Hydrophobic self-assembly of a perylenediimide-linked DNA dumbbell into supramolecular polymers.

The self-assembly of DNA dumbbell conjugates possessing hydrophobic perylenediimide (PDI) linkers separated by an eight-base pair A-tract has been investigated. Cryo-TEM images obtained from dilute solutions of the dumbbell in aqueous buffer containing 100 mM NaCl show the presence of structures corresponding to linear end-to-end assemblies of 10−30 dumbbell monomers. The formation of assemblies of this size is consistent with analysis of the UV−vis and fluorescence spectra of these solutions for the content of PDI monomer and dimer chromophores. Assembly size is dependent upon the concentration of dumbbell and salt as well as the temperature. Kinetic analysis of the assembly process by means of salt-jump stopped-flow measurements shows that it occurs by a salt-triggered isodesmic mechanism in which the rate constants for association and dissociation in 100 mM NaCl are 3.2 × 107 M−1s−1 and 1.0 s−1, respectively, faster than the typical rate constants for DNA hybridization. TEM and AFM images of samples de...