Very large scale immobilized polymer synthesis

• US 20050148027A1
• Filed: 11/23/2004
• Published: 07/07/2005
• 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:
  US10/997,439
• Publication Number:
  US 20050148027A1
• Time in Patent Office: Days
• US Class Current: 435/7.100
• 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 method and apparatus for preparation of a substrate containing a plurality of sequences. Photoremovable groups are attached to a surface of a substrate. Selected regions of the substrate are exposed to light so as to activate the selected areas. A monomer, also containing a photoremovable group, is provided to the substrate to bind at the selected areas. The process is repeated using a variety of monomers such as amino acids until sequences of a desired length are obtained. Detection methods and apparatus are also disclosed.

Claims

1. A method of preparing sequences on a substrate comprising the steps of:

a) exposing a first region of said substrate to an activator to remove a protective group;

b) exposing at least said first region to a first monomer;

c) exposing a second region to an activator to remove a protective group; and

d) exposing at least said second region to a second monomer.

2. The method as recited in claim 1 wherein said steps of exposing to an activator use an activator selected from the group consisting of ion beams, electron beams, gamma rays, x-rays, ultra-violet radiation, light, infra-red radiation, microwaves, electric currents, radiowaves, and combinations thereof.

3. The method as recited in claim 1 wherein said protective groups are photosensitive protective groups.

4. The method as recited in claim 1 wherein said steps of exposing to an activator are steps of applying light to selected regions of said substrate.

5. The method as recited in claim 1 wherein said first and the second monomers are amino acids.

6. The method as recited in claim 1 further comprising a step of screening sequences on said substrate for affinity with a receptor, said step of screening further comprising the step of exposing said substrate to said receptor and testing for the presence of said receptor in said first and said second region.

7. The method as recited in claim 6 wherein said receptor is an antibody.

8. The method as recited in claim 1 wherein said substrate is selected from the group consisting of polymerized Langmuir Blodgett film, functionalized glass, germanium, silicon, polymers, (poly)tetrafluoroethylene, polystyrene, gallium arsenide, and combinations thereof.

9. The method as recited in claim 1 wherein said protective group is selected from the group consisting of ortho-nitrobenzyl derivatives, 6-nitroveratryloxycarbonyl, 2-nitrobenzyloxycarbonyl, cinnamoyl derivatives, and mixtures thereof.

10. The method as recited in claim 1 wherein said first and second regions each have total areas of less than 1 cm².

11. The method as recited in claim 1 wherein said first and second regions each have total areas of between about 1 μ

m² and 10,000 μ

m².

12. The method as recited in claim 4 wherein said light is monochromatic coherent light.

13. The method as recited in claim 1 wherein said steps of exposing to an activator are carried out with a solution in contact with said substrate.

14. The method as recited in claim 13 wherein said solution further comprises said first or said second monomer.

15. The method as recited in claim 6 wherein said receptor further comprises a marker selected from the group consisting of radioactive markers and fluorescent markers and wherein said step of testing for the presence of the receptor is a step of detecting said marker.

16. The method as recited in claim 1 wherein the steps of exposing to an activator further comprise steps of:

a) placing a mask adjacent to said substrate, said mask having substantially transparent regions and substantially opaque regions at a wavelength of light; and

b) illuminating said mask with a light source, said light source producing at least said wavelength of light.

17. The method as recited in claim 1 wherein said steps are repeated so as to synthesize 10³ or more different sequences on said substrate.

18. The method as recited in claim 1 wherein said steps are repeated so as to synthesize 10⁶ or more different sequences on said substrate.

19. A method of synthesizing a plurality of chemical sequences, said chemical sequences comprising at least a first and a second monomer, comprising the steps of:

a) at a first region on a substrate having at least a first and a second region, said first and said second region comprising a substrate protective group, activating said first region to remove said substrate protective group in said first region;

b) exposing said first monomer to said substrate, said first monomer further comprising a first monomer protective group, said first monomer binding at said first region;

c) activating said second region to remove said substrate protective group in said second region;

d) exposing said second monomer to said substrate, said second monomer further comprising a second monomer protective group, said second monomer binding at said second region;

e) activating said first region to remove said first monomer protective group;

f) exposing a third monomer to said substrate, said third monomer binding at said first region to produce a first sequence;

g) activating said second region to remove said second monomer protective group; and

h) exposing a fourth monomer to said substrate, said fourth monomer binding at said second region to produce a second sequence, said second sequence different from said first sequence.

