188
• Time in Patent Office: 1,827 Days
• Field of Search: 422/82.05, 422/82.08, 422/63, 250/458.1, 250/328, 356/440, 436/524, 436/531, 436/94, 436/172
• US Class Current: 506/9
• 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 2219/00619 : using hydrophilic or hydrophobic regions
• 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 2219/00639 : the compounds being trapped in or bound to a porous medium
• 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: B01L 7/52 : with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples amplification or hybridisation processes per se C12Q1/68; controlling sequential reactions for synthesis B01J19/0046
• 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 1/04 : 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 1/062 : for alpha- or omega-carboxy functions
• 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: C08G 69/00 : Macromolecular compounds obtained by reactions forming a carboxylic amide link in the main chain of the macromolecule products obtained from isocyanates or isothiocyanates C08G18/00; polyamide-imides C08G73/14
• 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: C40B 80/00 : Linkers or spacers specially adapted for combinatorial chemistry or libraries, e.g. traceless linkers or safety-catch linkers
• CPC Class Codes: G01N 15/1433 : using image recognition
• CPC Class Codes: G01N 21/253 : for batch operation, i.e. multisample apparatus analytical automats G01N35/00
• 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: 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 7/26 : Processing photosensitive materials; Apparatus therefor G03F7/12 - G03F7/24 take precedence
• 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: H01L 25/50 : Multistep manufacturing processes of assemblies consisting of devices, each device being of a type provided for in group H01L27/00 or H01L29/00 H01L21/50 takes precedence
• CPC Class Codes: H01L 2924/00 : Indexing scheme for arrangements or methods for connecting or disconnecting semiconductor or solid-state bodies as covered by H01L24/00
• CPC Class Codes: H01L 2924/0002 : Not covered by any one of groups H01L24/00, H01L24/00 and H01L2224/00
• CPC Class Codes: Y02P 20/55 : Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups
• CPC Class Codes: Y10S 435/961 : including a step of forming, releasing, or exposing the antigen or forming the hapten-immunogenic carrier complex or the antigen per se
• CPC Class Codes: Y10S 435/968 : High energy substrates, e.g. fluorescent, chemiluminescent, radioactive
• CPC Class Codes: Y10S 435/969 : Multiple layering of reactants
• CPC Class Codes: Y10S 435/973 : Simultaneous determination of more than one analyte
• CPC Class Codes: Y10S 436/807 : Apparatus included in process claim, e.g. physical support structures
• CPC Class Codes: Y10S 436/809 : Multifield plates or multicontainer arrays
• CPC Class Codes: Y10T 428/31971 : Of carbohydrate
• CPC Class Codes: Y10T 436/2575 : Volumetric liquid transfer

Abstract

A synthetic strategy for the creation of large scale chemical diversity. Solid-phase chemistry, photolabile protecting groups, and photolithography are used to achieve light-directed spatially-addressable parallel chemical synthesis. Binary masking techniques are utilized in one embodiment. A reactor system, photoremovable protective groups, and improved data collection and handling techniques are also disclosed. A technique for screening linker molecules is also provided.

Claims

1. A system for determining affinity of a receptor to a ligand, comprising:

(a) a substrate that comprises a plurality of ligands at known locations;

(b) an optical arrangement that directs light to a surface of the substrate;

(c) a support upon which the substrate can be placed, wherein when the substrate is placed on the support and operatively aligned with respect to the optical arrangement, the optical arrangement simultaneously illuminates an area of the substrate, wherein the illuminated area is a fraction of each of a plurality of the known locations, which plurality of known locations is a subset of the known locations; and

(d) a detector that detects the amount of light from the illuminated area as a function of position.

2. The system of claim 1, wherein the optical arrangement generates a linear beam of light such that the illuminated area is linear.

3. The system of claim 2, wherein the detector comprises a linear array of detection elements.

4. The system of claim 3, wherein the linear array comprises a linear CCD array.

5. The system of claim 2, wherein the optical arrangement comprises a point light source and a cylindrical lens, the cylindrical lens focusing light from the light source to form the linear beam of light.

6. The system of claim 5, wherein the light source is a laser.

7. The system of claim 2, wherein the optical arrangement comprises a dichromic mirror that directs light to the substrate surface and directs the light fluoresced from the illuminated area to the detector.

8. The system of claim 2, wherein the optical arrangement comprises

(a) a point light source and a cylindrical lens, the cylindrical lens focusing light from the light source to form the linear beam of light; and

(b) a dichromic mirror that directs the linear beam of light to the substrate surface and directs the light fluoresced from the illuminated area to the detector.

9. A system for determining affinity of a receptor to a ligand, comprising:

(a) a substrate that comprises a plurality of ligands at known locations disposed to bind one or more fluorescently labeled receptors;

(b) a device adapted to hold the substrate;

(c) an optical arrangement that directs excitation light to the substrate, the optical arrangement simultaneously illuminating an area of the substrate, wherein

(i) the illuminated area comprises a fraction of each of a plurality of the known locations, which plurality of known locations comprise a subset of the known locations; and

(ii) the excitation light causes fluorescently labeled receptors bound to ligands within the illuminated area to emit fluorescent light; and

(d) a detector that detects the amount of light fluoresced from the illuminated area as a function of position.

10. The system of claim 9, wherein the optical arrangement generates a linear beam of light such that the illuminated area is linear.

11. The system of claim 10, wherein the detector comprises a linear array of detection elements.

12. The system of claim 11, wherein the linear array comprises a linear CCD array.

13. The system of claim 10, wherein the optical arrangement comprises a point light source and a cylindrical lens, the cylindrical lens focusing light from the light source to form the linear beam of light.

14. The system of claim 13, wherein the light source is a laser.

15. The system of claim 10, wherein the optical arrangement comprises a dichromic mirror that directs light to the substrate surface and directs the light fluoresced from the illuminated area to the detector.

16. The system of claim 10, wherein the optical arrangement comprises

(a) a point light source and a cylindrical lens, the cylindrical lens focusing light from the light source to form the linear beam of light; and

(b) a dichromic mirror that directs the linear beam of light to the substrate surface and directs the light fluoresced from the illuminated area to the detector.

17. The system of claim 9, wherein the device that holds the substrate comprises an x-y translation stage and stage controller that can move the substrate relative to a light source such that another area of the substrate can be illuminated.

18. The system of claim 9, further comprising

(a) a processor that receives an electrical signal from the detector and records the amount of light fluoresced from the illuminated area as a function of position;

and

(b) a display unit for displaying an image of locations of the substrate from which fluoresced light is detected.

19. The system of claim 9, wherein the receptors are selected from the group consisting of antibodies, cell membrane receptors, nucleic acids, polypeptides, cofactors, lectins, polysaccharides, enzymes, catalytic polypeptides, hormone receptors and cells.

20. The system of claim 9, wherein the plurality of ligands are selected from the group consisting of polypeptides, nucleic acids, oligosaccharides, enzymes, monoclonal antibodies, enzyme substrates, lectins, hormones and steroids.

21. The system of claim 9, wherein the plurality of ligands are a plurality of different nucleic acids.

22. The system of claim 20, wherein the plurality of ligands are polypeptides.

23. The system of claim 21, wherein the plurality of different nucleic acids comprises at least 100 different nucleic acids.

24. The system of claim 23, wherein the plurality of different nucleic acids comprises at least 1000 different nucleic acids.

25. The system of claim 24, wherein the plurality of different nucleic acids comprises at least 10,000 different nucleic acids.

26. The system of claim 25, wherein the plurality of different nucleic acids comprises at least 100,000 different nucleic acids.