Secondary amine-substituted coumarin compounds and their uses as fluorescent labels

1. A compound of Formula (I) or a salt thereof:

wherein:

X is O, S, Se, or NR n , where R n is H or C 1-6 alkyl;

R is H, halo, —CN, amino, —OH, C-amido, N-amido, —NO 2 , —SO 3 H, —SO 2 NH 2 , optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted alkoxy, optionally substituted aminoalkyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl;

R 1 is H, halo, —CN, —CO 2 H, amino, —OH, C-amido, N-amido, —NO 2 , —SO 3 H, —SO 2 NH 2 , optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted alkoxy, optionally substituted aminoalkyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl;

R 2 and R 4 are each independently H, halo, —CN, —CO 2 H, amino, —OH, C-amido, N-amido, —NO 2 , —SO 3 H, —SO 2 NH 2 , optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted alkoxy, optionally substituted aminoalkyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl;

R 3 is C 2-6 alkyl substituted with —CO 2 H or —SO 3 H or both, or optionally substituted heterocyclyl;

each R 5 is independently halo, —CN, —CO 2 H, amino, —OH, C-amido, N-amido, —NO 2 , —SO 3 H, —SO 2 NH 2 , optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted alkoxy, optionally substituted aminoalkyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl; and

m is 0, 1, 2, 3, or 4.

2. The compound of claim 1 , wherein X is O or S.

3. The compound of claim 1 , wherein R 3 is C2_6alkyl substituted with —CO 2 H or —SO 3 H, or both.

4. The compound of claim 1 , wherein m is 0, 1, or 2, and wherein each R 5 is independently optionally substituted C 1-6 alkyl, halo, —CN, —CO 2 H, amino, —OH, —SO 3 H, or —SO 2 NH 2 .

5. The compound of claim 4 , wherein R 5 is —SO 3 H or —SO 2 NH 2 , or C 2-6 alkyl substituted with —CO 2 H, —SO 3 H, or —SO 2 NH 2 .

6. The compound of claim 1 , wherein each of R and R 1 is independently H, halo, or C 1-6 alkyl.

7. The compound of claim 6 , wherein R is H.

8. The compound of claim 1 , wherein R 2 is H, optionally substituted alkyl, C 1-4 alkyl optionally substituted with —CO 2 H or —SO 3 H, or —SO 3 H.

9. The compound of claim 1 , wherein R 4 is H, optionally substituted alkyl, C 1-4 alkyl optionally substituted with —CO 2 H or —SO 3 H, or —SO 3 H.

10. The compound of claim 1 , wherein X is O or S; R is H; R 1 is H; R 3 is —(CH2) n COOH where n is 2, 3, 4, 5, or 6; R 5 is H, —SO 3 H, or —SO 2 NH 2 ; R 2 is H or —SO 3 H; and R 4 is H or —SO 3 H.

11. A compound of Formula (II) or a salt thereof:

wherein:

X′ is selected from O, S, and NR P , where R P is H or C 1-6 alkyl;

R 6 is H or C 1-4 alkyl;

R 7 is H, halo, —CN, —OH, optionally substituted C 1-4 alkyl, optionally substituted C 1-4 alkenyl, optionally substituted C 2-4 alkynyl, —CO 2 H, —SO 3 H, —SO 2 NH 2 , —SO 2 NH(C 1-4 alkyl), —SO 2 N(C 1-4 alkyl) 2 , and optionally substituted C 1-4 alkoxy;

R 8 and R 10 are each independently H, halo, —CN, —CO 2 H, amino, —OH, —SO 3 H, —SO 2 NH 2 , —SO 2 NH(C 1-4 alkyl), —SO 2 N(C 1-4 alkyl) 2 , optionally substituted C 1-6 alkyl, optionally substituted C 1-6 alkenyl, optionally substituted C 2-6 alkynyl, or optionally substituted C 1-6 alkoxy;

R 9 is C 2-6 alkyl substituted with —CO 2 H, —CO 2 C 1-4 alkyl, —CONH 2 , —CONH(C 1-4 alkyl), —CON(C 1-4 alkyl) 2 , —CN, —SO 3 H, —SO 2 NH 2 , —SO 2 NH(C 1-4 alkyl), or —SO 2 N(C 1-4 alkyl) 2 ;

each R 11 is independently halo, —CN, carboxy, amino, —OH, C-amido, N-amido, nitro, —SO 3 H, —SO 2 NH 2 , —SO 2 NH(C 1-4 alkyl), —SO 2 N(C 1-4 alkyl) 2 , optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, and optionally substituted C 1-6 alkoxy; and

q is 0, 1, or 2.

12. The compound of claim 1 , selected from the group consisting of:

and salts thereof.

13. A nucleotide or oligonucleotide labeled with a compound according to claim 1 .

14. The labeled nucleotide or oligonucleotide according to claim 13 wherein the compound is attached via R 3 of Formula (I).

15. The labeled nucleotide or oligonucleotide of claim 14 , wherein R 3 of Formula (I) is —(CH 2 ) n COOH where n is 2, 3, 4, 5, or 6, and the attachment forms an amide using the —COOH group.

16. The labeled nucleotide or oligonucleotide of claim 13 , wherein the label is attached to the C5 position of a pyrimidine base or the C7 position of a 7-deaza purine base through a linker moiety.

17. The labeled nucleotide or oligonucleotide according to claim 13 , further comprising a 3′ OH blocking group covalently attached to the ribose or 2-deoxyribose sugar of the nucleotide.

18. A kit comprising a first labeled nucleotide according to claim 14 and a second labeled nucleotide.

19. The kit of claim 18 , wherein the second labeled nucleotide is labeled with a different compound than the first labeled nucleotide or is unlabeled.

20. The kit of claim 18 , further comprising a third nucleotide and a fourth nucleotide, wherein each of the second, third, and fourth nucleotides is labeled with a different compound, wherein each label has a distinct absorbance maximum that is distinguishable from the other labels.

21. The kit of claim 18 , wherein the kit comprises four nucleotides, wherein a first of the four nucleotides is a labeled nucleotide according to claim 13 , a second of the four nucleotides carries a second label, a third nucleotide carries a third label, and a fourth nucleotide is unlabeled (dark).

22. The kit of claim 18 , wherein the kit comprises four nucleotides, wherein a first of the four nucleotides is a labeled nucleotide according to claim 13 , a second of the four nucleotides carries a second label, a third nucleotide carries a mixture of two labels, and a fourth nucleotide is unlabeled (dark).

23. A method of sequencing, comprising: incorporating a nucleotide according to claim 17 in a sequencing assay; and detecting the incorporated nucleotide.

24. The method of claim 23 , wherein the sequencing assay is performed on an automated sequencing instrument, and wherein the automated sequencing instrument comprises two light sources operating at different wavelengths.

25. The compound of claim 11 , wherein each of R 6 and R 7 is H.

26. The compound of claim 25 , wherein each of R 8 and R 10 is independently H, —CO 2 H, a —SO 3 H, or —SO 2 NH 2 .

27. The compound of claim 26 , wherein R 9 is —(CH 2 ) y —CO 2 H, where y is 2, 3, 4, or 5.