Processes for detecting or quantifying analytes of interest

• US 9,279,147 B2
• Filed: 07/29/2004
• Issued: 03/08/2016
• Est. Priority Date: 06/30/2001
• Status: Expired due to Term

• Current Assignee: Enzo Life Sciences Incorporated (Enzo Biochem Incorporated)
• Original Assignee: Enzo Life Sciences Incorporated (Enzo Biochem Incorporated)
• Inventors: Rabbani, Elazar, Stavrianopoulos, Jannis G., Donegan, James J., Coleman, Jack
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): Tung, Joyce
• Application Number:
  US10/902,640
• Publication Number:
  US 20050202456A1
• Time in Patent Office: 4,240 Days
• Field of Search: 435/6, 435/91.2, 435/4, 435/6.12, 536/23.1, 536/23.4, 536/22.1
• US Class Current: 1/1
• 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 2219/00599 Solution-phase processes
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• 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: C12N 15/1006 by means of a solid support carrier, e.g. particles, polymers
• CPC Class Codes: C12N 15/1058 Directional evolution of libraries, e.g. evolution of libraries is achieved by mutagenesis and screening or selection of mixed population of organisms
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2545/114 involving a quantitation step
• CPC Class Codes: C12Q 2563/179 the label being a nucleic acid
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/514 characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array
• CPC Class Codes: C12Q 2565/537 : characterised by the capture oligonucleotide acting as a primer
• CPC Class Codes: C40B 40/00 : Libraries per se, e.g. arrays, mixtures
• 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: G01N 33/68 : involving proteins, peptides or amino acids involving lipoproteins G01N33/92

Abstract

This invention provides novel compositions and processes for analyte detection, quantification and amplification. Nucleic acid arrays and libraries of analytes are usefully incorporated into such compositions and processes. Universal detection elements, signaling entities and the like are employed to detect and if necessary or desirable, to quantify analytes. Amplification of target analytes are also provided by the compositions and processes of this invention.

Claims

1. A process for detecting or quantifying non-nucleic acid analytes of interest, said process comprising the steps of:

1) providing

a) an array on a solid surface comprising a plurality of discrete areas;

wherein

at least two of said discrete areas each comprise a nucleotide sequence fixed or immobilized to said discrete areas,

said at least two discrete areas comprise a first discrete area and a second discrete area, and

said nucleotide sequence on said first discrete area is different from said nucleotide sequence on said second discrete area;

b) chimeric compositions consisting of;

i) a nucleic acid portion; and

ii) a non-nucleic acid portion;

wherein

said nucleic acid portion of each chimeric composition is complementary to a nucleotide sequence of said array,

said nucleic acid portion of the chimeric composition that is complementary to the nucleotide sequence located at said first discrete area has a different sequence from that of said nucleic acid portion of the chimeric composition complementary to the nucleotide sequence located at said second discrete area,

said non-nucleic acid portion of the chimeric composition that has a nucleic acid portion that is complementary to the nucleotide sequence of said first discrete area has a binding affinity for a first non-nucleic acid analyte of interest and said non-nucleic acid portion of the chimeric composition that has a nucleic acid portion that is complementary to the nucleotide sequence of said second discrete area has a binding affinity for a second non-nucleic acid analyte of interest,

said first non-nucleic acid analyte is different from said second non nucleic acid analyte,

when said non-nucleic acid portion of a chimeric composition is a peptide or protein, said nucleic acid portion of said chimeric composition does not comprise a sequence which is either identical or complementary to a sequence that codes for said peptide or protein, and

said nucleic acid portion i) and said non-nucleic acid portion ii) are covalently attached to each other;

c) a sample containing or suspected of containing said non-nucleic acid analytes of interest, wherein

said non-nucleic acid analytes of interest comprise oligopeptides, polypeptides, oligosaccharides, polysaccharides, lipids, ligands, or combinations thereof; and

d) signal generating means;

2) contacting said array with said chimeric compositions to hybridize the nucleic acid portions of said chimeric compositions to complementary nucleotide sequences fixed or immobilized to said array;

3) contacting said array with the sample under conditions permissive of binding said non-nucleic acid analytes to said non-nucleic acid portion;

4) contacting said bound non-nucleic acid analytes with said signal generating means; and

5) detecting or quantifying the presence of said non-nucleic acid analytes by measuring said signal generating means bound to said array.

