Compounds and methods for fluorescent labeling

1. A compound having a formula selected from the group consisting of:

wherein

Y 4 is C, S, or SO;

each X 1 , X 2 , X 3 and X 4 is a member independently selected from the group consisting of H, halogen, cyano, halo(C 1 -C 8 )alkyl, (C 1 -C 8 )alkyl, (C 1 -C 8 )alkoxy, (C 1 -C 8 )alkylthio, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, SO 3 H and CO 2 H, or any two adjacent X 1 , X 2 , X 3 , and X 4 are combined to form a fused aromatic or heteroaromatic ring that is optionally further substituted with from one to four substituents selected from the group consisting of halogen cyano, carboxy, sulfo, hydroxy, amino, mono(C 1 -C 6 )alkylamino, di(C 1 -C 6 )alkylamino, (C 1 -C 6 )alkyl, (C 1 -C 6 )alkylthio and (C 1 -C 6 )alkoxy;

the moiety

is a member selected from the group consisting of:

optionally substituted with a member independently selected from the group consisting of halogen, cyano, halo(C 1 -C 8 )alkyl, (C 1 -C 8 )alkoxy, (C 1 -C 8 )alkylthio, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, aryl, heteroaryl, SO 2 H and CO 2 H;

each R 1 , R 2 , R 13 , R 14 or R 15 is a member independently selected from the group consisting of H, halogen, cyano, halo(C 1 -C 8 )alkyl, (C 1 -C 8 )alkyl, (C 1 -C 8 )alkylthio, (C 1 -C 8 )alkoxy, aryl and heteroaryl, or R 14 and R 15 are combined with the atoms which attach them to form a 5- or 6-membered aromatic ring;

each R 5 or R 6 is a member independently selected from the group consisting of H, (C 1 -C 8 )alkyl, aryl, heteroaryl, aryl(C 1 -C 4 )alkyl and heteroaryl(C 1 -C 4 )alkyl;

R 7 is H or a hydroxyl protecting group;

R 8 is NR 9 W(Y 2 P L), hydroxy, or a leaving group that can be displaced by a nucleophilic reagent;

W is a linking group selected from the group consisting of a (C 2 -C 50 )alkylene, heteroalkylene, (C 2 -C 50 )cycloalkylene, heterocycloalkylene, (C 6 -C 50 )arylene group, a heteroarylene group, (C 2 -C 50 )alkylenearylene group, a heteroalkylenearylene group, optionally substituted with at least one substituent independently selected from the group consisting of(C 1 -C 8 )alkyl, hydroxy, protected hydroxy, alkoxy, amino, protected amino, hydrazino, thio, protected thio and aryl;

R 9 is H, alkyl or combined with W to form a heterocycloalkylene, heterocycloalkylenearylene, or heterocycloalkyleneheteroarylene linking group;

Y 2 is a linking group selected from the group consisting of:

wherein dashed line indicates the point of attachment to L and the wavy line indicates the point of attachment to the rest of the molecule;

each R 10 is independently (C 1 -C 8 )alkyl or (C 1 -C 8 )alkoxy;

the subscript p is an integer of from 0 to 1;

L is solid support when p is 1 and L is a member selected from the group consisting of an O-phosphoramidite or a reactive functional group when p is 0; and

the subscript n is an integer of from 4 to about 20.

2. The compound in accordance with claim 1 , selected from the group consisting of 5-(12,15-Dihydroxy-1-oxospiro[3-hydroisobenzofuran-3,9′-xanthene]-11-yl)pentanoic acid; 2,3,4,5,6-Pentafluorophenyl 5-(12,15-dihydroxy-1-oxospiro[3-hydroisobenzofuran-3,9′-xanthene]-11-yl)pentanoate; 5-(12,15-Dihydroxy-1-oxospiro[3-hydroisobenzofuran-3,9′-xanthene]-11-yl)-N-(6-hydroxyhexyl)pentanamide; 5-(12, 15-Dihydroxy-1-oxospiro[3-hydroisobenzofuran-3,9′-xanthene]-11-yl)-N-{6-[bis(4-methoxyphenyl)phenylmethoxy]hexyl}pentanamide; 11-[4-(N-{6-[bis(4-methoxyphenyl)phenylmethoxy]hexyl}carbamoyl)butyl]-15-(2,2-dimethylpropanoyloxy)-1-oxospiro[3-hydroisobenzofuran-3,9′-xanthene]-12-yl 2,2-dimethylpropanoate; 15-(2,2-dimethylpropanoyloxy)-11-{4-[N-(6-hydroxyhexyl)carbamoyl]butyl}-1-oxospiro[3-hydroisobenzofuran-3,9′-xanthene]-12-yl 2,2-dimethylpropanoate; and 11-{4-[N-(6-{[bis(methylethyl)amino](2-cyanoethoxy)phosphinooxy}hexyl)carbamoyl]butyl}-15-(2,2-dimethylpropanoyloxy)-1-oxospiro[3-hydroisobenzoftiran-3,9′-xanthene]-12-yl 2,2-dimethylpropanoate.

