DNA Binding of the Nonintercalative Ligands SN-6132, SN-6131 and SN-6113: Minor Variations of the Ligand Structure May Cause Changes in the Base Pair Preference

Abstract The DNA binding selectivity of three ligands of a series of antitunor agents of bisquaternary ammonium heterocycles has been investigated by means of CD spectroscopy and melting measurements. From the spectroscopic results and binding data it is concluded that the agents SN-6132, SN-6131 and SN-6113 have relatively high affinity to AT base pair sequences whereas the binding to GC pairs is very low. The binding selectivity to AT base pair sequences decreases in the order netropsin >SN-6132>SN-6113>SN-6131. Poly(dA) · poly(dT) has the highest binding preference for SN-6132 relative to that of SN-6131. The different binding behavior of the ligands is related to their distinct changes in the chemical structure and to the DNA minor groove properties which determines the adaptability of the ligands in the groove.