Porphyrin binding to quadrupled T4G4

We have recently reported the cation-induced self-assembly of DNA oligomers of the general sequence C4T4G4T1-4G4 into high-molecular weight multistranded structures [Marotta, S.P., Tamburri, P.A., and Sheardy, R.D. (1996) Biochemistry 35, 10484-10492]. The architecture of the proposed structure consists of a series of four leafed G4 tetrads tethered together via one or two T1-4 strands and thus resembles a long four-sided hollow tube with periodic "pockets". These pockets possess electrostatic, hydrogen bonding, and hydrophobic contact points and should be ideal candidates for the binding of small molecules. To assess the potential of using porphyrins as probes for these structures, we have investigated the interaction of tetrakis(4-N-methylpyridyl)porphine (H2TMPyP) with the simple quadruplex formed by T4G4 and with the duplex formed by CGCGATATCGCG. Visible absorption, circular dichroism, and fluorescent energy transfer studies indicate that H2TMPyP binds to both the duplex and quadruplex via intercalation at low [porphyrin]/[DNA molecule] ratios, i.e., in the presence of excess potential DNA binding sites. Analyses of Scatchard plots show that H2TMpyP binds with high affinity to both DNA secondary structures but binds to the quadruplex with an affinity 2 times greater than that of the duplex.