23. The method as recited in claim 19 wherein said protective groups are photosensitive protective groups.

24. The method as recited in claims 19 or 20 wherein said steps of activating and deactivating are steps of applying light to selected regions of said substrate.

25. The method as recited in claims 19 or 20 wherein said first and said second monomers are amino acids.

26. The method as recited in claims 19, 20 or 21 further comprising a step of screening said first and said second sequences for affinity with a first receptor, said step of screening further comprising a step of exposing said substrate to said first receptor and testing for the presence of said first receptor.

27. The method as recited in claim 26 wherein said step of screening is a step of screening with antibodies.

28. The method as recited in claims 19, 20 or 21 wherein said substrate is selected from the group consisting of a polymerized Langmuir Blodgett film, functionalized glass, germanium, silicon, polymers, (poly)tetrafluoroethylene, gallium arsenide, gallium phosphide, silicon oxide, silicon nitride and combinations thereof.

29. The method as recited in claim 19 wherein said protective group, said first monomer protective group, and said second monomer protective group are selected from the group consisting of ortho-nitrobenzyl derivatives, 6-nitroveratryloxycarbonyl, 2-nitrobenzyloxycarbonyl, and mixtures thereof.

31. The method as recited in claims 19 or 20 wherein said first and second regions each have total areas of less than 1 cm².

32. The method as recited in claims 19 or 20 wherein said first and second regions each have total areas of between about 1 μ

m² and 10,000 μ

m².

33. The method as recited in claim 24 wherein said light is monochromatic coherent light.

34. The method as recited in claim 19 wherein said steps of activating are carried out with a solution in contact with said substrate.

35. The method as recited in claim 34 wherein said solution further comprises a monomer.

36. The method as recited in claim 26 wherein said receptor further comprises a marker selected from the group consisting of radioactive markers and fluorescent markers and wherein said step of testing for the presence of the receptor is a step of detecting said marker.

37. The method as recited in claims 19 or 20 wherein two of said first, said second, said third, and said fourth monomers are the same monomers.

40. The method as recited in claim 26 further comprising the step of exposing said substrate to a second, labeled receptor, said second, labeled receptor binding at multiple sites on said first receptor.

41. The method as recited in claim 40 wherein said first receptor is an antibody of a first animal species and said second receptor is an antibody derived from a second species and directed at said first species.

42. The method as recited in claim 19 wherein:

a) said first monomer protective group is removable upon exposure to a first wavelength of light;

b) said second monomer protective group is removable upon exposure to a second wavelength of light;

c) said step of activating said first region to remove said first monomer protective group is a step of exposing substantially all of said substrate to said first wavelength of light; and

d) said step of activating said second region to remove said second monomer protective group is a step of exposing substantially all of said substrate to said second wavelength of light.

43. A method as recited in claims 19 or 21 wherein said protective groups are of the form:

20. A method of synthesizing a plurality of chemical sequences, said chemical sequences comprising at least a first and a second monomer, comprising the steps of:

a) on a substrate having at least a first and a second region deactivating said first region to provide a first protective group in said first region;

b) exposing said first monomer to said substrate, said first monomer binding at said second region;

c) removing said protective group in said first region;

d) deactivating said second region to provide a second protective group in said second region;

e) exposing said second monomer to said substrate, said second monomer binding at said first region;

f) removing said protective group in said second region;

g) deactivating said first region to provide a protective group in said first region;

h) exposing a third monomer to said substrate, said third monomer binding at said second region to produce a first sequence;

i) removing said protective group in said first region; and

j) exposing a fourth monomer to said substrate, said fourth monomer binding at said first region to produce a second sequence, said second sequence different than said first sequence.

30. The method as recited in claim 20 wherein said protective group is a cinnamate group.

21. A method of synthesizing at least a first polymer sequence and a second polymer sequence on a substrate, said first polymer sequence having a different monomer sequence from said second polymer sequence, comprising the steps of:

a) inserting a first mask between said substrate and an energy source, said mask having first regions and second regions, said first regions permitting passage of energy from said source, said second regions blocking energy from said source;

b) directing energy from said source at said substrate, said energy removing a protective group from first portions of said first polymer under said first regions of said first mask;

c) exposing a second portion of said first polymer to said substrate to create a first polymer sequence;

d) inserting a second mask between said substrate and said energy source, said second mask having first regions and second regions;

e) directing energy from said source at said substrate, said energy removing said protective group under said first regions of said second mask from first portions of said second polymer; and

f) exposing a second portion of said second polymer to said substrate, said second portion of said second polymer binding with said first portion of said second polymer to create a polymer 8 second sequence.

