Fluorescent dyes and methods of use thereof

1. A method for fluorescently labeling a target molecule, comprising the steps of:

providing a fluorescent dye compound having the formula:

wherein

R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 8 , R 9 , and R 10 are independently H, F, Cl, Br, I, CN, nitro, azido, hydroxyl, amino, hydrazino, (substituted) aryl, (substituted) aryloxy, alkenyl, alkynyl, alkyl, alkoxy, alkylamino, dialkylamino, arylamino, diarylamino, alkyl(aryl)amino, alkanoylamino, alkylthio, alkylcarbonyl, aryl carbonyl, alkylthiocarbonyl, arylthiocarbonyl, alkyloxycarbonyl, aroxycarbonyl, alkylaminocarbonyl, arylaminocarbonyl, dialkylaminocarbonyl, diarylaminocarbonyl, alkyl(aryl)aminocarbonyl, arylcarboxamido, or Q, the alkyl or alkoxy portions of which are saturated or unsaturated, linear or branched, unsubstituted or further substituted by F, Cl, Br, I, CN, OH, alkenyl, alkynyl, alkylcarbonyl, amide, thioamide, or Q;

wherein Q is selected from the group consisting of a carboxyl group (CO 2 − ), a carbonate ester (COER 11 ), a sulfonate ester (SO 2 ER 11 ), a sulfoxide (SOR 11 ), a sulfone (SO 2 CR 11 R 12 R 13 ), a sulfonamide (SO 2 NR 11 R 12 ), a phosphate (PO 4 − ), a phosphate monoester (PO 3 − ER 11 ), a phosphate diester (PO 2 ER 11 ER 12 ), a phosphonate (PO 3 − ), a phosphonate monoester (PO 2 − ER 11 ), a phosphonate diester (POER 11 ER 12 ), a thiophosphate (PSO 3 − ), a thiophosphate monoester (PSO 2 − ER 11 ), a thiophosphate diester (PSOER 11 ER 12 ), a thiophosphonate (PSO 2 − ), a thiophosphonate monoester (PSO − ER 11 ), a thiophosphonate diester (PSER 11 ER 12 ), a phosphonamide (PONR 11 R 12 NR 14 R 15 ), a phosphonamide thioanalogue (PSNR 11 R 12 NR 14 R 15 ), a phosphoramide (PONR 11 R 12 NR 13 NR 14 R 15 ), a phosphoramide thioanalogue (PSNR 11 R 12 NR 13 NR 14 R 15 S), a phosphoramidite (PO 2 R 14 NR 11 R 12 ), and a phosphoramidite thioanalogue (POSR 14 NR 11 R 12 ),

wherein E can independently be O or S, and

wherein the aryl portions of any of the above are optionally substituted by F, Cl, Br, I, CN, OH, alkenyl, alkynyl, alkylcarbonyl, amide, or thioamide;

wherein R 1 in combination with R 2 , R 3 in combination with R 4 , R 5 in combination with R 6 , or R 9 in combination with R 10 can independently form a 5-10 member ring structure which is saturated or unsaturated, and which is optionally further substituted with an alkyl, an aryl, an alkenyl, an alkynyl, an alkoxy, an aryloxy, a hydroxyl, F, Cl, Br, I, CN, a nitro, an alkylsulfonyl, an arylsulfonyl, an alkylsulfinyl, an arylsulfinyl, a (thio)carbonyl, a (thio)carboxylic acid, a (thio)carboxylic acid ester, a nitro, an amino, a (thio)amide, an azido, a hydrazino, or a (thio)phosphonate where each alkyl group or alkoxy group is independently saturated or unsaturated, linear or branched, or substituted or unsubstituted and each aryl group wherein is independently optionally substituted with F, Cl, Br, I, CN, OH, an alkyl, an alkenyl, an alkynyl, an alkoxy, an aryoxy, an alkylthio, an arylthio, a nitro, an azido, a hydrazino, a carboxyl, a thiocarboxyl, a carbonyl, a thiocarbonyl, a carboxylic acid ester, a thiocarboxylic acid ester, or an amino, amide, thioamide, or Q;

R 11 , R 12 , R 13 , R 14 and R 15 are independently hydrogen, a halogen, an amino group, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, or substituted or unsubstituted, an alkoxy group wherein said alkoxy group is saturated or unsaturated, branched or linear, or substituted or unsubstituted, an aryl group wherein said aryl group is unsubstituted or substituted; wherein R 11 in combination with R 12 , R 14 in combination with R 15 , R 11 in combination with R 13 , R 11 in combination with R 14 , R 12 in combination with R 15 , or R 13 in combination with R 14 can independently form a 5-10 member ring;

X is O, OR 16 , NR 17 R 18 or N + R 17 R 18 ; Y is O, OR 16 , NR 19 R 20 or N + R 19 R 20 , wherein R 16 , R 17 , R 18 , R 19 and R 20 are independently H, alkyl, alkenyl, alkynyl, or aryl; or R 17 in combination with R 18 , or R 19 in combination with R 20 can independently form a 5-10 member ring structure which is optionally further substituted with alkyl, alkenyl, alkynyl, aryl, alkoxy, F, Cl, Br, I, carboxylic acid or carboxylic acid ester, where the alkyl group is saturated or unsaturated, linear or branched, and is optionally further substituted by F, Cl, Br, I, CN, OH, alkenyl, alkynyl, nitro, azido, hydrazino, alkoxy, aryoxy, alkylthio, arylthio, thiocarboxyl, carbonyl, thiocarbonyl, thiocarboxylic acid ester, amino, amide, thioamide, or Q, and the aryl group wherein is optionally substituted by F, Cl, Br, I, CN, OH, alkoxy, aryoxy, alkylthio, arylthio, nitro, azido, hydrazino, carboxyl, thiocarboxyl, carbonyl, thiocarbonyl, carboxylic acid ester, thiocarboxylic acid ester, amino, amide, thioamide, or Q;

