Thermal response of DNA supramolecular polymers assembled with hydrophobic sticky ends

We report the self-assembly and thermal dissociation of DNA dumbbell conjugates having a perylenediimide (PDI) linker on each end separated by 6-16 A-T base pairs. In the presence of NaCl these dumbbells form one-dimensional supramolecular assemblies as a consequence of the hydrophobic association of their PDI sticky ends. The dependence of assembly formation on dumbbell concentration, salt concentration, and temperature can be conveniently monitored by UV-vis spectroscopy. The melting of these linear assemblies follows two limiting mechanisms, depending on the length of the dumbbells. Upon heating in the presence of salt, the assemblies formed by the longer dumbbells undergo a sequential transition from assembly to base-paired monomer to random coiled monomer, whereas the assemblies formed by the shorter dumbbells undergo disassembly and base-pair melting cooperatively. In all cases, the intramolecular hydrophobic association of the PDI chromophores is observed at elevated temperature. The thermal behavior of these one-dimensional assemblies is compared to that of other sticky-ended assemblies.