A xanthene dye having the formula: in which R 1, R 2, R 4, R 5, R 6, R 7, R 8, R 9, R 10 and R 11 are independently selected from substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, halogen, H, NO 2, CN, NR 15 R 16 and Z 2 R 16; R 3 is NR 15 R 16; wherein Z 2 is O or S; each R 15 is a member independently selected from H, substituted or unsubstituted alkyl, and substituted or unsubstituted heteroalkyl; each R 16 is a member independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, C(Z 3)R 17, and R 15 and R 16, together with the nitrogen to which they are attached, can also be a nitrogen-containing reactive group, wherein said reactive group is a member selected from -NHNH 2, -N=C=S and -N=C=O; wherein Z 3 is a member selected from O, S and NH; R 17 is a member selected from substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, OR 18 and NR 19 R 20; wherein R 18 is a member selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and C R 21; wherein R 21 is substituted or unsubstituted alkyl or substituted or unsubstituted heteroalkyl; R 19 and R 20 are members independently selected from H, substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl; Y is C or S 2; and X is (NR 22 R 23) or wherein R 22 and R 23 are members independently selected from H, substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl; and R 12 and R 13 together with the nitrogen to which they are attached are joined to form a ring, wherein said R 12 or R 13 comprises an oxygen-containing reactive group or a moiety produced by reaction of the oxygen-containing reactive group with a reactive group of complementary reactivity on a carrier molecule. R 1, R 2, R 4, R 5, R 6, R 7, R 8, R 9, R 10 and R 11 are independently selected from substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, halogen, H, NO 2, CN, NR 15 R 16 and Z 2 R 16; R 3 is NR 15 R 16; wherein Z 2 is O or S; each R 15 is a member independently selected from H, substituted or unsubstituted alkyl, and substituted or unsubstituted heteroalkyl; each R 16 is a member independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, C(Z 3)R 17, and R 15 and R 16, together with the nitrogen to which they are attached, can also be a nitrogen-containing reactive group, wherein said reactive group is a member selected from -NHNH 2, -N=C=S and -N=C=O; wherein Z 3 is a member selected from O, S and NH; R 17 is a member selected from substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, OR 18 and NR 19 R 20; wherein R 18 is a member selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and C R 21; wherein R 21 is substituted or unsubstituted alkyl or substituted or unsubstituted heteroalkyl; R 19 and R 20 are members independently selected from H, substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl; Y is C or S 2; and X is (NR 22 R 23) or wherein R 22 and R 23 are members independently selected from H, substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl; and R 12 and R 13 together with the nitrogen to which they are attached are joined to form a ring, wherein said R 12 or R 13 comprises an oxygen-containing reactive group or a moiety produced by reaction of the oxygen-containing reactive group with a reactive group of complementary reactivity on a carrier molecule.