wherein R 17 in combination with R 6 , R 18 in combination with R 7 , R 19 in combination with R 8 , and R 20 in combination with R 9 , can independently form a 5- to 10-member ring structure that is saturated or unsaturated and optionally further substituted with an alkyl, an aryl, an alkenyl, an alkynyl, an alkoxy, an aryloxy, a hydroxyl, F, Cl, Br, I, CN, a nitro, a carbonyl, a thiocarbonyl, a thiocarboxylic acid, a thiocarboxylic acid ester, a nitro, an amino, a (thio)amide, an azido, a hydrazino, or Q, wherein the alkyl group herein is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein the alkoxy group is saturated or unsaturated, branched or linear, substituted or unsubstituted; and wherein the aryl group is optionally substituted with F, Cl, Br, I, CN, OH, alkenyl, alkynyl, alkoxy, aryoxy, alkylthio, arylthio, nitro, azido, hydrazino, carboxyl, thiocarboxyl, carbonyl, thiocarbonyl, carboxylic acid ester, thiocarboxylic acid ester, amino, amide, thioamide, or Q;

A is O, S or NR 21 , wherein R 21 is a hydrogen, an alkyl, an aryl, an alkenyl, an alkynyl, an alkylcarbonyl, an arylcarbonyl, an alkylaminocarbonyl, or an arylaminocarbonyl, the alkyl or aryl portions of which is optionally substituted by an alkyl, an aryl, an alkenyl, an alkynyl, F, Cl, Br, I, CN, OH, an alkoxy, an aryoxy, an alkylthio, an arylthio, a nitro, an azido, a hydrazino, a thiocarboxyl, a carbonyl, a thiocarbonyl, a thiocarboxylic acid ester, or an amino, amide, thioamide, or Q;

B is an alkyl, an alkenyl, an alkynyl, or an aryl linker, the alkyl or aryl portions of which is optionally substituted by an alkyl, an alkenyl, an alkynyl, an aryl, F, Cl, Br, I, CN, OH, an alkoxy, an aryoxy, an alkylthio, an arylthio, a nitro, an azido, a hydrazino, a carboxyl, a thiocarboxyl, a carbonyl, a thiocarbonyl, a carboxylic acid ester, a thiocarboxylic acid ester, or an amino, amide, thioamide, or Q; or

B in combination with A form an amide, a thioamide, a carboxylic acid ester, a carboxylic acid thioester, a thiocarboxylic acid ester, an imine, a hyrazone, or Q; and

Z is a reactive group selected from the group consisting of an isocyanate, an isothiocyanate, a monochlorotriazine, a dichlorotriazine, a 4,6-dichloro-1,3,5-triazines, a mono- or di-halogen substituted pyridine, a mono- or di-halogen substituted diazine, a maleimide, a haloacetamide, an aziridine, a sulfonyl halide, a carboxylic acid, an acid halide, a phosphonyl halide, a phosphoramidite (PO 2 R 14 NR 11 R 12 ), a phosphoramidite thioanalogue (POSR 14 NR 11 R 12 ), a hydroxysuccinimide ester, a hydroxysulfosuccinimide ester, an imido ester, an azido, a nitrophenol ester, an azide, a 3-(2-pyridyl dithio)-propionamide, a glyoxal, an aldehyde, a thiol, an amine, a hydrazine, a hydroxyl, a terminal alkene, a terminal alkyne, a platinum coordinate group and an alkylating agent,

wherein the carbon lengths for said alkenyl, alkynyl, and alkyl groups are in the range of 1 to 16;

providing a target molecule to be labeled, wherein the target molecule is selected from the group consisting of a nucleic acid, a nucleotide, and a peptide nucleic acid; and

contacting the fluorescent dye compound with the target molecule such that reactive group Z reacts with the target molecule to form a covalent bond between reactive group Z and the target molecule.

2. The method of claim 1 , wherein -A-B—Z is

wherein n is 1-10.

3. The method of claim 2 , wherein n is 1-4.

4. The method of claim 2 , wherein -A-B—Z is

5. The method of claim 1 , wherein -A-B—Z is

6. The method of claim 1 , wherein the fluorescent dye compound has the structure

7. The method of claim 6 , wherein R 6 and R 9 are both H or CH 3 .

8. The method of claim 6 , wherein X and Y are

(a) OH and O, respectively;

(b) NHCH 2 CH 3 and NCH 2 CH 3 , respectively; or

(c) N(CH 3 ) 2 and N + (CH 3 ) 2 , respectively.

9. The method of claim 1 , wherein the fluorescent dye compound is selected from the group consisting of:

10. The method of claim 9 , wherein the fluorescent dye compound is selected from the group consisting of:

11. The method of claim 1 , wherein the fluorescent dye compound is selected from the group consisting of:

12. The method of claim 1 , wherein the fluorescent dye compound is selected from the group consisting of:

wherein E − is an anion.

13. The method of claim 1 , wherein the target molecule is a nucleic acid.

14. The method of claim 1 , wherein the target molecule is a peptide nucleic acid.

15. The method of claim 1 , wherein the target molecule is a nucleotide.

16. The method of claim 1 , wherein the carbon lengths for said alkenyl, alkynyl, and alkyl groups are in the range of 1 to 10.

17. The method of claim 13 , wherein the carbon lengths for said alkenyl, alkynyl, and alkyl groups are in the range of 1 to 10.