DISTAMYCIN AND PENTA-N-METHYLPYRROLECARBOXAMIDE BINDING-SITES ON NATIVE DNA - A COMPARISON OF METHIDIUMPROPYL-EDTA-FE(II) FOOTPRINTING AND DNA AFFINITY CLEAVING

Using 2 direct methods the binding locations and site sizes of distamycin and penta-N-methylpyrrolecarboxamide were studied on 3 DNA restriction fragments from pBR322 plasmid. Methidiumpropyl-EDTA .cntdot. Fe(II) footprinting and DNA affinity cleaving methods report common binding locations and site sizes for the tri- and pentapeptides bound to heterogeneous DNA. The tripeptide distamycin binds 5-base-pair sites with a preference for poly(dA) .cntdot. poly(dT) regions. The pentapeptide binds 6-7-base-pair sites with a preference for poly(dA).cntdot.poly(dT) regions. These results are consistent with distamycin binding as an isogeometric helix to the minor groove of DNA with the 4 carboxamide N-H hydrogen bonding 5 A + T base pairs. The data supports a model where each of the carboxamide N-H can hydrogen bond to 2 bases, either O(2) of thymine or N(3) of adenine, located on adjacent base pairs on opposite strands of the helix. In most (but not all) cases the tri- and pentapeptide can adopt 2 orientations at each A + T rich binding site.