Photolithographic and other means for manufacturing arrays

• US 6,416,952 B1
• Filed: 09/01/2000
• Issued: 07/09/2002
• 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: Pirrung, Michael C., Fodor, Stephen P. A., Stryer, Lubert, Read, J. Leighton
• Primary Examiner(s): FREDMAN, JEFFREY NORMAN
• Application Number:
  US09/654,206
• Time in Patent Office: 676 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 536/22.1
• 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 2219/00621 : 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 2219/00644 : 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 1/6837 : 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 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 method of using a fluorescent label to detect binding with polypeptide probes of known sequence, said method comprising:

(a) attaching said label to a target polypeptide to form a labeled polypeptide;

(b) contacting said labeled target polypeptide with a collection of polypeptide probes of known sequences wherein said polypeptide probes are attached to a substrate at positionally defined locations; and

(c) determining the sequences of the probes that bind with said target, said collection comprising at least 100 different probes per square centimeter of substrate.

2. The method of claim 1, wherein said polypeptide probes are members selected from the group consisting of antibodies, monoclonal antibodies, antibody fragments, whole cells lysates, receptors, murine antibodies, goat antibodies, proteins exhibiting binding specificity and combinations thereof.

4. The method of claim 1, wherein each of said polypeptide probes occupies an area on said substrate of less than about 1 cm² to about 1×

10<sup>−

5</sup> cm².

5. The method of claim 4, wherein each of said polypeptide probes occupies an area on said substrate of less than about 1×

10<sup>−

1</sup> cm² to about 1×

10<sup>−

4</sup> cm².

6. The method of claim 5, wherein each of said polypeptide probes occupies an area on said substrate of less than about 1×

10<sup>−

2</sup> cm² to about 1×

10<sup>−

3</sup> cm².

7. The method of claim 1, wherein said polypeptide probes occupy a density of about 400 different polypeptides/cm².

8. The method of claim 1, wherein said polypeptide probes occupy a density of about 1000 different polypeptides/cm².

9. The method of claim 1, wherein said substrate contains more than 100 different polypeptides per cm².

10. The method of claim 1, wherein said substrate contains more than 1,000 different polypeptides per cm².

11. The method of claim 1, wherein said substrate contains more than 10,000 different polypeptides per cm².

3. A method of using a fluorescent label to detect binding with polypeptide probes of known sequence, said method comprising:

(a) attaching said label to a target polypeptide to form a labeled polypeptide;

(b) contacting said labeled target polypeptide with a collection of polypeptide probes of known sequences wherein said polypeptide probes are attached to a substrate at positinally defined locations; and

(c) identifying the probes that bind with said target, said collection comprising more than 100 different probes per square centimeter of substrate.

12. A method of mapping a plurality of polypeptides relative to one another, said method comprising:

(a) preparing a substrate having attached thereto at positionally defined locations a plurality of sequence specific probes comprising at least about 100 probes per square centimeter of substrate;

(b) subjecting each of said polypeptides to contact with the probes attached to said substrate under binding conditions; and

(c) determining the relative locations of said binding of said polypeptides to determine the overlap of said plurality of polypeptides.

13. The method of claim 12, wherein said specific probes are members selected from the group consisting of antibodies, monoclonal antibodies, antibody fragments, whole cells lysates, receptors, murine antibodies, goat antibodies, proteins exhibiting binding specificity and combinations thereof.

14. The method of claim 12, wherein each of said specific probes occupies an area on said substrate of less than about 1 cm² to about 1×

10<sup>−

5</sup> cm².

15. The method of claim 14, wherein each of said specific probes occupies an area on said substrate of less than about 1×

10<sup>−

1</sup> cm² to about 1×

10<sup>−

4</sup> cm².

16. The method of claim 15, wherein each of said specific probes occupies an area on said substrate of less than about 1×

10<sup>−

2</sup> cm² to about 1×

10<sup>−

3</sup> cm².

