Fluorescent dye compounds, conjugates and uses thereof

• US 7,985,602 B2
• Filed: 08/14/2007
• Issued: 07/26/2011
• Est. Priority Date: 09/16/2004
• Status: Active Grant

• Current Assignee: Applera Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Inventors: Zou, Ruiming, Upadhya, Krishna G., Benson, Scott C., Graham, Ronald J.
• Primary Examiner(s): AULAKH, CHARANJIT
• Application Number:
  US11/838,793
• Publication Number:
  US 20090093062A1
• Time in Patent Office: 1,442 Days
• Field of Search: 436/800, 546/58, 546/61, 546/102
• US Class Current: 436/800
• CPC Class Codes: C07D 219/06 Oxygen atoms
• 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: C09B 15/00 Acridine dyes
• CPC Class Codes: C09K 11/06 containing organic luminescent materials
• CPC Class Codes: C09K 2211/1011 Condensed systems
• CPC Class Codes: C09K 2211/1029 containing one nitrogen atom as the heteroatom
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: G01N 33/582 with fluorescent label
• CPC Class Codes: Y10S 436/80 Fluorescent dyes, e.g. rhodamine
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

The present teachings generally relate to fluorescent dyes, linkable forms of fluorescent dyes, energy transfer dyes, reagents labeled with fluorescent dyes and uses thereof.

Claims

1. An energy transfer dye comprising a donor dye covalently attached to an acceptor dye, wherein the donor dye is capable of absorbing light at a first wavelength and emitting excitation energy in response, the acceptor dye is capable of absorbing the excitation energy emitted by the donor dye and fluorescing at a second wavelength in response, and the donor dye is a compound selected from the group consisting of structures (I), (II), (III) and (IV)

2. The energy transfer dye of claim 1, wherein the donor dye is covalently attached to the acceptor dye through a linker.

3. The energy transfer dye of claim 2, wherein the linker is non-nucleotidic.

4. The energy transfer dye of claim 2, wherein the linker is nucleotidic.

5. The energy transfer dye according to any one of claims 1-4, wherein the acceptor dye is a compound comprising a structure selected from the group consisting of structures (I), (II), (III) and (IV)

6. The energy transfer dye of claim 5, wherein the donor dye is selected from the group consisting of 5-carboxyfluorescein (5-FAM), 6-carboxyfluorescein (6-FAM), rhodamine green (R110), 5-carboxyrhodamine, 6-carboxyrhodamine, N,N′

-diethyl-2′

,7′

-dimethyl-5-carboxy-rhodamine (5-R6G), N,N′

-diethyl-2′

,7′

-dimethyl-6-carboxyrhodamine (6-R6G), N,N,N′

,N′

-tetramethyl-5-carboxyrhodamine (5-TAMRA), Cy3, N,N,N′

,N′

-tetramethyl-5-carboxyrhodamine (6-TAMRA), 5-carboxy-X-rhodamine (5-ROX), 6-carboxy-X-rhodamine (6-ROX), 5-carboxy-2′

,4′

,5′

,7′

,4,7-hexachlorofluorescein, 6-carboxy-2′

, 4′

,5,7′

,4,7-hexachlorofluorescein, 5-carboxy-2′

,7′

-dicarboxy-4′

,5′

-dichloro-fluorescein, 6-carboxy -1′

,2′

-dicarboxy-4′

,5′

-dichlorofluorescein, 5-carboxy-2′

,4′

,5′

,7′

-tetrachlorofluorescein, 1′

,2′

-benzo-4′

-fluoro-7′

,4,7-trichloro-5-carboxyfluorescein, 1′

,2′

-benzo-4′

-fluoro-7′

,4,7-trichloro-6-carboxyfluorescein and 1′

,2′

,7′

,8′

-dibenzo-4,7-dichloro-5-carboxyfluorescein.

7. The compound of claim 1, wherein each of R₆ and R₇ is independently selected from the group consisting of fluorine, chlorine and bromine.

8. The compound of claim 7, wherein each of R₆ and R₇ is fluorine.

9. The compound of claim 7, wherein each of R₆ and R₇ is chlorine.

10. The compound of claim 7, wherein each of R₆ and R₇ is bromine.

11. The compound of claim 1, wherein R₆ is —

H and R₇ is selected from the group consisting of —

H, —

CO₂H, —

CO₂R, —

SO₃H, —

SO₃R, —

CH₂CO₂H, —

CH₂CO₂R, —

CH₂SO₃H, —

CH₂SO₃R, —

CH₂NH₂, and —

CH₂NHR.

12. The compound of claim 1, wherein R₆ is —

H and R₇ is selected from the group consisting of —

H, —

SO₃H, —

SO₃R, —

CH₂CO₂H, —

CH₂CO₂R, —

CH₂NH₂, and —

CH₂NHR.

13. The compound of claim 1, wherein R₃ is —

H and R₂ is selected from the group consisting of —

H, —

SO₃H, —

SO₃R, —

CH₂CO₂H, —

CH₂CO₂R, —

CH₂NH₂, and —

CH₂NHR.

14. The compound of claim 1, wherein R is selected from the group consisting of C₁-C₆ alkyl, substituted C₁-C₆ alkyl, C₁-C₆ alkoxy, substituted C₁-C₆ alkoxy, C₁-C₆ alkoxyaryl, substituted C₁-C₆ alkoxyaryl, phenyl, substituted phenyl, biphenyl, substituted biphenyl, benzyl, substituted benzyl, benzoyl, substituted benzoyl, a linking group and trifluoracetyl.