Tris-benzimidazole derivatives: Design, synthesis and DNA sequence recognition

Two tris-benzimidazole derivatives have been designed and synthesized based on the known structures of the bis-benzimidazole stain Hoechst 33258 compl exed to short oligonucleotide duplexes derived from single crystal X-ray st udies and from NMR. In both derivatives the phenol group has been replaced by a methoxy-phenyl substituent. Whereas one tris-benzimidazole carries a N -methyl-piperazine at the 6-position, the other one has this group replaced by a 2-amino-pyrrolidine ring. This latter substituent results in stronger DNA binding. The optimized synthesis of the drugs is described. The two tr is-benzimidazoles exhibit high AT-base pair (bp) selectivity evident in foo tprinting experiments which show that five to six base pairs are protected by the tris-benzimidazoles as compared to four to five protected by the bis -benzimidazoles. The tris-benzimidazoles bind well to sequences like 5-TAAA C, 5'-TTTAC and 5'-TTTAT, but it is also evident that they can bind weakly to sequences such as 5'-TATGTT-3' where the continuity of an AT stretch is interrupted by a single G-C base pair. (C) 2001 Elsevier Science Ltd. All r ights reserved.