A fluorescent cyanine dye of the following general formula is disclosed: wherein: X1 and X2 are independently selected from the group consisting of —O—, —S—, —C(CH3)2 or —C═CH2; Y1 and Y2 are nonmetal atoms required to form a benzo-condensed or naphtho-condensed ring; Q is a conjugated moiety that increases the fluorescent quantum yield and the stability of the compound; R1 and R2 are independently selected from the group consisting of H, C1-C4, alkyl, alkylensulfonic group or alkylensulfonate group wherein the alkylene group has from 1 to 4 carbon atoms; R3, R4 and R5 are independently selected from the group consisting of H, a sulfonic group, a sulfonate group, alkylensulfonic, alkylensulfonate and —SO2NH(CH2)m—W—(CH2)nZ, wherein alkylene has 1 to 4 carbon atoms, with the proviso that at least one of R1 to R5 contains a sulfonic or sulfonate group; W is absent or is a group selected from —SO2NH, —O—, —COO—, or —CONH—; n=0-12 and m=0-12 with the provisos that m+n≦12 and at least one of m and n≠0; 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. Nucleophile functionalities include —NH2, —OH, and —SH groups; groups capable of reacting with such functionalities include —COCl, —COOCOR, —CONHNH2, N-hydroxysuccinimido esters, —NCS, —CHO, —COCH2I, phosphoramidite and maleimido.