22. The method as recited in claim 21 wherein said energy is selected from the group consisting of ion beams, electron beams, gamma rays, x-rays, ultra-violet radiation, light, infra-red radiation, microwaves, electric fields, radiowaves, and combinations thereof.

38. The method as recited in claim 21 wherein the step of inserting a second mask is a step of translating said first mask from a first position to a second position.

39. The method as recited in claim 21 wherein the step of inserting a second mask is a step of rotating said first mask.

44. A method of screening a plurality of amino acid sequences for binding with a receptor comprising the steps of:

a) on a glass plate having at least a first surface, said at least a first surface comprising a photoprotective material selected from the group consisting of nitroveratryloxy carbonyl and nitrobenzyloxy carbonyl, reacting said at least a first surface with t-butoxycarbonyl for storage, said glass plate substantially transparent to at least ultraviolet light;

b) exposing said at least a first surface to TFA to remove said t-butoxycarbonyl;

c) placing said glass plate on a reactor, said reactor comprising a reactor space, said at least a first surface exposed to said reactor space;

d) placing a mask at a first position on said glass plate, said mask comprising first locations and second locations, said first locations substantially transparent to at least ultraviolet light and said second locations substantially opaque to at least ultraviolet light, said second locations comprising a light blocking material on a first surface of said mask, said first surface of said mask placed in contact with said glass plate;

e) filling said reactor space with a reaction solution;

f) illuminating said mask with at least ultraviolet light, said ultraviolet light removing said photoprotective material from said at least a first surface of said glass plate under said first locations of said mask;

g) exposing said first surface to a first amino acid, said first amino acid binding to regions of said at least a first surface from which said photoprotective material was removed, said first amino acid comprising said photoprotective group at a terminus thereof;

h) placing a mask in contact with said glass plate at a second position;

i) illuminating said mask with at least ultraviolet light, said ultraviolet light removing said photoprotective material from said at least a first surface of said glass plate under said first locations of said mask;

j) exposing said at least a first surface to a second amino acid, said second amino acid binding to regions of said at least a first surface from which said photoprotective material was removed, said second amino acid comprising said photoprotective group at a terminus thereof;

k) placing a mask in contact with said glass plate at a third position;

l) illuminating said mask with at least ultraviolet light, said ultraviolet light removing said photoprotective material from said at least a first surface of said glass plate under said first locations of said mask;

m) exposing said at least a first surface to a third amino acid, said third amino acid binding to regions of said at least a first surface from which said photoprotective material was removed;

n) placing a mask in contact with said glass plate at a fourth position;

o) illuminating said mask with at least ultraviolet light, said ultraviolet light removing said photoprotective material from said at least a first surface of said glass plate under said first locations of said mask;

p) exposing said at least a first surface to a fourth amino acid, said fourth amino acid binding to regions of said at least a first surface from which said photoprotective material was removed, said at least a first surface comprising at least first, second, third, and fourth amino acid sequences;

q) exposing said at least a first surface to an antibody of interest, said antibody of interest binding more strongly to at least one of said first, said second, said third, or said fourth amino acid sequences;

r) exposing said at least a first surface to a receptor, said receptor recognizing said antibody of interest and binding at multiple locations thereof, said receptor comprising fluorescein;

s) exposing said at least a first surface to light, said first surface fluorescing in at least a region where said more strongly bound amino acid sequence is located; and

t) detecting and recording fluoresced light intensity as a function of location across said at least a first surface.

45. A method of identifying at least one peptide sequence for binding with a receptor comprising the steps of:

a) on a substrate having a plurality of polypeptides, each having a photoremovable protective group, irradiating first selected polypeptides to remove said protective group;

b) contacting said polypeptides with a first amino acid to create a first sequence, second polypeptides on said substrate comprising a second sequence; and

c) identifying which of said first or said second sequence binds with said receptor.

