An interstrand-wedged duplex composed of alternating DNAbase pairs and covalently attached intercalators

Abstract

An interstrand-wedged duplex involving alternating base pairs and covalently attached intercalators viaD-threoninols was constructed. In this novel duplex structure, natural DNA base pairs and artificially introduced planar molecules such as azobenzene derivatives are lined up one by one. Although each base pair is sandwiched by two intercalators and vice versa, the duplex is extremely stable compared with the corresponding native DNA duplex. Analysis by ¹H-NMR showed that all of the expected internal base pairs are strongly formed even when the base pairs are sandwiched between azobenzene moieties. More interestingly, the stability of this new duplex structure decreased greatly when a mismatched base pair was introduced, indicating that this interstrand-wedged duplex has a high sequence specificity. Furthermore, the structure became very unstable when azobenzene moieties were photoisomerized to the cis form. It is expected that this new duplex motif will be very useful for the construction of a variety of functional nanostructures and nanodevices. The concept proposed here is a novel combination of the specificity of DNA hybridization and the versatility of synthesized organic molecules.