Biocompatible N, N-Disubstituted Sulfonamide-Containing Fluorescent Dye Labels

A compound represented by the following structural formula:

• or a salt thereof, wherein:
• X1 and X2 are independently selected from the group consisting of C(CH2K1)(CH2K2), O, S and Se;
• K1 and K2 are independently selected from the group consisting of H, a C1-C20 aliphatic group and a C1-C20 aliphatic group substituted with —OR*, N(R*)2 or —SR*;
• or K1 and K2 together are part of a substituted or unsubstituted carbocyclic, or heterocyclic ring;
• Y1 and Y2 are each independently a benzo-condensed ring or a naphtha-condensed ring;
• n1 is 1, 2, or 3;
• R2, R11 and R12 are independently H, F, Br, Cl, C1-C6 alkyl, C1-C6 alkoxy, aryloxy, a nitrogen-containing heterocyclic ring, a nitrogen-containing heteroaromatic ring, a sulfonate, an iminium ion, or any two adjacent R12 and R11 substituents or R2 and R11 substituents, when taken in combination, form a 4-, 5-, or 6-membered substituted or unsubstituted carbocyclic ring, substituted or unsubstituted non-aromatic carbocyclic ring or a substituted or unsubstituted carbocyclic aryl ring, wherein the carbocyclic rings are each independently optionally substituted one or more times by C1-C6 alkyl, halogen, or OR* or SR*;
• R1 and R13 are (CH2)xCH3, when x is an integer selected from 0 to 6;
• or R1 and R13 are independently (CH2)nSO3 or (CH2)nSO3H when n is an integer selected from 2 to 6;
• R3, R4 and R5 are independently selected from the group consisting of H, carboxylate, carboxylic acid, carboxylic ester, amine, amide, sulfonamide, hydroxyl, alkoxyl, a sulphonic acid moiety and a sulphonate moiety;
• R6 is selected from the group consisting of a substituted or unsubstituted C1-C20 aliphatic group, a substituted or unsubstituted aryl, a substituted or unsubstituted alkylaryl;
• wherein R6 is optionally substituted with halogen, OR*, N(R*)2 or SR*, when Q is absent, a carbonyl group, a substituted or unsubstituted C1-C6 alkyl group, wherein 0-2 of the methylene groups of the alkyl group are replaced by NH, O or S, or a substituted or unsubstituted C1-C6 carbocyclic, non-aromatic carbocyclic, heterocyclic or non-aromatic heterocyclic ring wherein the heterocyclic rings contains 1-2 heteroatoms;
• or
• R6 is H, when Q is a carbonyl;
• and
• R7 is selected from the group consisting of H, a substituted or unsubstituted C1-C20 aliphatic group, a substituted or unsubstituted aryl, a substituted or unsubstituted alkylaryl, wherein R7 is optionally substituted with halogen, OR*, N(R*)2 or SR*;
• or
• R6 and R7, taken together form a 4-, 5-, 6- or 7-membered heterocyclic or non-aromatic heterocyclic ring optionally substituted with halogen, OR*, N(R*)2 or SR*;
• or
• NR6, Q and CHR7 together form a substituted or unsubstituted or heterocyclic or non-aromatic heterocyclic ring system wherein the rings contain 1 or 2 heteroatoms, wherein rings are optionally substituted with —OR*, N(R*)2 or —SR*;
• and
• W is absent or is a group selected from the group consisting of —SO2NR6-Q-CHR7—, —O—, —COO—, and —CONH—;
• h=0-70;
• k=0 or 1;
• d=0-12;
• m=0-12;
• p=0-12;
• Z is, or contains a N, O or S nucleophile functionality or is, or contains a functionality capable of reacting with N, O or S nucleophiles;
• and
• each R* is independently —H or C1-20 alkyl.

A compound represented by the following structural formula:

