Interactions of thionin with DNA strands: Intercalation versus external stacking

We have investigated thionin in a glycerol/water glass bound to DNA quadruplexes and DNA duplexes with pressure-tuning hole-burning spectroscopy at 2 K. For free thionin as a reference we could identify the two tautomeric structures (imino and amino form) in the inhomogeneous absorption bands. The measurement of local compressibilities from the spectral hole shifts under pressure allowed the assignment of binding modes of thionin to the DNA strands. Thionin binds via external stacking to the dimeric hairpin quadruplex and binds to the monomeric quadruplex only by Coulombic interaction, whereas it intercalates into a linear GC-duplex structure. However, differences in the local compressibilities revealed that only the amino form is able to intercalate into the DNA duplex.