We have studied the influence of terminal substituents, amidinium group and N-methylpiperazine ring, of 2-phenylbenzimidazole compounds (1-6; Figure 1) on their DNA-binding modes. Experimental results reveal that 1-3 are accepted in intercalation pockets owing to structural flexibility of the N-methylpiperazine ring, while 4-6 bind to the groove of DNA because of steric hindrance between the amidinium group and the DNA phosphate-sugar backbone.
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