Purine based fluorescent dyes
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Abstract
The present invention provides novel purine-based fluorescent dyes that may be used for staining, localizing and otherwise labeling target molecules, such as nucleic acids, for detection, amplification and quantification.
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Citations
89 Claims
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1. A dye having the formula:
- View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 81, 82, 83, 84, 85, 86, 87, 88, 89)
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2. The dye of claim 1, wherein at least one of R1, R2, R3, R5, R6, R7, R8, R10, R11, R13, R14, R15, R16, R17 or R18 comprises a reactive group.
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3. The dye of claim 2, wherein said reactive group comprises a nucleophilic reactive group, an electrophilic reactive group, a terminal alkene, a terminal alkyne, a coordinate group or an alkylating agent.
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4. The dye of claim 3, wherein said nucleophilic reactive group comprises a thiol, amine, hydrazine or hydroxyl group.
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5. The dye of claim 3, wherein said electrophilic reactive group comprises an isocyanate, isothiocyanate, monochlorotriazine, dichlorotriazine, 4,6-dichloro-1,3,5-triazines, mono- or di-halogen substituted pyridine, mono- or di-halogen substituted diazine, maleimide, haloacetamide, aziridine, sulfonyl halide, acid halide, hydroxysuccinimide ester, hydroxysulfosuccinimide ester, imido ester, azidonitrophenol, azide, 3-(2-pyridyl dithio)proprionamide, glyoxal or aldehyde group.
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6. The dye of claim 1, wherein said dye is linked to a target molecule.
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7. The dye of claim 6, wherein said target molecule comprises a nucleoside, nucleotide, oligonucleotide, polynucleotide, peptide nucleic acid, protein, peptide, enzyme, antigen, antibody, hormone, hormone receptor, cellular receptor, lymphokine, cytokine, hapten, lectin, avidin, strepavidin, digoxygenin, carbohydrate, oligosaccharide, polysaccharide, lipid, glycolipid, viral particle, viral component, bacterial cell, bacterial component, eucaryotic cell, eukaryotic cell component, natural drug, synthetic drug, glass particle, glass surface, plastic particle, plastic surface, siliceous particle, siliceous surface, organic molecule, dye or a derivative thereof.
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8. The dye of claim 7, wherein said nucleoside, nucleotide, oligonucleotide, or polynucleotide comprises one or more ribonucleoside moieties, ribonucleotide moieties, deoxyribonucleoside moieties, deoxyribonucleotide moieties, modified ribonucleosides, modified ribonucleotides, modified deoxyribonucleosides, modified deoxyribonucleotides, ribonucleotide analogues, deoxyribonucleotide analogues or any combination thereof.
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9. The dye of claim 6, wherein said dye is linked to said target molecule through a linker arm.
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10. The dye of claim 9, wherein said linker arm is attached to said target molecule through a bond which comprises a covalent bond, a non-covalent bond, a polar bond or a coordinate bond.
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11. The oligonucleotide or polynucleotide of claim 8, wherein said oligonucleotide or polynucleotide comprises two or more dye molecules attached to separate nucleotides of said oligonucleotide or polynucleotide.
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12. The oligonucleotide or polynucleotide of claim 11, wherein said two or more dye molecules comprise the same dye molecules.
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13. The oligonucleotide or polynucleotide of claim 11, wherein said two or more dye molecules comprise different dye molecules.
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14. A composite dye comprising the dye of claim 7, said dye being joined or attached to a second dye molecule.
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15. The dye of claim 1, wherein said dye is attached to a target specific moiety.
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16. The dye of claim 15, wherein said target specific moiety comprises a protein or a nucleic acid.
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17. The dye of claim 16, wherein said protein comprises an antibody or a fragment thereof.
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18. The dye of claim 16, wherein said nucleic acid comprises unmodified nucleotides, modified nucleotides, nucleotide analogues or any combination thereof.
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19. The dye of claim 1, wherein said alkyl or alkoxy groups independently comprise from 1-18 carbons.
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20. The dye of claim 19, wherein said alkyl or alkoxy groups independently comprise from 1-6 carbons.
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25. The dye of claim 3 wherein said electrophilic reactive group comprises an isocyanate, isothiocyanate, monochlorotriazine, dichlorotriazine, 4,6-dichloro-1,3,5-triazines, mono- or di-halogen substituted pyridine, mono- or di-halogen substituted diazine, maleimide, haloacetamide, aziridine, sulfonyl halide, acid halide, hydroxysuccinimide ester, hydroxysulfosuccinimide ester, imido ester, azidonitrophenol, azide, 3-(2-pyridyl dithio)proprionamide, glyoxal or aldehyde group.