2. The process of claim 1, wherein said solid surface is porous.

3. The process of claim 2, wherein said porous solid surface comprises polyacrylamide or agarose.

4. The process of claim 1, wherein said solid surface is non-porous.

5. The process of claim 4, wherein said nonporous solid surface comprises glass or plastic.

6. The process of claim 1, wherein said solid surface is transparent, translucent, opaque or reflective.

7. The process of claim 1, wherein said fixed or immobilized nucleotide sequences comprise DNA, RNA, a DNA analog, an RNA analog, or combinations thereof.

8. The process of claim 7, wherein said nucleotide sequences comprise PNA.

9. The process of claim 7 or 8, wherein said nucleotide sequences are modified on any of the sugar, phosphate or base moieties.

10. The process of claim 1, wherein said nucleic acid portion comprises DNA, RNA, a DNA analog, an RNA analog, or combinations thereof.

11. The process of claim 10, wherein said nucleic acid portion comprises PNA.

12. The process of claim 10 or 11, wherein said nucleic acid portion is modified on any of the sugar, phosphate or base moieties.

13. The process of claim 1, wherein said non-nucleic acid portions comprise peptides, proteins, ligands, enzyme substrates, hormones, receptors, drugs, or a combination of any of the foregoing.

14. The process of claim 1, wherein said signal generating means comprises a direct signal generating means.

15. The process of claim 14, wherein said direct signal generating means comprises a fluorescent compound, a phosphorescent compound, a chemiluminescent compound, a chelating compound, an electron dense compound, a magnetic compound, an intercalating compound, an energy transfer compound, or a combination of any of the foregoing.

16. The process of claim 1, wherein said signal generating means comprises an indirect signal generating means.

17. The process of claim 16, wherein said indirect signal generating means comprises an antibody, an antigen, a hapten, a receptor, a hormone, a ligand, an enzyme, or a combination of any of the foregoing.

18. The process of claim 17, wherein said indirect signal generating means comprises an enzyme that catalyzes a reaction comprising a fluorogenic reaction, a chromogenic reaction or a chemiluminescent reaction.

73. The process of claim 1, wherein said non-nucleic acid analytes comprise ligands comprising nonpeptide antigens, hormones, enzymes, substrates, vitamins, drugs, nonpeptide signal molecules, or combinations thereof.

19. A process for detecting or quantifying non-nucleic acid analytes of interest, said process comprising the steps of:

1) providing

a) an array on a solid surface comprising a plurality of discrete areas;

wherein

at least two of said discrete areas each comprise a nucleotide sequence fixed or immobilized to said discrete areas,

said at least two discrete areas comprise a first discrete area and a second discrete area, and

said nucleotide sequence on said first discrete area is different from said nucleotide sequence on said second discrete area;

b) chimeric compositions consisting of;

a nucleic acid portion; and

a non-nucleic acid portion;

wherein

said nucleic acid portion of each chimeric composition is complementary to a nucleotide sequence of said array,

said nucleic acid portion of the chimeric composition that is complementary to the nucleotide sequence located at said first discrete area has a different sequence from that of said nucleic acid portion of the chimeric composition complementary to the nucleotide sequence located at said second discrete area,

said non-nucleic acid portion of the chimeric composition that has a nucleic acid portion that is complementary to the nucleotide sequence of said first discrete area has a binding affinity for a first non-nucleic acid analyte of interest and said non-nucleic acid portion of the chimeric composition that has a nucleic acid portion that is complementary to the nucleotide sequence of said second discrete area has a binding affinity for a second non-nucleic acid analyte of interest,

said first non-nucleic acid analyte is different from said second non-nucleic acid analyte,

when said non-nucleic acid portion of a chimeric composition is a peptide or protein, said nucleic acid portion of said chimeric composition does not comprise a sequence which is either identical or complementary to a sequence that codes for said peptide or protein, and

said nucleic acid portion i) and said non-nucleic acid portion ii) are covalently attached to each other;

c) a sample containing or suspected of containing said non-nucleic acid analytes of interest, wherein

said non-nucleic acid analytes of interest comprise oligopeptides, polypeptides, oligosaccharides, polysaccharides, lipids, ligands, or combinations thereof; and

d) signal generating means;

