PHOSPHONYLATED FLUORESCENT DYES AND CONJUGATES

• US 20080207887A1
• Filed: 11/08/2007
• Published: 08/28/2008
• Est. Priority Date: 08/13/2004
• Status: Abandoned Application

• Current Assignee: Elitech Holding BV (Bruker Corporation)
• Original Assignee: Epoch Biosciences Inc. (Ngen, Inc.)
• Inventors: Lukhtanov, Eugeny, Vorobiev, Alexei
• Application Number:
  US11/937,448
• Publication Number:
  US 20080207887A1
• Time in Patent Office: Days
• US Class Current: 536/24.3
• CPC Class Codes: C07F 9/1411 with hydroxyalkyl compounds with further substituents on alkyl
• CPC Class Codes: C07F 9/5728 condensed with carbocyclic rings or carbocyclic ring systems
• CPC Class Codes: C07F 9/5765 condensed with carbocyclic rings or carbocyclic ring systems
• CPC Class Codes: C07F 9/58 Pyridine rings
• CPC Class Codes: C07F 9/6533 Six-membered rings
• CPC Class Codes: C07F 9/65335 condensed with carbocyclic rings or carbocyclic ring systems
• CPC Class Codes: C07F 9/6541 condensed with carbocyclic rings or carbocyclic ring systems
• CPC Class Codes: C07F 9/6547 condensed with carbocyclic rings or carbocyclic ring systems
• CPC Class Codes: C07F 9/65522 condensed with carbocyclic rings or carbocyclic ring systems
• CPC Class Codes: C07F 9/65583 each of the hetero rings containing nitrogen as ring hetero atom
• CPC Class Codes: C07F 9/65586 at least one of the hetero rings does not contain nitrogen as ring hetero atom
• CPC Class Codes: C07F 9/6561 containing systems of two or more relevant hetero rings condensed among themselves or condensed with a common carbocyclic ring or ring system, with or without other non-condensed hetero rings
• CPC Class Codes: C07F 9/65842 Cyclic amide derivatives of acids of phosphorus, in which one nitrogen atom belongs to the ring
• CPC Class Codes: C09B 11/24 Phthaleins containing amino groups ; Phthalanes; Fluoranes; Phthalides; Rhodamine dyes; Phthaleins having heterocyclic aryl rings; Lactone or lactame forms of triarylmethane dyes
• CPC Class Codes: C09B 15/00 Acridine dyes
• CPC Class Codes: C09B 57/00 Other synthetic dyes of known constitution

Abstract

Reagents are provided for the introduction of phosphonate groups into fluorescent dyes. Methods are also provided for preparing dye conjugates.

Claims

1-20. -20. (canceled)

21. A fluorescent dye reagent having the formula:

Fl—

P¹

wherein

Fl is a fluorescent dye component; and

P¹ is functionalized phosphonate group having the formula;

22. A fluorescent dye reagent of claim 21, wherein said fluorescent dye component is selected from the group consisting of coumarins, benzocoumarins, xanthenes, benzo[a]xanthenes, benzo[b]xanthenes, benzo[c]xanthenes, cyanines, acridines, dipyrrometheneboron difluorides, phenoxazines, benzo[a]phenoxazines, benzo[b]phenoxazines and benzo[c]phenoxazines.

23. A fluorescent dye reagent of claim 21, wherein said fluorescent dye component is selected from the group consisting of coumarin dyes, resorufin dyes, dipyrrometheneboron difluoride dyes, ruthenium bipyridyl dyes, energy transfer dyes, polymethine dyes, thiazole orange dyes and N-aryl-1,8-naphthalimide dyes.

24. A fluorescent dye reagent of claim 21, wherein said fluorescent dye component is a xanthene or benzoxanthene dye selected from the group consisting of fluorescein dyes, rhodamine dyes and rhodol dyes.

34. An oligonucleotide probe having an attached fluorescent dye reagent of claim 21, wherein attachment of the fluorescent dye reagent to the oligonucleotide is through a functional group present on pa.

35. An oligonucleotide probe having an attached quencher and an attached fluorescent dye reagent of claim 21, wherein attachment of the fluorescent dye reagent to the oligonucleotide is through a functional group present on pa.

36. An oligonucleotide probe having an attached quencher, minor groove binding agent, and an attached fluorescent dye reagent of claim 21, wherein attachment of the fluorescent dye reagent to the oligonucleotide is through a functional group present on P^a.

43. A fluorescent dye reagent of claim 24, wherein said fluorescent dye component has formula I(a):

44. A fluorescent dye reagent of claim 43, wherein A¹ and A² are each OR′

.

45. A fluorescent dye reagent of claim 43, wherein A¹ is OR′

and A² is N(Z)₂.

46. A fluorescent dye reagent of claim 43, wherein A¹ and A² are each N(Z)₂.

47. A fluorescent dye reagent of claim 44, wherein each R′

is selected from the group consisting of H and C₁-C₈ alkyl.

48. A fluorescent dye reagent of claim 21, wherein L¹ is an alkylene linking group.

49. A fluorescent dye reagent of claim 21, wherein P^a is a reactive electrophilic group.

50. A fluorescent dye reagent of claim 49, wherein said reactive electrophilic group is an activated ester group.

51. A fluorescent dye reagent of claim 50, wherein said activated ester group is selected from the group consisting of pentafluorophenyl esters and N-hydroxysuccinimide esters.

25-33. -33. (canceled)

37-42. -42. (canceled)