Formation of Polymeric Assembly by Anti-directed Oligo-DNA Dimers

Abstract

We synthesized two types of “anti-directed” oligo-DNA dimer conjugates consisting of a photo-functional core group, in this case naphthalene as a model, and two strands of sequential oligo-DNAs (pentamer, GCTGC or GCAGC) linked at the 1,5-positions of naphthalene and at the 5′ ends of the oligo-DNAs through a phosphorodiester bond, forming Np(GCTGC)2 and Np(GCAGC)2. These conjugates are designed to be complementary to each other and are capable of forming a one-dimensional polymeric supramolecular assembly in aqueous solution. Duplex formation of the oligo-DNA strands in a solution of an equimolar mixture of the conjugates was confirmed by measurement of the hypochromicity, ethidium bromide (EB) intercalation tests, and circular dichroism (CD) spectra. From the CD spectra measurements of the solution, it was suggested that the oligo-DNA strands formed a B-type duplex-like conformation in aqueous solution. The equimolar mixture of the conjugates showed a temperature-dependent CD spectra change corresponding to the melting temperature of the B-type duplex. The formation of the polymeric assembly from the equimolar mixture of the conjugates was suggested by size-exclusion chromatography. The obtained results are useful for the construction of nanometre-scale structures using DNAs as building blocks.