Consideration on the metachromatic spectra of to luidine blue dimers formed on DNA oligomers

Metachromatic staining with toluidine blue (TB) has been used as a cytological tool for tissue recognition and cancer diagnosis. Recently, its strong potential for infertility diagnosis was also reported. Metachromatic staining is important in biological applications, but the origin of spectral changes has not been fully understood, although dye aggregation on biological materials is thought to be the cause. In this study, we investigated the dimer structure of TB formed on DNA oligomers by using a computational method, particularly focusing on the spectral changes caused by TB dimer formation. The structure of the TB-DNA complexes was constructed on the basis of the calculated molecular structure of TB and crystal data of A-and B-form DNA oligomers, assuming that there was an electrostatic interaction between them. The resulting spectral shift was then evaluated using the extended-dipole model. The examination of B-DNA revealed that possible TB dimers result in a hypsochromic spectral shift of absorption. On the other hand, the dimerization of TB on A-DNA was found to be quite difficult, because the helical geometry of A-DNA restricted the binding sites of TB. These results suggest that the metachromatic color observed during biological staining is significantly affected by the helical geometry of DNA.