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81. A method for detecting the presence, location or quantity of a target comprising the steps of:
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a) providing;
i) a sample where the presence, location or quantity of a target is desired to be detected;
ii) any of the dyes of claims 1, 21, 41 or 61;
b) allowing any targets present in said sample i) to bind with said dye ii); and
c) detecting said dye ii) bound to any of said target in the sample i), thereby detecting the presence, location or quantity of said target.
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82. The method of claim 81, wherein said target comprises an oligonucleotide, polynucleotide, peptide nucleic acid, protein, peptide, enzyme, antigen, antibody, hormone, hormone receptor, cellular receptor, lymphokine, cytokine, hapten, lectin, avidin, strepavidin, digoxygenin, carbohydrate, oligosaccharide, polysaccharide, lipid, glycolipid, viral particle, viral component, bacterial cell, bacterial component, eucaryotic cell, eukaryotic cell component, natural drug, synthetic drug, organic molecule, or a derivative thereof.
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83. The method of claim 81 wherein said target has been bound to a solid matrix.
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84. The method of claim 83, wherein said solid matrix comprises a bead, filter, gel, cuvette, test tube, dish, microscope slide, plate, microtitre plate, microarray,
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85. The method of claim 81 wherein said target is detected in situ.
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86. The method of claim 81 wherein said detection takes place without binding of target to a solid matrix.
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87. The method of claim 86, wherein said detection takes place by a change in properties of said dye after binding takes place between said dye and said target.
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88. The method of claim 87, wherein said change is an increase or decrease in the amount of fluorescence of said dye.
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89. The method of claim 83, wherein a further step is carried out where unbound dye is removed.
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2. The dye of claim 1, wherein at least one of R1, R2, R3, R5, R6, R7, R8, R10, R11, R13, R14, R15, R16, R17 or R18 comprises a reactive group.
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21. A dye having the formula:
- View Dependent Claims (22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40)
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22. The dye of claim 21 wherein at least one of R1, R2, R3, R4, R5, R6, R7, R16, R17 and R18 comprises a reactive group.
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23. The dye of claim 22 wherein said reactive group comprises a nucleophilic reactive group, an electrophilic reactive group, a terminal alkene, a terminal alkyne, a coordinate group or an alkylating agent.
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24. The dye of claim 23 wherein said nucleophilic reactive group comprises a thiol, amine, hydrazine or hydroxyl group.
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26. The dye of claim 21, wherein said dye is linked to a target molecule.
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27. The dye of claim 26, wherein said target molecule comprises a nucleoside, nucleotide, oligonucleotide, polynucleotide, peptide nucleic acid, protein, peptide, enzyme, antigen, antibody, hormone, hormone receptor, cellular receptor, lymphokine, cytokine, hapten, lectin, avidin, strepavidin, digoxygenin, carbohydrate, oligosaccharide, polysaccharide, lipid, glycolipid, viral particle, viral component, bacterial cell, bacterial component, eucaryotic cell, eukaryotic cell component, natural drug, synthetic drug, glass particle, glass surface, plastic particle, plastic surface, silicaceous particle, silicaceous surface, organic molecule, dye or a derivative thereof.
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28. The dye of claim 27, wherein said nucleoside, nucleotide, oligonucleotide, or polynucleotide comprises one or more ribonucleoside moieties, ribonucleotide moieties, deoxyribonucleoside moieties, deoxyribonucleotide moieties, modified ribonucleosides, modified ribonucleotides, modified deoxyribonucleosides, modified deoxyribonucleotides, ribonucleotide analogues, deoxyribonucleotide analogues or any combination thereof.
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29. The dye of claim 26, wherein said dye is linked to said target molecule through a linker arm.
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30. The dye of claim 29, wherein said linker arm is attached to said target molecule through a bond which comprises a covalent bond, a non-covalent bond, a polar bond or a coordinate bond.
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31. The oligonucleotide or polynucleotide of claim 28, wherein said oligonucleotide or polynucleotide comprises two or more dye molecules attached to separate nucleotides of said oligonucleotide or polynucleotide.
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32. The oligonucleotide or polynucleotide of claim 31, wherein said two or more dye molecules comprise the same dye molecules.
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33. The oligonucleotide or polynucleotide of claim 31, wherein said two or more dye molecules comprise different dye molecules.
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34. A composite dye comprising the dye of claim 27, said dye being joined or attached to a second dye molecule.
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35. The dye of claim 31, wherein said dye is attached to a target specific moiety.
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36. The dye of claim 35, wherein said target specific moiety comprises a protein or a nucleic acid.
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37. The dye of claim 36, wherein said protein comprises an antibody or a fragment thereof.
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38. The dye of claim 36, wherein said nucleic acid comprises unmodified nucleotides, modified nucleotides, nucleotide analogues or any combination thereof.
