Shape-selective recognition of a model Okazaki fragment by geometrically-constrained bis-distamycins

Okazaki fragments represent interesting targets for the design of anticance r drugs because of their selective occurrence during DNA replication, a pro cess often elevated in aggressive malignancies. Structural studies have ind icated a bend occurs in the helical axis at the junction region (JR) that j oins 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 investig ated the binding of geometrically-constrained bis-distamycins to a model Ok azaki fragment, [OKA], with a sequence derived from the genome of simian vi rus 40 (SV40). Both the JR and the DDR of [OKA] contain consecutive A/T bas e pairs that could accommodate distamycin binding. Of the six bis-distamyci ns selected for analysis, the two with a para configuration of the distamyc ins on the benzene or pyridine scaffold bound [OKA] tightly (K-d similar to 10(-6) M from gel-shift assays; K-d similar to 10(-8) M from Delta T-M) wh ile 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 co mplementary to the minor groove of the model Okazaki fragment.