17. The method of claim 12, wherein said specific probes occupy a density of about 400 different polypeptides/cm².

18. The method of claim 12, wherein said specific probes occupy a density of about 1000 different polypeptides/cm².

19. The method of claims 12, wherein said substrate contains more than 100 different specific probes per cm².

20. The method of claim 12, wherein said substrate contains more than 1,000 different specific probes per cm².

21. The method of claim 12, wherein said substrate contains more than 10,000 different specific per cm².

22. A method for identifying polypeptide probes, said method comprising:

(a) binding non-identical polypeptide probes attached to a substrate at a density of at least 100 of said probes per square centimeter with target polypeptides;

(b) identifying a first polypeptide probe that binds in step (a) with said target polypeptide;

(c) further identifying other polypeptide probes which binds in step (a) beginning with a second polypeptide probe; and

(d) continuing said identification to identify at least about 100 probes that bind with said target polypeptides.

23. The method of claim 22, wherein said first polypeptide probe is selected from the group consisting of a monoclonal antibody, an antibody fragment, a whole cell lysate, a receptor, a murine antibody, a goat antibody, a protein exhibiting binding specificity, an enzyme binding site, an antibody binding site and a combination thereof.

24. The method of claim 22, wherein said target polypeptides are members selected from the group consisting of antibodies, monoclonal antibodies, antibody fragments, whole cells lysates, receptors, murine antibodies, goat antibodies, proteins exhibiting binding specificity and combinations thereof.

25. The method of claim 22, wherein each of said polypeptide probes occupies an area on said substrate of less than about 1 cm² to about 1×

10^{31 5} cm².

26. The method of claim 25, wherein each of said polypeptide probes occupies an area on said substrate of less than about 1×

10<sup>−

1</sup> cm² to about 1×

10<sup>−

4</sup> cm².

27. The method of claim 26, wherein each of said polypeptide probes occupies an area on said substrate of less than about 1×

10<sup>−

2</sup> cm² to about 1×

10<sup>−

3</sup> cm².

28. The method of claim 22, wherein said polypeptide probes occupy a density of more than 400 different polypeptides/cm².

29. The method of claim 22, wherein said polypeptide probes occupy a density of more than 1000 different polypeptides/cm².

30. The method of claim 22, wherein said method produces a substrate that contains more than 100 different polypeptides per cm².

31. The method of claim 22, wherein said method produces a substrate that contains more than 1,000 different polypeptides per cm².

32. The method of claim 22, wherein said method produces a substrate that contains more than 10,000 different polypeptides per cm².

33. A method for detecting sequences in two or more collections of polypeptides, the method comprising:

(a) providing an array of polypeptides bound to a solid surface, each said polypeptide comprising a determinable sequence;

(b) sequentially or simultaneously contacting the array of polypeptides with;

(i) a first collection of labeled polypeptides comprising a sequence that will bind to a polypeptide of said array, and

(ii) at least a second collection of labeled polypeptide comprising a sequence that will bind to a polypeptide of said array;

wherein the first and second labels are distinguishable from each other; and

(c) detecting binding of the first and second labeled polypeptides to polypeptides of said arrays.

34. The method of claim 33, wherein said first collection of labeled polypeptides are members selected from the group consisting of antibodies, monoclonal antibodies, antibody fragments, whole cells lysates, receptors, murine antibodies, goat antibodies, proteins exhibiting binding specificity and combinations thereof.

35. The method of claim 33, wherein the solid support comprises an array of beads.

36. The method of claim 33, wherein the first and second labels are fluorescent labels.

37. The method of claim 33, wherein each polypeptide in said array of polypeptides occupies an area on said substrate of less than about 1 cm² to about 1×

10<sup>−

5</sup> cm².

38. The method of claim 37, wherein each polypeptide in said array of polypeptides occupies an area on said substrate of less than about 1×

10<sup>−

1</sup> cm² to about 1×

10<sup>−

4</sup> cm².

39. The method of claim 38, wherein each polypeptide in said array of polypeptides occupies an area on said substrate of less than about 1×

10<sup>−

2</sup> cm² to about 1×

10<sup>−

3</sup> cm².

40. The method of claim 33, wherein said array of polypeptides occupy a density of more than 400 different polypeptides/cm².

41. The method of claim 33, wherein said array of polypeptides occupy a density of about 1000 different polypeptides/cm².

42. The method of claim 33, wherein said method produces a substrate that contains more than 100 different polypeptides per cm².

43. The method of claim 33, wherein said method produces a substrate that contains more than 1,000 different polypeptides per cm².

44. The method of claim 33, wherein said method produces a substrate that contains more than 10,000 different polypeptides per cm².