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39. The dye of claim 21, wherein said alkyl or alkoxy groups independently comprise from 1-18 carbons.
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40. The dye of claim 39, wherein said alkyl or alkoxy groups independently comprise from 1-6 carbons.
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22. The dye of claim 21 wherein at least one of R1, R2, R3, R4, R5, R6, R7, R16, R17 and R18 comprises a reactive group.
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41. A dye having the formula:
- View Dependent Claims (42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60)
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42. The dye of claim 41 wherein at least one of R1, R2, R3, R4, R5, R6, R16, R17 or R18 comprises a reactive group.
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43. The dye of claim 42 wherein said reactive group comprises a nucleophilic reactive group, an electrophilic reactive group, a terminal alkene, a terminal alkyne, a coordinate group or an alkylating agent.
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44. The dye of claim 43 wherein said nucleophilic reactive group comprises a thiol, amine, hydrazine or hydroxyl group.
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45. The dye of claim 43 wherein said electrophilic reactive group comprises an isocyanate, isothiocyanate, monochlorotriazine, dichlorotriazine, 4,6-dichloro-1,3,5-triazines, mono- or di-halogen substituted pyridine, mono- or di-halogen substituted diazine, maleimide, haloacetamide, aziridine, sulfonyl halide, acid halide, hydroxysuccinimide ester, hydroxysulfosuccinimide ester, imido ester, azidonitrophenol, azide, 3-(2-pyridyl dithio)proprionamide, glyoxal or aldehyde group.
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46. The dye of claim 41, wherein said dye is linked to a target molecule.
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47. The dye of claim 46, wherein said target molecule comprises a nucleoside, nucleotide, oligonucleotide, polynucleotide, peptide nucleic acid, protein, peptide, enzyme, antigen, antibody, hormone, hormone receptor, cellular receptor, lymphokine, cytokine, hapten, lectin, avidin, strepavidin, digoxygenin, carbohydrate, oligosaccharide, polysaccharide, lipid, glycolipid, viral particle, viral component, bacterial cell, bacterial component, eucaryotic cell, eukaryotic cell component, natural drug, synthetic drug, glass particle, glass surface, plastic particle, plastic surface, silicaceous particle, silicaceous surface, organic molecule, dye or a derivative thereof.
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48. The dye of claim 47, wherein said nucleoside, nucleotide, oligonucleotide, or polynucleotide comprises one or more ribonucleoside moieties, ribonucleotide moieties, deoxyribonucleoside moieties, deoxyribonucleotide moieties, modified ribonucleosides, modified ribonucleotides, modified deoxyribonucleosides, modified deoxyribonucleotides, ribonucleotide analogues, deoxyribonucleotide analogues or any combination thereof.
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49. The dye of claim 46, wherein said dye is linked to said target molecule through a linker arm.
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50. The dye of claim 49, wherein said linker arm is attached to said target molecule through a bond which comprises a covalent bond, a non-covalent bond, a polar bond or a coordinate bond.
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51. The oligonucleotide or polynucleotide of claim 48, wherein said oligonucleotide or polynucleotide comprises two or more dye molecules attached to separate nucleotides of said oligonucleotide or polynucleotide.
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52. The oligonucleotide or polynucleotide of claim 51, wherein said two or more dye molecules comprise the same dye molecules.
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53. The oligonucleotide or polynucleotide of claim 51, wherein said two or more dye molecules comprise different dye molecules.
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54. A composite dye comprising the dye of claim 47, said dye being joined or attached to a second dye molecule.
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55. The dye of claim 41, wherein said dye is attached to a target specific moiety.
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56. The dye of claim 55, wherein said target specific moiety comprises a protein or a nucleic acid.
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57. The dye of claim 56, wherein said protein comprises an antibody or a fragment thereof.
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58. The dye of claim 56, wherein said nucleic acid comprises unmodified nucleotides, modified nucleotides, nucleotide analogues or any combination thereof.
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59. The dye of claim 41, wherein said alkyl or alkoxy groups independently comprise from 1-18 carbons.
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60. The dye of claim 59, wherein said alkyl or alkoxy groups independently comprise from 1-6 carbons.
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42. The dye of claim 41 wherein at least one of R1, R2, R3, R4, R5, R6, R16, R17 or R18 comprises a reactive group.
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61. A dye comprising the structure:
- View Dependent Claims (62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80)
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62. The dye of claim 61 wherein at least one of R1, R2, R3, R4, R5, R6, R7, R8, R10, R13, R14, R15, R16 or R17 comprises a reactive group.
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63. The dye of claim 62 wherein said reactive group comprises a nucleophilic reactive group, an electrophilic reactive group, a terminal alkene, a terminal alkyne, a coordinate group or an alkylating agent.
