Phenyl xanthene dyes

• US 8,383,841 B2
• Filed: 01/09/2009
• Issued: 02/26/2013
• Est. Priority Date: 05/09/2003
• Status: Active Grant

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Inventors: Lam, Joe Y. L., Menchen, Steven M., Zou, Ruiming, Benson, Scott C.
• Primary Examiner(s): POWERS, FIONA
• Application Number:
  US12/351,504
• Publication Number:
  US 20090172899A1
• Time in Patent Office: 1,509 Days
• Field of Search: None
• US Class Current: 549/382
• CPC Class Codes: C07D 311/82 Xanthenes
• CPC Class Codes: C07D 491/14 Ortho-condensed systems
• CPC Class Codes: C09B 11/06 Hydroxy derivatives of triarylmethanes in which at least one OH group is bound to an aryl nucleus and their ethers or esters
• CPC Class Codes: C09B 11/12 without any OH group bound to an aryl nucleus
• CPC Class Codes: C09B 11/22 containing OH groups bound to an aryl nucleus and their ethers and esters
• 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 11/26 Triarylmethane dyes in which at least one of the aromatic nuclei is heterocyclic phthaleins C09B11/24
• CPC Class Codes: C09B 13/00 Oxyketone dyes
• CPC Class Codes: C09B 57/00 Other synthetic dyes of known constitution
• CPC Class Codes: C09B 62/0025 Specific dyes not provided for in groups C09B62/004 - C09B62/018

Abstract

Fluorescent phenyl xanthene dyes are described that comprise any fluorescein, rhodamine or rhodol comprising a particular C9 phenyl ring. One or both of the ortho groups on the lower C9 phenyl ring is ortho substituted with a group selected from alkyl, heteroalkyl, alkoxy, halo, haloalkyl, amino, mercapto, alkylthio, cyano, isocyano, cyanato, mercaptocyanato, nitroso, nitro, azido, sulfeno, sulfinyl, and sulfino. In one embodiment, halo and/or hydroxy groups are used. Optimal dyes contain a lower C9 phenyl ring in which both ortho groups are the same and the lower ring exhibits some form a symmetry relative to an imaginary axis running from the phenyl rings point of attachment to the remainder of the xanthene dye through a point para to the point of attachment. The phenyl xanthene dyes may be activated. Furthermore, the phenyl xanthene dyes may be conjugated to one or more substances including other dyes. The phenyl xanthene dyes are useful for a number of purposes, including labels for use in automated DNA sequencing as well the formation of fluorescent “bar codes” for polymeric particles used in the multiplexed analysis of analytes.

Claims

1. A fluorescent phenyl xanthene dye comprising a rhodamine that comprises one of the following core structures:

2. The fluorescent phenyl xanthene dye according to claim 1, wherein R¹¹, R¹², R¹³, R¹⁴ and R¹⁵ are defined according to one of the following alternatives:

(i) R¹¹ and R¹⁵ are each the same halo group and R¹², R¹³ and R¹⁴ are each hydrogen;

(ii) R¹¹, R¹³ and R¹⁵ are each the same halo group and R¹² and R¹⁴ are each hydrogen;

(iii) R¹¹, R¹², R¹⁴ and R¹⁵ are each the same halo group and R¹³ is hydrogen;

or

(iv) R¹¹, R¹², R¹³, R¹⁴ and R¹⁵ are each the same halo group.

3. The fluorescent phenyl xanthene dye according to claim 1, wherein:

R¹, R², R²′

, R⁴, R⁴′

, R⁵, R⁵′

, R⁷, R⁷′ and

R⁸, when taken alone, are each, independently of one another, selected from hydrogen, a substituent having up to 40 atoms, and —

S-LG, or alternatively, R¹ may be taken together with R², or R⁷ may be taken together with R⁸ to form an optionally substituted benzo, naptho or polycyclic aryleno group;

R³′

, R³″

, R⁶′ and

R⁶″

, when taken alone, are each, independently of one another, selected from hydrogen, a substituent having up to 40 atoms, and —

S-LG, or alternatively, R³″

may be taken together with R⁴, R³′

may be taken together with an adjacent R² or R²′

, R⁶″

may be taken together with R⁵ or R⁶′

may be taken together with an adjacent R⁷ or R⁷′

to form an optionally substituted 5- or 6-membered ring, with the proviso that at least one of R³′

, R³″

, R⁶′

or R⁶″

must be the lipophilic substituent;

each S is, independently of the others, selected from a direct bond and a spacing moiety; and

each LG is, independently of the others, a linking group.

4. A composition comprising a phenyl xanthene dye according to claim 1 and at least one second substance, wherein said phenyl xanthene dye is covalently linked to said second substance by way of a linker of the formula —

S¹LK-S²—

, where S¹ is a direct bond or a spacing moiety, LK is a linkage, and S² is a direct bond or a spacing moiety.

5. The composition according to claim 4, wherein said second substance is selected from a biomolecule, a glass substrate, a metal substrate and a polymer substrate.

6. The composition according to claim 4, wherein said second substance is another dye and the phenyl xanthene dye is part of an energy transfer network.