Shape-Selective Recognition of a Model Okazaki Fragment By Geometrically-Constrained Bis-Distamycins

Abstract

Okazaki fragments represent interesting targets for the design of anticancer drugs because of their selective occurrence during DNA replication, a process often elevated in aggressive malignancies. Structural studies have indicated a bend occurs in the helical axis at the junction region (JR) that joins the DNA duplex region (DDR) and the RNA-DNA hybrid duplex region (HDR) of model Okazaki fragments. To identify a structural motif that provides a shape complementary to the Okazaki fragment minor groove, we have investigated the binding of geometrically-constrained bis-distamycins to a model Okazaki fragment, [OKA], with a sequence derived from the genome of simian virus 40 (SV40). Both the JR and the DDR of [OKA] contain consecutive A/T base pairs that could accommodate distamycin binding. Of the six bis-distamycins selected for analysis, the two with a para configuration of the dis-tamycins on the benzene or pyridine scaffold bound [OKA] tightly (Kd ∼ 1O−8 M from ΔTM) while the four with a meta orientation did not bind. The two mono-distamycins studied also did not bind [OKA], Molecular modeling of the complex between the para bis-distamycin MT-9 and [OKA] revealed MT-9 adopted an S-shape complementary to the minor groove of the model Okazaki fragment.