Water soluble squaraine dyes for use as colorimetric stains in gel electrophoresis

Here we report that the difficulties encountered in the synthesis of a dual-pendant sulfonate bis(indolenine)squaraine dye can be overcome through the use of equimolar amounts of the common reaction catalyst, thus creating an organic salt between the sulfonate groups and the protonated catalyst. Thus, a range of water-soluble dyes can further be prepared, by simply altering the catalyst. Crystal structures of four subsequent derivatives, prepared in this manner, are reported and show that, although the squaraine moieties remain essentially planar, the packing lattices can vary significantly, and the expectation that both sulfonic acid groups will protonate a stoichiometric amount of the available organic base catalyst is also demonstrated by one structure to not be fully true. Two of the dyes, whose crystal structures are reported, proved to be suitable as colorimetric stains for protein separation in sodium dodecylsulphate polyacrylamide gel electrophoresis (SDS-PAGE), and an optimal method for staining is reported. Results obtained for a fifth dye, crystal structure not obtained, are also reported. In all cases the results were compared against non-colloidal Coomassie Brilliant Blue (CBB) and it was found that the limit of detection for all squaraine derivatives examined were comparable with that of CBB although the resolution between protein bands was better. In addition, it was discovered that gels stained with the fifth dye (presented in this study) could be imaged in UV excitation/fluorescent imaging mode. The image robustness (or colour fastness) of all squaraines was found to be good for only a few hours.

► We report the synthesis of water soluble sulfonate bis(indolenine)squaraine salts. ► We report the crystal structures of four squaraine derivatives. ► The dyes are suitable as stains for protein separation in gel electrophoresis. ► The image robustness (or colour fastness) of the stained gels is good for a few hours.