• or a salt thereof, wherein:
• X1 and X2 are independently selected from the group consisting of C(CH2K1)(CH2K2), O, S and Se;
• K1 and K2 are independently selected from the group consisting of H, a C1-C20 aliphatic group and a C1-C20 aliphatic group substituted with —OR*, N(R*)2 or —SR*;
• or K1 and K2 together are part of a substituted or unsubstituted carbocyclic, or heterocyclic ring;
• Y1 and Y2 are each independently a benzo-condensed ring or a naphtha-condensed ring;
• n1 is 1, 2, or 3;
• R2, R11 and R12 are independently H, halogen, C1-C6 alkyl, C1-C6 alkoxy, aryloxy, a nitrogen-containing heterocyclic ring, a nitrogen-containing heteroaromatic ring, a sulfonate, an iminium ion, a group containing SO2NR6-Q-CHR7—(CH2)m;
• i is 0 or 1;
• and m=0-12 or any two adjacent R12 and R11 substituents or R2 and R11 substituents, when taken in combination, form a 4-, 5-, or 6-membered substituted or unsubstituted carbocyclic ring, substituted or unsubstituted non-aromatic carbocyclic ring or a substituted or unsubstituted carbocyclic aryl ring, wherein the carbocyclic rings are each independently optionally substituted one or more times by C1-C6 alkyl, halogen, or OR* or SR*;
• R1 and R13 are (CH2)xCH3, when x is an integer selected from 0 to 6;
• or R1 and R13 are independently (CH2)nSO3− or (CH2)nSO3H when n is an integer selected from 2 to 6;
• R3, R4 and R5 are independently selected from the group consisting of H, carboxylate, carboxylic acid, carboxylic ester, amine, amide, sulfonamide, hydroxyl, alkoxyl, a sulphonic acid moiety and a sulphonate moiety;
• R6 is selected from the group consisting of a substituted or unsubstituted C1-C20 aliphatic group, a substituted or unsubstituted aryl, a substituted or unsubstituted alkylaryl, wherein R6 is optionally substituted with halogen, OR*, N(R*)2 or SR* when Q is absent, a carbonyl group, a substituted or unsubstituted C1-C6 alkyl group;
• wherein 0-2 of the methylene groups of the alkyl group are replaced by NH, O or S, or a substituted or unsubstituted C1-C6 carbocyclic, non-aromatic carbocyclic, heterocyclic or non-aromatic heterocyclic ring wherein the heterocyclic rings contains 1-2 heteroatoms;
• or
• R6 is H, when Q is a carbonyl;
• and
• R7 is selected from the group consisting of H, a substituted or unsubstituted C1-C20 aliphatic group, a substituted or unsubstituted aryl, a substituted or unsubstituted alkylaryl, wherein R7 is optionally substituted with halogen, OR*, N(R*)2 or SR*;
• or
• R6 and R7, taken together form a 4-, 5-, 6- or 7-membered heterocyclic or non-aromatic heterocyclic ring optionally substituted with halogen, OR*, N(R*)2 or SR*;
• or
• NR6, Q and CHR7 together form a substituted or unsubstituted or heterocyclic or non-aromatic heterocyclic ring system wherein the rings contain 1 or 2 heteroatoms, wherein rings are optionally substituted with —OR*, N(R*)2 or —SR*;
• and
• W is absent or is a group selected from the group consisting of —SO2NR6-Q-CHR7—, —O—, —COO—, and —CONH—;
• h=0-70;
• k=0 or 1;
• d=0-12;
• m=0-12;
• p=0-12;
• and
• Z is, or contains a N, O or S nucleophile functionality or is, or contains a functionality capable of reacting with N, O or S nucleophiles;
• and each R* is independently —H or C1-20 alkyl.

A compound represented by the following structural formula:

• or a salt thereof, wherein:
• X1 and X2 are independently selected from the group consisting of C(CH2K1)(CH2K2), 0, S and Se;
• K1 and K2 are independently selected from the group consisting of H, a C1-C20 aliphatic group and a C1-C20 aliphatic group substituted with —OR*, N(R*)2 or —SR*;
• or K1 and K2 together are part of a substituted or unsubstituted carbocyclic, or heterocyclic ring;
• Y1 and Y2 are each independently a benzo-condensed ring or a naphtha-condensed ring;
• n1 is 1, 2, or 3;
• R2, R11 and R12 are independently a group containing SO2NR6-Q-CHR7—(CH2)m;
• i is 0 or 1;
• and m=0-12, alkyl, aryl, alkoxy, halogen, S-aryl or S-alkyl,
• R1 and R13 are H;
• R3, R4 and R5 are independently selected from the group consisting of H, carboxylate, carboxylic acid, carboxylic ester, amine, amide, sulfonamide, hydroxyl, alkoxyl, a sulphonic acid moiety and a sulphonate moiety;
• R6 is selected from the group consisting of a substituted or unsubstituted C1-C20 aliphatic group, a substituted or unsubstituted aryl, a substituted or unsubstituted alkylaryl, wherein R6 is optionally substituted with halogen, OR*, N(R*)2 or SR* when Q is absent, a carbonyl group, a substituted or unsubstituted C1-C6 alkyl group, wherein 0-2 of the methylene groups of the alkyl group are replaced by NH, O or S, or a substituted or unsubstituted C1-C6 carbocyclic, non-aromatic carbocyclic, heterocyclic or non-aromatic heterocyclic ring wherein the heterocyclic rings contains 1-2 heteroatoms;
• or
• R6 is H, when Q is a carbonyl;
• and
• R7 is selected from the group consisting of H, a substituted or unsubstituted C1-C20 aliphatic group, a substituted or unsubstituted aryl, a substituted or unsubstituted alkylaryl, wherein R7 is optionally substituted with halogen, OR*, N(R*)2 or SR*;
• or
• R6 and R7, taken together form a 4-, 5-, 6- or 7-membered heterocyclic or non-aromatic heterocyclic ring optionally substituted with halogen, OR*, N(R*)2 or SR*;
• or
• NR6, Q and CHR7 together form a substituted or unsubstituted or heterocyclic or non-aromatic heterocyclic ring system wherein the rings contain 1 or 2 heteroatoms, wherein rings are optionally substituted with —OR*, N(R*)2 or —SR*;
• and
• W is absent or is a group selected from the group consisting of —SO2NR6-Q-CHR7—, —O—, —COO—, and —CONH—;
• h=0-70;
• k=0 or 1;
• d=0-12;
• m=0-12;
• p=0-12;
• Z is, or contains a N, O or S nucleophile functionality or is, or contains a functionality capable of reacting with N, O or S nucleophiles;
• and
• each R* is independently —H or C1-20 alkyl.