2) contacting said chimeric compositions with the sample under conditions permissive of binding said non-nucleic acid analytes to said non-nucleic acid portion;

3) contacting said array with said chimeric compositions to hybridize the nucleic acid portions of said chimeric compositions to complementary nucleotide sequences fixed or immobilized to said array;

4) contacting said bound non-nucleic acid analytes with said signal generating means; and

5) detecting or quantifying the presence of said non-nucleic acid analytes by measuring said signal generating means bound to said array.

20. The process of claim 19, wherein said solid surface is porous.

21. The process of claim 20 wherein said porous solid surface comprises polyacrylamide or agarose.

22. The process of claim 19, wherein said solid surface is non-porous.

23. The process of claim 22, wherein said non-porous solid surface comprises glass or plastic.

24. The process of claim 19, wherein said solid surface is transparent, translucent, opaque or reflective.

25. The process of claim 19, wherein said fixed or immobilized nucleotide sequences comprise DNA, RNA, a DNA analog, an RNA analog, or combinations thereof.

26. The process of claim 25, wherein said nucleotide sequences comprise PNA.

27. The process of claim 25 or 26, wherein said nucleic acid portion is modified on any of the sugar, phosphate or base moieties.

28. The process of claim 19, wherein said nucleic acid portion comprises DNA, RNA, a DNA analog, an RNA analog, or combinations thereof.

29. The process of claim 28, wherein said nucleic acid portion comprises PNA.

30. The process of claim 28 or 29, wherein said nucleic, acid portion is modified on any of the sugar, phosphate or base moieties.

31. The process of claim 19, wherein said non-nucleic acid portions comprise peptides, proteins, ligands, enzyme substrates, hormones, receptors, drugs, or a combination of any of the foregoing.

32. The process of claim 19, wherein said signal generating means comprises a direct signal generating means.

33. The process of claim 32, wherein said direct signal generating means comprises a fluorescent compound, a phosphorescent compound, a chemiluminescent compound, a chelating compound, an electron dense compound, a magnetic compound, an intercalating compound, an energy transfer compound, or a combination of any of the foregoing.

34. The process of claim 19, wherein said signal generating means comprises an indirect signal generating means.

35. The process of claim 34, wherein said indirect signal generating means comprises an antibody, an antigen, a hapten, a receptor, a hormone, a ligand, an enzyme, or a combination of any of the foregoing.

36. The process of claim 35, wherein said indirect signal generating means comprises an enzyme that catalyzes a reaction comprising a fluorogenic reaction, a chromogenic reaction or a chemiluminescent reaction.

74. The process of claim 19, wherein said non-nucleic acid analytes comprise ligands comprising non-peptide antigens, hormones, enzymes, substrates, vitamins, drugs, non-peptide signal molecules, or combinations thereof.

37. A process for detecting or quantifying non-nucleic acid analytes of interest, said process comprising the steps of:

1) providing

a) an array on a solid surface comprising a plurality of discrete areas;

wherein

at least two of said discrete areas each comprise a nucleotide sequence fixed or immobilized to said discrete areas,

said at least two discrete areas comprise a first discrete area and a second discrete area, and

said nucleotide sequence on said first discrete area is different from said nucleotide sequence on said second discrete area;

b) chimeric compositions consisting of;

i) a nucleic acid portion; and

ii) a non-nucleic acid portion;

wherein

said nucleic acid portion of each chimeric composition is complementary to a nucleotide sequence of said array,

said nucleic acid portion of the chimeric composition that is complementary to the nucleotide sequence located at said first discrete area has a different sequence from that of said nucleic acid portion of the chimeric composition complementary to the nucleotide sequence located at said second discrete area,

said non-nucleic acid portion of the chimeric composition that has a nucleic acid portion that is complementary to the nucleotide sequence of said first discrete area has a binding affinity for a first non-nucleic acid analyte of interest and said non-nucleic acid portion of the chimeric composition that has a nucleic acid portion that is complementary to the nucleotide sequence of said second discrete area has a binding affinity for a second non-nucleic acid analyte of interest,

