Perylenediimide-Linked DNA Dumbbells: Long-Distance Electronic Interactions and Hydrophobic Assistance of Base-Pair Melting

The synthesis and properties of synthetic DNA dumbbells having A-tract base pair domains consisting of 6−16 base pairs connected by perylenediimide (PDI) linkers are reported. The dumbbells were prepared in good yield by chemical ligation of nicked-dumbbell precursors having six or more A-T base pairs. The dumbbell structures have been investigated by a combination of electronic spectroscopy and molecular dynamics simulations. UV−visible spectra are indicative of the formation of monomeric dumbbells at room temperature in aqueous buffer in the absence of added salt. The long-wavelength region of the circular dichroism (CD) spectra is a composite of induced CD of the PDI monomers and intramolecular exciton-coupled CD between the two PDI chromophores. Weak exciton coupled CD can be observed between PDI chromophores separated by 13 base pairs, thus extending the reach of dumbbell molecular rulers. Upon heating, the dumbbells undergo base pair melting and intramolecular PDI−PDI association. Analysis of the temperature-dependent spectral data provides evidence for a three-state model in which base pair melting of the intact dumbbell results in the formation of an intermediate species which is in equilibrium with a collapsed dumbbell having intramolecular PDI−PDI stacking. The low melting temperatures of the shorter dumbbells are attributed to the partial compensation of PDI−PDI association for base pair dissociation.