Support bound probes and methods of analysis using the same

• US 6,610,482 B1
• Filed: 04/24/2000
• Issued: 08/26/2003
• 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): ZITOMER, STEPHANIE W
• Application Number:
  US09/557,875
• Time in Patent Office: 1,219 Days
• Field of Search: 435/6, 536/22.1, 536/23.1
• 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 2219/00621 : 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. An array of oligonucleotides, the array comprising:

a planar solid support having at least a first surface; and

at least 1000 different oligonucleotides attached to the first surface of the solid support in an area of less than 1 cm², wherein each of the different oligonucleotides is attached to the surface of the solid support in a different localized area, and has a different determinable sequence.

2. The array of claim 1, wherein each different oligonucleotides is from about 4 to about 20 nucleotides in length.

3. The array of claim 1, wherein each different oligonucleotide is at least 12 nucleotides in length.

4. The array of claim 1, wherein each different oligonucleotide is 2-100 nucleotides in length.

5. The array of claim 1, wherein the array comprises at least 1,000 different oligonucleotides attached to the first surface of the solid support.

6. The array of claim 1, wherein the array comprises at least 10,000 different oligonucleotides attached to the first surface of the solid support.

7. The array of claim 1, wherein each of the different localized areas is physically separated from each other of the localized areas.

8. The array of claim 1, wherein said planar solid support is glass.

9. The array of claim 1, wherein said oligonucleotides are attached to the first surface of the solid support through a linker group.

10. The array of claim 1, wherein the oligonucleotides in the different localized areas are at least 20% pure.

11. The array of claim 1, wherein the oligonucleotides in the different localized areas are covalently attached to the support.

12. The array of claim 1, wherein the oligonucleotides in the different localized areas are at least 80% pure and greater than 25 bases in length.

13. The array of claim 1, wherein the oligonucleotides in the different localized areas are greater than 50 bases in length.

14. The array of claim 1, wherein the oligonucleotides in the different localized areas are of known sequences.

15. The array of claim 1, wherein said array is produced by a binary synthesis process, said process comprising the steps of:

providing a planar solid support, said solid support having a plurality of compounds immobilized on a surface thereof, said compounds having protecting groups coupled thereto;

deprotecting a first portion of said plurality of compounds on said surface and not a second portion of said plurality of compounds;

reacting said first portion of said plurality of compounds with a first component of said oligonucleotide;

deprotecting at least a third portion of said plurality of compounds on said surface, said third portion comprising a fraction of said first portion of said plurality of compounds;

reacting said at least third portion of said plurality of compounds with a second component of said oligonucleotide; and

optionally repeating said binary synthesis steps to produce said oligonucleotide array.

16. An array of nucleic acids, the array comprising:

a planar support having at least a first surface; and

at least 1000 different nucleic acids attached to the first surface of the solid support within an area of 1 cm2, wherein each of the different nucleic acids is attached to the surface of the solid support in a different known location, has a different determinable sequence.

17. The array of claim 16, wherein each different nucleic acid is at least 12 nucleotides in length.

18. The array of claim 16, wherein the array comprises at least 1,000 different nucleic acids attached to the first surface of the solid support.

19. The array of claim 16, wherein the array comprises at least 10,000 different nucleic acids attached to the first surface of the solid support.

20. The array of claim 16, wherein each of the different localized areas is physically separated from each of the other known locations.

21. The array of claim 16, wherein said planar solid support is glass.

22. The array of claim 16, wherein said nucleic acids are attached to the first surface of the solid support through a linker group.

23. The array of claim 16, wherein the nucleic acids in the different localized areas comprise nucleic acids that are at least 20% pure.

24. The array of claim 16, wherein the nucleic acids in the different localized areas comprise nucleic acids that are covalently bound to the support.

25. The array of claim 16, wherein the nucleic acids in the different localized areas are greater than 25 bases in length.

26. The array of claim 16, the nucleic acids in the different localized areas are greater than 50 bases in length.

27. The array of claim 16, wherein said array is produced by a binary synthesis process, said process comprising the steps of:

providing a planar, solid support, said support having a plurality of compounds immobilized on a surface thereof, said compounds having protecting groups coupled thereto;

deprotecting a first portion of said plurality of compounds on said surface and not a second portion of said plurality of compounds;

reacting said first portion of said plurality of compounds with a first reactant;

deprotecting at least a third portion of said plurality of compounds on said surface, said third portion comprising a fraction of said first portion of said plurality of compounds;

reacting said at least third portion of said plurality of compounds with a second reactant; and

optionally repeating said binary synthesis steps to produce said nucleic acid array.

28. The array of claim 16, wherein the nucleic acids are covalently attached to the support.

31. The array of claim 16, wherein the different localized areas are square in shape.

32. The array of claim 16, wherein the substrate is glass.

33. The array of claim 16, wherein the substrate is silicon dioxide.

34. The array of claim 16, wherein the substrate is (poly)tetrafluoroethylene, (poly)vinylidenedifluoride, polystryene or polycarbonate.