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64. The dye of claim 63 wherein said nucleophilic reactive group comprises a thiol, amine, hydrazine or hydroxyl group.
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65. The dye of claim 63 wherein said electrophilic reactive group comprises an isocyanate, isothiocyanate, monochlorotriazine, dichlorotriazine, 4,6-dichloro-1,3,5-triazines, mono- or di-halogen substituted pyridine, mono- or di-halogen substituted diazine, maleimide, haloacetamide, aziridine, sulfonyl halide, acid halide, hydroxysuccinimide ester, hydroxysulfosuccinimide ester, imido ester, azidonitrophenol, azide, 3-(2-pyridyl dithio)proprionamide, glyoxal or aldehyde group.
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66. The dye of claim 61, wherein said dye is linked to a target molecule.
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67. The dye of claim 66, wherein said target molecule comprises a nucleoside, nucleotide, oligonucleotide, polynucleotide, peptide nucleic acid, protein, peptide, enzyme, antigen, antibody, hormone, hormone receptor, cellular receptor, lymphokine, cytokine, hapten, lectin, avidin, strepavidin, digoxygenin, carbohydrate, oligosaccharide, polysaccharide, lipid, glycolipid, viral particle, viral component, bacterial cell, bacterial component, eucaryotic cell, eukaryotic cell component, natural drug, synthetic drug, glass particle, glass surface, plastic particle, plastic surface, silicaceous particle, silicaceous surface, organic molecule, dye or a derivative thereof.
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68. The dye of claim 67, wherein said nucleoside, nucleotide, oligonucleotide, or polynucleotide comprises one or more ribonucleoside moieties, ribonucleotide moieties, deoxyribonucleoside moieties, deoxyribonucleotide moieties, modified ribonucleosides, modified ribonucleotides, modified deoxyribonucleosides, modified deoxyribonucleotides, ribonucleotide analogues, deoxyribonucleotide analogues or any combination thereof.
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69. The dye of claim 66, wherein said dye is linked to said target molecule through a linker arm.
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70. The dye of claim 69, wherein said linker arm is attached to said target molecule through a bond which comprises a covalent bond, a non-covalent bond, a polar bond or a coordinate bond.
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71. The oligonucleotide or polynucleotide of claim 68, wherein said oligonucleotide or polynucleotide comprises two or more dye molecules attached to separate nucleotides of said oligonucleotide or polynucleotide.
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72. The oligonucleotide or polynucleotide of claim 71, wherein said two or more dye molecules comprise the same dye molecules.
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73. The oligonucleotide or polynucleotide of claim 71, wherein said two or more dye molecules comprise different dye molecules.
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74. A composite dye comprising the dye of claim 67, said dye being joined or attached to a second dye molecule.
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75. The dye of claim 61, wherein said dye is attached to a target specific moiety.
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76. The dye of claim 75, wherein said target specific moiety comprises a protein or a nucleic acid.
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77. The dye of claim 76, wherein said protein comprises an antibody or a fragment thereof.
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78. The dye of claim 76, wherein said nucleic acid comprises unmodified nucleotides, modified nucleotides, nucleotide analogues or any combination thereof.
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79. The dye of claim 61, wherein said alkyl or alkoxy groups independently comprise from 1-18 carbons.
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80. The dye of claim 79, wherein said alkyl or alkoxy groups independently comprise from 1-6 carbons.
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62. The dye of claim 61 wherein at least one of R1, R2, R3, R4, R5, R6, R7, R8, R10, R13, R14, R15, R16 or R17 comprises a reactive group.
Specification
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Current AssigneeEnzo Life Sciences Incorporated (Enzo Biochem Incorporated)
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Original AssigneeEnzo Life Sciences Incorporated (Enzo Biochem Incorporated)
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InventorsSzczepanik, Maciej
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Granted Patent
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Time in Patent OfficeDays
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Field of Search
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US Class Current435/6
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CPC Class CodesC07D 401/14 containing three or more he...C07D 405/14 containing three or more he...C07D 417/06 linked by a carbon chain co...C07D 417/14 containing three or more he...C07D 473/00 Heterocyclic compounds cont...C07F 9/65616 containing the ring system ...C09B 23/0091 having only one heterocycli...C09B 23/04 one >CH- group, e.g. cyanin...C09B 23/06 three >CH- groups, e.g. car...C09B 23/083 five >CH- groupsC09B 23/105 two >CH- groupsC09B 23/145 the ethylene chain carrying...C09B 23/146 (Benzo)thiazolstyrylamino dyesC12Q 1/6816 characterised by the detect...C12Q 2563/107 fluorescence