Poly-intercalators Carrying Threading Intercalator Moieties as Novel DNA Targeting Ligands

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Abstract

Threading intercalators are a novel class of intercalators that carry two substituents along the diagonal positions of an aromatic ring. These substituents are projecting out in DNA grooves when bound to DNA. Poly-intercalators carrying threading intercalating parts are quite novel and were recently found to show a unique DNA binding behavior. We review herein two types of poly-intercalators. First, tris-intercalators carrying a threading intercalator part in the middle of the molecule are described. These intercalators appear to intercalate into double stranded DNA in a special binding manner, which we call the penetrating mode, in which all the three intercalating units are arranged linearly with one of them penetrating into the DNA ladder. We synthesized two tris-intercalators (3 and 4) of this type and studied their binding behavior for double stranded DNA. All the experimental results were consistent with the proposed penetrating mode. Another type of threading poly-intercalators is a macrocyclic bis-threading intercalator (5). We found that this compound can bis-intercalate to double stranded DNA when the base pairing is disrupted temporarily to form a complex with a unique structure like a catenane. On the basis of a study of the interaction of such intercalators we envisage that DNA is a flexible and dynamic entity. These novel families of poly-intercalators will expand the scope of DNA poly-intercalation chemistry with possible medicinal applications.

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