Dyes linked to target molecules, oligonucleotides or polynucleotides comprising dye molecules, composite dyes and other compositions useful for detecting or quantifying desirable target molecules
The present invention provides dyes, reactive dyes and labeled reagents that may be used in the detection or quantification of desirable target molecules, such as proteins and nucleic acids. Dyes are provided that may be used free in solution where the binding of the dye to the target molecule provides signal generation. Dyes are also provided that comprise reactive groups that may be used to attach the dyes to probes that will bind to desirable target molecules. The novel dyes of the present invention have been modified by the addition of charged and polar groups to provide beneficial properties.
1. A dye having the formula:
wherein said dye is linked to a target molecule.
2. The dye of claim 1 , 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, streptavidin, digoxigenin, carbohydrate, oligosaccharide, polysaccharide, lipid, glycolipid, viral particle, viral component, bacterial cell, bacterial component, eukaryotic cell, eukaryotic cell component, natural drug, synthetic drug, glass particle, glass surface, plastic particle, plastic surface, silicaceous particle, silicaceous surface, organic molecule, or second dye.
3. The dye of claim 1 , wherein said target molecule 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.
4. The dye of claim 1 , wherein said dye is linked to said target molecule through a linker arm.
5. The dye of claim 4 , 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.
6. A dye having the formula:
wherein said dye further comprises a reactive group comprising a nucleophilic reactive group, an electrophilic reactive group, a terminal alkene, a terminal alkyne, a coordinate group or an alkylating agent; and
wherein said dye is linked to a target molecule through said reactive group.
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, streptavidin, digoxigenin, carbohydrate, oligosaccharide, polysaccharide, lipid, glycolipid, viral particle, viral component, bacterial cell, bacterial component, eukaryotic cell, eukaryotic cell component, natural drug, synthetic drug, glass particle, glass surface, plastic particle, plastic surface, silicaceous particle, silicaceous surface, organic molecule, or second dye.
8. The dye of claim 6 , wherein said target molecule 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.
9. The dye of claim 6 , wherein said dye is linked to said target molecule through a linker arm.
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.
11. The dye of claim 6 , wherein said target molecule is an oligonucleotide or polynucleotide that further comprises at least a second dye, wherein said dye and said second dye are attached to separate nucleotides of said oligonucleotide or polynucleotide.
12. The dye of claim 6 , wherein said target molecule comprises a second dye.
13. The dye of claim 12 , wherein either the dye or the second dye further comprises a nucleophilic reactive group, an electrophilic reactive group, a terminal alkene, a terminal alkyne, a coordinate group or an alkylating agent.
14. The dye of claim 6 , wherein said dye is linked to a target specific moiety through said reactive group.
15. The dye of claim 14 , wherein said target specific moiety comprises a protein or a nucleic acid.
16. The dye of claim 15 , wherein said target specific moiety comprises an antibody or a fragment thereof.
17. The dye of claim 14 , wherein said target specific moiety comprises a nucleic acid comprising an unmodified nucleotide, a modified nucleotide, a nucleotide analogue or any combination thereof.
18. A composition comprising a first portion and a second portion wherein said first portion comprises a dye and said second portion comprises a target molecule, said dye having the formula:
wherein said dye further comprises one or more charged groups or polar groups,
and wherein said dye is linked to said target molecule.
19. The composition of claim 18 , wherein at least one of said one or more charged groups or polar groups is monomeric.
20. The composition of claim 18 , wherein at least one of said one or more charged groups or polar groups is polymeric.
21. The composition of claim 18 , wherein at least one of said one or more charged groups or polar groups is anionic.
22. The composition of claim 18 , wherein at least one of said one or more charged groups or polar groups is cationic.
23. The composition of claim 18 , wherein said dye further comprises one or more anionic charged groups or polar groups and one or more cationic charged groups or polar groups.
24. The composition of claim 18 , 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, streptavidin, digoxigenin, carbohydrate, oligosaccharide, polysaccharide, lipid, glycolipid, viral particle, viral component, bacterial cell, bacterial component, eukaryotic cell, eukaryotic cell component, natural drug, synthetic drug, glass particle, glass surface, plastic particle, plastic surface, silicaceous particle, silicaceous surface, organic molecule, or second dye.
25. The composition of claim 18 , wherein said target molecule 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.
26. The composition of claim 18 , wherein said dye is linked to said target molecule through a linker arm.
27. The composition of claim 26 , 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.
28. The composition of claim 18 , wherein said target molecule is an oligonucleotide or polynucleotide that further comprises at least a second dye, wherein said dye and said second dye are attached to separate nucleotides of said oligonucleotide or polynucleotide.
29. The composition of claim 28 , wherein said dye and said second dye are the same dye molecule.
30. The composition of claim 28 , wherein said dye and said second dye are different dye molecules.
31. The composition of claim 18 , wherein said target molecule comprises a second dye.
32. The composition of claim 31 , wherein either the dye or the second dye further comprises a nucleophilic reactive group, an electrophilic reactive group, a terminal alkene, a terminal alkyne, a coordinate group or an alkylating agent.
33. The composition of claim 18 , wherein said second portion further comprises a target specific moiety.
34. The composition of claim 33 , wherein said target specific moiety comprises a protein or a nucleic acid.
35. The composition of claim 34 , wherein said target specific moiety comprises an antibody or a fragment thereof.
36. The composition of claim 34 , wherein said target specific moiety comprises a nucleic acid comprising an unmodified nucleotide, a modified nucleotide, a nucleotide analogue or any combination thereof.
37. The dye or composition of any one of claim 1 , 6 or 18 , comprising
38. The dye or composition of any one of claim 1 , 6 or 18 , comprising
39. The dye or composition of any one of claim 1 , 6 or 18 , comprising
40. The dye or composition of any one of claim 1 , 6 or 18 , comprising
41. The dye or composition of claim 6 or 18 , comprising
42. The dye or composition of claim 6 or 18 , comprising
43. The dye or composition of claim 6 or 18 , comprising
44. The dye or composition of claim 6 or 18 , comprising