46. The method as recited in claim 45 wherein said step of identifying further comprises a step of detecting the presence of a marker selected from the group consisting of radioactive markers and fluorescent markers in said receptor.

47. The method as recited in claim 45 wherein said step of irradiating is a step of masking a light source with a mask, said mask comprising first transparent regions and second opaque regions.

48. The method as recited in claim 47 wherein the step of identifying further comprises the steps of:

a) exposing a first receptor to said substrate; and

b) exposing a receptor to said first receptor to said substrate, said receptor to said first receptor comprising a marker.

49. The method as recited in claim 48 wherein said marker is selected from the group consisting of radioactive markers and fluorescent markers.

50. The method as recited in claim 48 wherein said first receptor is an antibody from a first species and said receptor to said first receptor is an antibody from a second species directed at said first species.

52. A method for screening as recited in claim 48 wherein said area is less than about 0.1 cm².

53. A method as recited in claim 48 wherein said area is less than about 10,000 μ

m².

54. A method as recited in claim 48 wherein said area is less than about 100 μ

m².

51. A method for screening a plurality of polymers for biological activity comprising exposing a receptor to a substrate having said plurality of said polymers on a surface thereof, each of said polymers occupying an area of less than about 1 cm².

55. Apparatus for preparation of a plurality of polymers comprising:

a) a substrate with a surface, said surface comprising a reactive portion, said reactive portion activated upon exposure to an energy source so as to react with a monomer; and

b) means for selectively protecting and exposing portions of said surface from said energy source.

56. Apparatus as recited in claim 55 wherein said reactive portion further comprises a protective group, said protective group of the form:

57. Apparatus as recited in claim 55 wherein said reactive portion further comprises linker molecules.

58. Apparatus as recited in claim 57 wherein said linker molecules are selected from the group consisting of ethylene glycol oligomers, diamines, diacids, amino acids, and combinations thereof.

59. Apparatus as recited in claim 55 wherein said means for selectively protecting further comprises a mask.

60. Apparatus as recited in claim 55 wherein said means for selectively protecting further comprises a light valve.

61. Apparatus as recited in claim 55 wherein said energy source is a light source.

62. Apparatus as recited in claim 55 wherein said reactive portion further comprises a composition selected from the group consisting of nitroveratryloxy carbonyl, nitrobenzyloxy carbonyl, dimethyl-dimethoxybenzyloxy carbonyl, 5-bromo-7-nitroindolinyl, hydroxy-2-methyl cinnamoyl, and 2-oxymethylene anthraquinone.

63. Apparatus for preparation of a substrate having a plurality of amino acid sequences thereon, said apparatus comprising:

a) a substrate with a surface;

b) a protective group on said surface, said protective group removable upon exposure to an energy source, said energy source selected from the group consisting of light, electron beams, and x-ray radiation;

c) means for directing said energy source at selected locations on said surface; and

d) means for exposing amino acids to said surface for binding to said surface.

64. Apparatus for screening polymers comprising a substrate with a surface, said surface comprising at least two predefined regions, said predefined regions containing different monomer sequences thereon, said predefined regions each occupying an area of less than about 0.1 cm².

65. Apparatus as recited in claim 64 wherein said area is less than about 0.01 cm².

66. Apparatus as recited in claim 64 wherein said area is less than 10000 μ

m².

67. Apparatus as recited in claim 64 wherein said area is less than about 100 μ

m².

68. Apparatus as recited in claims 64, 65, 66, or 67 wherein said monomer sequences are substantially pure within said predefined regions.

74. A substrate as recited in claim 64 wherein said ligands are substantially pure within said predefined regions.

69. A substrate for screening for biological activity, said substrate comprising 10³ or more different ligands on a surface thereof in predefined regions.

70. A substrate as recited in claim 69 wherein said substrate comprises 10⁴ or more different ligands in predefined regions.

71. A substrate as recited in claim 69 wherein said substrate comprises 10⁵ or more different ligands in predefined regions.

72. A substrate as recited in claim 69 wherein said substrate comprises 10⁶ or more different ligands in predefined regions.

73. A substrate as recited in claims 69, 70, 71, or 72 wherein the ligands are peptides.

75. Apparatus for screening for biological activity comprising:

a) a substrate comprising a plurality of polymer sequences, said polymer sequences attached to a surface of said substrate at known locations on said substrate, each of said sequences occupying an area of less than about 0.1 cm²;

b) means for exposing said substrate to a receptor, said receptor marked with a fluorescent marker, said receptor binding with at least one of said sequences; and

c) means for detecting a location of said fluorescent marker on said substrate.

