Structural and Dynamic Characterization of the Heterodimeric and Homodimeric Complexes of Distamycin and l-Methylimidazole-2-carboxamide—Netropsin Bound to the Minor Groove of DNA

NMR spectroscopy combined with molecular modeling was used to characterize a heterodimeric complex with Dst and 2-ImN bound in the minor groove of d(GCCTAACAAGG)·d(CCTTGTTAGGC) (1:1:1 2-ImN·Dst·DNA complex). The imidazole-pyrrole-pyrrole ligand 2-ImN spans 5′-GTTA-3′ of the TAACA·TGTTA binding site with the imidazole nitrogen specifically recognizing the guanine amino group. The Dst ligand lies along the 5·-AACA-3· sequence and complements the 2-ImN ligand in the formation of the antiparallel side-by-side heterodimeric complex. Titrations of the same site with Dst or 2-ImN alone yield homodimeric complexes (2:1 ligand·DNA) of lower stability than the 1:1:1 2-ImN·Dst·DNA complex. Dst and 2-ImN binding to d(CGCAAACTGGC)·d(GCCAGTTTGCG) was also investigated. The 1:1:1 2-ImN·Dst·DNA complex is again the most stable complex with the AAACT·AGTTT site and is similar to the TAACA·TGTTA complex. No monomeric binding of either 2-ImN or Dst was observed to either site.