35. The method of claim 16, wherein the substrate is optically transparent.

36. The array of claim 16, wherein the substrate is functionalized with groups that attach to the plurality of different nucleic acids.

29. An array of nucleic acids, the array comprising:

a planar solid support having at least a first surface; and

a plurality of different nucleic acids attached to the first surface of the solid support at a density exceeding 10,000 different nucleic acids/cm², wherein each of the different nucleic acids is attached to the surface of the solid support in a different localized areas, and has a different determinable sequence.

30. An array of nucleic acids, the array comprising:

a planar support having at least a first surface; and

a plurality of different nucleic acids attached to the first surface of the solid support at a density exceeding 400 different nucleic acids/cm², wherein each of the different nucleic acids is attached to the surface of the solid support in a different localized area, has a different determinable sequence, wherein the surface and the support are made from different materials.

37. An array of biological polymers, the array comprising:

a solid support; and

a plurality of different biological polymers attached to a surface of the solid support at a density greater than 400 different polymers/cm², wherein each of the different biological polymers has a known or determinable sequence and is positionally distinguishable from other polymers.

38. The array of claim 37, wherein the biological polymers are peptides.

39. The array of claim 37, wherein each different biological polymer is greater than 25 monomers in length.

40. The array of claim 37, wherein each different biological polymer is greater than 50 monomers in length.

41. The array of claim 37, wherein the array contains more than 1,000 different biological polymers.

42. The array of claim 37, wherein the array comprises a density of at least 1,000/cm².

43. The array of claim 37, wherein the array comprises a density of at least 10,000/cm².

44. The array of claim 37, wherein each of the different biological polymers is physically separated from other polymers.

45. The array of claim 37, wherein said solid support is planar glass.

46. The array of claim 37, wherein said biological polymers are attached to the surface of the solid support through a linker group.

47. The array of claim 37, wherein the sequence of each of the different biological polymers is known.

48. The array of claim 37, wherein the different biological polymers are nucleic acids and the density is at least 1,000 nucleic acids/cm².

49. The array of claim 37, wherein the substrate is rigid.

50. The array of claim 37, wherein the array is produced by a binary synthesis process.

51. The array of claim 39, wherein the biological polymers are nucleic acids.

58. The array of claim 37, wherein the solid support has a surface which can be composed of the same or different material as the substrate and the support or the surface comprises polymers, plastics, resins, polysaccharide, silicon, silicon based materials, carbon, metals, inorganic glasses, membranes, particles, strands, precipitates, gels, sheets, tubing, spheres, containers, capillaries, pads, slices, films, plates or slides.

60. The array of claim 37, wherein the solid support has a surface which can be composed of the same or different material as the substrate and the support or the surface comprises polymers, plastics, resins, polysaccharide, silicon, silicon based materials, carbon, metals, inorganic glasses, membranes, particles, strands, precipitates, gels, sheets, tubing, spheres, containers, capillaries, pads, slices, films, plates or slides.

52. An array of biological polymers, the array comprising:

a planar solid support; and

a plurality of different polypeptides or nucleic acids attached to a surface of the planar solid support at a density of more than 400 different polymers/cm², wherein each of the different polypeptides or nucleic acids has a known or sequence and is positionally distinguishable from other polypeptides or nucleic acids.

53. The array of claim 52 wherein the density is at least 1,000 different polypeptides or nucleic acids/cm².

54. The array of claim 52 wherein the density is at least 10,000 different polypeptides or nucleic acids/cm².

55. The array of claim 52, wherein each different polypeptide or nucleic acid is greater than 25 monomers in length.

56. The array of claim 52, wherein each different polypeptide or nucleic acid is greater than 50 monomers in length.

57. The array of claim 52, wherein each different polypeptide or nucleic acid is covalently attached to the planar solid support.

59. The array of claim 52, wherein the solid support has a surface which can be composed of the same or different material as the substrate and the support or the surface comprises polymers, plastics, resins, polysaccharide, silicon, silicon based materials, carbon, metals, inorganic glasses, membranes, particles, strands, precipitates, gels, sheets, tubing, spheres, containers, capillaries, pads, slices, films, plates or slides.

61. The array of claim 52, wherein the solid support has a surface which can be composed of the same or different material as the substrate and the support or the surface comprises polymers, plastics, resins, polysaccharide, silicon, silicon based materials, carbon, metals, inorganic glasses, membranes, particles, strands, precipitates, gels, sheets, tubing, spheres, containers, capillaries, pads, slices, films, plates or slides.

62. An array of biological polymers, the array comprising:

a solid support; and

a plurality of different biological polymers attached to a surface of the solid support at a density greater than 400 different polymers/cm², wherein each of the different biological polymers has a known or determinable sequence and is in a localized area.