said first non-nucleic acid analyte is different from said second non-nucleic acid analyte,

when said non-nucleic acid portion of a chimeric composition is a peptide or protein, said nucleic acid portion of said chimeric composition does not comprise a sequence which is either identical or complementary to a sequence that codes for said peptide or protein, and

said nucleic acid portion i) and said non-nucleic acid portion ii) are covalently attached to each other;

c) a sample containing or suspected of containing said non-nucleic acid analytes of interest, wherein

said non-nucleic acid analytes of interest comprise oligopeptides, polypeptides, oligosaccharides, polysaccharides, lipids, ligands, or combinations thereof; and

d) signal generating means;

2) contacting said array with said chimeric compositions to hybridize the nucleic acid portions of said chimeric compositions to complementary nucleotide sequences fixed or immobilized to said array;

3) labeling said non-nucleic acid analytes of interest with said signal generating means;

4) contacting said array with the labeled non-nucleic acid analytes to bind said non-nucleic acid analytes to said non-nucleic acid portion; and

5) detecting or quantifying the presence of said non-nucleic acid analytes by measuring said signal generating means bound to said array.

38. The process of claim 37, wherein said solid surface is porous.

39. The process of claim 38, wherein said porous solid surface comprises polyacrylamide or agarose.

40. The process of claim 37, wherein said solid surface is non-porous.

41. The process of claim 40, wherein said non-porous solid surface comprises glass or plastic.

42. The process of claim 37, wherein said solid surface is transparent, translucent, opaque or reflective.

43. The process of claim 37 wherein said fixed or immobilized nucleotide sequences comprise DNA, RNA, a DNA analog, an RNA analog, or combinations thereof.

44. The process of claim 43, wherein said nucleotide sequences comprise PNA.

45. The process of claim 43 or 44, wherein said nucleic acid portion is modified on any of the sugar, phosphate or base moieties.

46. The process of claim 37, wherein said nucleic acid portion comprises DNA, RNA, a DNA analog, an RNA analog, or combinations thereof.

47. The process of claim 46, Wherein said nucleic acid portion comprises PNA.

48. The process of claim 46 or 47, wherein said nucleic acid portion is modified on any of the sugar, phosphate or base moieties.

49. The process of claim 37, wherein said non-nucleic acid portions comprise peptides, proteins, ligands, enzyme substrates, hormones, receptors, drugs, or a combination of any of the foregoing.

50. The process of claim 37, wherein said signal generating means comprises a direct signal generating means.

51. The process of claim 50, wherein said direct signal generating means comprises a fluorescent compound, a phosphorescent compound, a chemiluminescent compound, a chelating compound, an electron dense compound, a magnetic compound, an intercalating compound, an energy transfer compound, or a combination of any of the foregoing.

52. The process of claim 37, wherein said signal generating means comprises an indirect signal generating means.

53. The process of claim 52, wherein said indirect signal generating means comprises an antibody, an antigen, a hapten, a receptor, a hormone, a ligand, an enzyme, or a combination of any of the foregoing.

54. The process of claim 53, wherein said indirect signal generating means comprises an enzyme that catalyzes a reaction comprising a fluorogenic reaction, a chromogenic reaction or a chemiluminescent reaction.

75. The process of claim 37, wherein said non-nucleic acid analytes comprise ligands comprising non-peptide antigens, hormones, enzymes, substrates, vitamins, drugs, non-peptide signal molecules, or combinations thereof.

