Porphyrin Binding to Quadruplexed T4G4

Abstract

We have recently reported the cation-induced self-assembly of DNA oligomers of the general sequence C₄T₄G₄T_1-4G₄ into high-molecular weight multistranded structures [Marotta, S. P., Tamburri, P. A., and Sheardy, R. D. (1996) Biochemistry35, 10484−10492]. The architecture of the proposed structure consists of a series of four leafed G₄ tetrads tethered together via one or two T_1-4 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.