76. Apparatus for forming a plurality of polymer sequences comprising:

a) a substrate, said substrate having at least a first surface and a second surface, said second surface comprising a photoremovable protective material, said substrate substantially transparent to at least light of a first wavelength;

b) a reactor body, said reactor body having a mounting surface with a reaction fluid cavity therein, said second surface maintained in a sealed relationship with said mounting surface; and

c) a light source for producing light of at least said first-wavelength and directed at a surface of said substrate.

77. Apparatus as recited in claim 76 wherein said light source is directed at said first surface.

78. Apparatus as recited in claim 76 further comprising a mask, said mask placed between said light source and said first surface, said mask having first regions substantially transparent to said first wavelength of light and second regions substantially opaque to said first wavelength of light.

79. Apparatus as recited in claim 76 wherein said cavity comprises a fluid inlet and a fluid outlet, said fluid inlet connected to a pump for flowing reaction fluids through said cavity.

80. Apparatus as recited in claim 76 wherein said cavity further comprises a plurality of raised sections.

81. Apparatus as recited in claim 78 wherein said mask further comprises a glass plate.

82. Apparatus as recited in claim 81 wherein said opaque regions on said mask comprise chrome.

83. Apparatus as recited in claim 76 wherein at least a portion of said second surface comprises a second photoremovable protective group, said second photoremovable protective group activatable upon exposure to light of a second wavelength.

84. Apparatus as recited in claim 76 further comprising first and second gaskets on said mounting surface and means for maintaining a vacuum between said first and second gaskets.

85. Apparatus as recited in claim 76 wherein said substrate has a thickness of less than 1 mm.

86. Apparatus as recited in claim 76 wherein said substrate has a thickness of less than 0.5 mm.

87. Apparatus as recited in claim 76 wherein said substrate has a thickness of less than 0.05 mm.

88. Apparatus as recited in claim 78 wherein said mask is in direct contact with said substrate.

89. Apparatus as recited in claim 88 wherein opaque regions of said mask are placed in direct contact with said substrate.

90. Apparatus as recited in claim 76 further comprising a liquid crystal light valve for selectively controlling exposure of light to said substrate.

91. Apparatus as recited in claim 76 further comprising a fiber optic faceplate between said light source and said substrate.

92. Apparatus as recited in claim 76 further comprising a molecular microcrystal between said light source and said substrate.

93. Apparatus as recited in claim 76 wherein said cavity comprises light absorptive materials.

94. Apparatus as recited in claim 93 wherein said light absorptive material is N,N-diethylamino 2,4-dinitrobenzene.

95. Apparatus as recited in claim 76 wherein said cavity is filled with a carrier solution.

96. Apparatus as recited in claim 95 wherein said carrier material comprises a material selected from the group of 1-hydroxybenzotriazole, dimethylformamide, diisopropylethylamine, and benzotriazolyl-n-oxy-tris (dimethylamino) phosphoriumhexafluorophosphate.

97. Apparatus as recited in claim 76 wherein said substrate is a fiber optic faceplate.

98. Apparatus for detection of fluorescent marked regions on a substrate comprising:

a) a light source for directing light at a surface of said substrate;

b) a means for detecting light fluoresced from said surface in response to said light source;

c) means for translating said substrate from a first position to a second position; and

d) means for storing fluoresced light intensity as a function of location on said substrate, said means for storing connected to said means for translating and said means for detecting.

99. Apparatus as recited in claim 98 further comprising video display means for displaying light intensity as a function of location on said substrate.

100. Apparatus as recited in claim 98 wherein said means for detecting comprises a photomultiplier tube and a photon counter.

101. Apparatus as recited in claim 99 wherein said means for directing light further comprises a dichroic mirror, said mirror reflecting light at a wavelength of said light source and passing said fluoresced light.

102. Apparatus as recited in claim 100 wherein said light source is a laser light source.

103. Apparatus as recited in claim 101 wherein said means for storing is a programmed digital computer.

104. Apparatus as recited in claim 102 further comprising a microscope, said light source directed at said substrate through said microscope, said means for detecting receiving light from said microscope.