55. A process for detecting or quantifying non-nucleic acid analytes of interest, said process comprising the steps of:

1) providing

a) an array on a solid surface comprising a plurality of discrete areas;

wherein

at least two of said discrete areas each comprise a nucleotide sequence fixed or immobilized to said discrete areas,

said at least two discrete areas comprise a first discrete area and a second discrete area, and

said nucleotide sequence on said first discrete area is different from said nucleotide sequence on said second discrete area;

b) chimeric compositions consisting of;

i) a nucleic acid portion; and

ii) a non-nucleic acid portion;

wherein

said nucleic acid portion of each chimeric composition is complementary to a nucleotide sequence of said array,

said nucleic acid portion of the chimeric composition that is complementary to the nucleotide sequence located at said first discrete area has a different sequence from that of said nucleic acid portion of the chimeric composition complementary to the nucleotide sequence located at said second discrete area,

said non-nucleic acid portion of the chimeric composition that has a nucleic acid portion that is complementary to the nucleotide sequence of said first discrete area has a binding affinity for a first non-nucleic acid analyte of interest and said non-nucleic acid portion of the chimeric composition that has a nucleic acid portion that is complementary to the nucleotide sequence of said second discrete area has a binding affinity for a second non-nucleic acid analyte of interest,

said first non-nucleic acid analyte is different from said second non-nucleic acid analyte,

when said non-nucleic acid portion of a chimeric composition is a peptide or protein, said nucleic acid portion of said chimeric composition does not comprise a sequence which is either identical or complementary to a sequence that codes for said peptide or protein, and

said nucleic acid portion i) and said non-nucleic acid portion n) are covalently attached to each other;

c) a sample containing or suspected of containing said non-nucleic acid analytes of interest, wherein

said non-nucleic acid analytes of interest comprise oligopeptides, polypeptides, oligosaccharides, polysaccharides, lipids, ligands, or combinations thereof; and

d) signal generating means;

2) labeling said non-nucleic acid analytes of interest with said signal generating means;

3) contacting said chimeric compositions with the labeled non-nucleic acid analytes to bind said non-nucleic acid analytes to said non-nucleic acid portion;

4) contacting said array with said chimeric compositions to hybridize the nucleic acid portions of said chimeric compositions to complementary nucleotide sequences fixed or immobilized to said array; and

5) detecting or quantifying the presence of said non-nucleic acid analytes by measuring said signal generating means bound to said array.

56. The process of claim 55, wherein said solid surface is porous.

57. The process of claim 56, wherein said porous solid surface comprises polyacrylamide or agarose.

58. The process of claim 55, wherein said solid surface is non-porous.

59. The process of claim 58, wherein said non-porous solid surface comprises glass or plastic.

60. The process of claim 55, wherein said solid surface is transparent, translucent, opaque or reflective.

61. The process of claim 55, wherein said fixed or immobilized nucleotide sequences comprise DNA, RNA, a DNA analog, an RNA analog, or combinations thereof.

62. The process of claim 61, wherein said nucleotide sequences comprise PNA.

63. The process of claim 61 or 62, wherein said nucleic acid portion is modified on any of the sugar, phosphate or base moieties.

64. The process of claim 55, Wherein said nucleic acid portion comprises DNA, RNA, a DNA analog, an RNA analog, or combinations thereof.

65. The process of claim 64, wherein said nucleic acid portion comprises PNA.

66. The process of claim 64 or 65, wherein said nucleic acid portion is modified on any of the sugar, phosphate or base moieties.

67. The process of claim 55, wherein said non-nucleic acid portions comprise peptides, proteins, ligands, enzyme substrates, hormones, receptors, drugs, or a combination of any of the foregoing.

68. The process of claim 55, wherein said signal generating means comprises a direct signal generating means.

69. The process of claim 68, wherein said direct signal generating means comprises a fluorescent compound, a phosphorescent compound, a chemiluminescent compound, a chelating compound, an electron dense compound, a magnetic compound, an intercalating compound, an energy transfer compound, or a combination of any of the foregoing.

70. The process of claim 55, wherein said signal generating means comprises an indirect signal generating means.

71. The process of claim 70, wherein said indirect signal generating means comprises an antibody, an antigen, a hapten, a receptor, a hormone, a ligand, an enzyme, or a combination of any of the foregoing.

72. The process of claim 71, wherein said indirect signal generating means comprises an enzyme that catalyzes a reaction comprising a fluorogenic reaction, a chromogenic reaction or a chemiluminescent reaction.

76. The process of claim 55, wherein said non-nucleic acid analytes comprise ligands comprising non-peptide antigens, hormones, enzymes, substrates, vitamins, drugs, non-peptide signal molecules, or combinations thereof.