3. The compound in accordance with claim 1 , wherein R 8 is NR 9 W(Y 2 p L).

4. The compound in accordance with claim 1 , wherein R 9 and W are combined together to form a linking group comprising a prolinol group.

5. The compound in accordance with claim 3 , wherein p is 0.

6. The compound in accordance with claim 3 , wherein p is 1.

7. The compound in accordance with claim 3 , wherein;

each X 1 , X 2 , X 3 and X 4 is a member independently selected from the group consisting of H, halogen, cyano, halo(C 1 -C 8 )alkyl, (C 1 -C 8 )alkyl, (C 1 -C 8 )alkoxy, (C 1 -C 8 )alkylthio, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, SO 3 H and CO 2 H.

8. The compound in accordance with claim 7 , wherein Y 4 is C.

9. A composition comprising a compound according to claim 1 covalently attached to a solid support.

10. A method for preparing a compound of claim 1 , wherein R 8 is NR 9 W(Y 2 p L), and L is a reactive functional group; said method comprising contacting a compound of claim 1 wherein R 8 is a leaving group with a nucleophilic linking group component HNR 9 W(Y 2 p L).

11. A method for preparing a compound of claim 1 , wherein R 8 is NR 9 W(Y 2 p L), and L is a O-phosphoramidite, said method comprising contacting a compound of claim 7 , wherein R 8 is NR 9 W(Y 2 p L), and L is a reactive functional group; with a phosphoramidite reagent under conditions sufficient to covalently attach a phosphoramidite moiety.

12. A method for preparing a labeled biological agent, said method comprising contacting an unlabeled biological agent with a compound of claim 1 under conditions sufficient to covalently attach said compound to said biological agent and form said labeled biological agent.

13. The method in accordance with claim 12 , wherein said biological agent is a nucleotide, a modified nucleotide, a oligonucleotide, or a modified oligonucleotide.

14. The method in accordance with claim 13 , wherein said oligonucleotide comprises one or more modified nucleotide bases.

15. A nucleic acid covalently modified with a substituent having the formula selected from the group consisting of:

wherein,

A 3 is OH or a protected hydroxyl group;

each R 5 and R 6 is independently selected from H, (C 1 -C 8 )alkyl, aryl and aryl(C 1 -C 4 )alkyl;

R 7 is H or a hydroxyl protecting group;

each R 1 , R 2 , R 13 , R 14 and R 15 is a member independently selected from the group consisting of H, halogen, cyano, halo(C 1 -C 8 )alkyl, (C 1 -C 8 )alkyl, (C 1 -C 8 )alkylthio, (C 1 -C 8 )alkoxy, aryl and heteroaryl; or R 14 and R 15 is combined with the atoms which attach them to form a 5- or 6-membered aromatic ring;

n is an integer from 4 to about 20;

Y 4 is C, S, or SO;

each X 1 , X 2 , X 3 and X 4 is a member independently selected from the group consisting of H, halogen, cyano, halo(C 1 -C 8 )alkyl, (C 1 -C 8 )alkyl, (C 1 -C 8 )alkoxy, (C 1 -C 8 )alkylthio, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, SO 3 H and CO 2 H, or any two adjacent X 1 , X 2 , X 3 , and X 4 are combined to form a fused aromatic or heteroaromatic ring that is optionally further substituted with from one to four substituents selected from halogen cyano, carboxy, sulfo, hydroxy, amino, mono(C 1 -C 6 )alkylamino, di(C 1 -C 6 )alkylamino, (C 1 -C 6 )alkyl, (C 1 -C 6 )alkylthio and (C 1 -C 6 )alkoxy; and

the wavy line indicates the point of attachment to said nucleic acid or said linking group joining said nucleic acid to said substituent.

16. The nucleic acid in accordance with claim 15 , further comprising an attached quencher, and attached minor groove binder, or a combination thereof.

17. The nucleic acid in accordance with claim 16 , wherein said substituent is attached at the 3′-end of said nucleic acid and said quencher and said minor groove binder are attached at the 5′-end of said nucleic acid.

18. The nucleic acid in accordance with claim 16 , wherein said substituent is attached at the 5′-end of said nucleic acid and said quencher and said minor groove binder are attached at the 3′-end of said nucleic acid.

19. The compound in accordance with claim 1 , wherein said compound has an emission wavelength of from about 400 nm to about 1200 nm.

20. The compound in accordance with claim 1 , wherein said compound has an emission wavelength of from about 400 nm to about 850 nm.