Porphyrin binding to DNA investigated by cyclodextrin supramolecular system

The interactive mode of meso-tetrakis- (4- N-trimethylaminobenzyl) porphyrin (TAPP) with DNA has been investigated by the cyclodextrin (CD)-porphyrin supramolecular system. The binding of TAPP with DNA is inhibited by the anion CD derivative, sulfurbutyl-beta-cyclodextrin (SB-beta-CD); however, the neutral CD cannot influence the binding. As for the inclusion procedure of the CDs-TAPP system, the (1)H-NMR data suggests that the hydrophobic segment of TAPP enters into the cavity of CD, which means that the hydrophobic part of TAPP is not the binding site in the TAPP-DNA interaction. Therefore, the binding model cannot be the intercalation and is not related to the grooves of DNA. In addition, experimental data show that the charge attraction, which exists in the inclusion procedure of SB-beta-CD and TAPP hampers the binding of TAPP with DNA. The negative groups of SB-beta-CD compete with the phosphate groups of the DNA backbone, and have an attraction to the positive groups of TAPP. This competitive attraction supports the theory that the binding mode of TAPP with DNA is "electrostatic binding". Furthermore, there are two binding sites between one TAPP molecule and one DNA standard. We produce a possible binding structure (a suprahelical structure of DNA) for this TAPP-DNA complex. This structure is in good agreement with the literature.