Synthesis and properties of phosphonic acid containing cyanine and squaraine dyes for use as fluorescent labels

Cyanine and squaraine dyes that contain one or two phosphonate groups attached directly to the aromatic residues of the dyes were synthesized. Absorption and fluorescence properties of the dyes were determined. Succinimidyl active esters were prepared from the dyes and were used to label proteins and oligonucleotides. Some of the dyes permit the preparation of brighter conjugates than do commercially available analogues such as Cy3 and Cy5.