Structure of d(ITITACAC) complexed with distamycin at 1.6 A resolution

Abstract

The crystal structure of the DNA octamer d(ITITACAC)(2) complexed with distamycin has been determined at 1.6 A resolution and refined to a final R(work) and R(free) of 17.0 and 20.7%, respectively. Two molecules of distamycin bind to the DNA duplex in an antiparallel side-by-side fashion. Each drug molecule covers five base pairs of the DNA duplex, with its amide groups hydrogen-bonding to bases in the proximal DNA strand. These two antiparallel drug molecules are stacked together with the pyrrole rings of one molecule stacking against the amide groups of the other. The present structure emphasizes the features of alternating DNA octamers in interaction with distamycin.