Chains, dimers, and sandwiches: melting behavior of DNA nanoassemblies.

We have studied, in experiment and theory, the melting behavior of DNA nanoassemblies of perylenediimide-bis-oligonucleotides (PON), in which two short oligonucleotide chains (16- or 24-mers) are attached to the extremities of a spacer molecule. By varying both the sequence orientation (exchange of 3' and 5' ends neighboring the spacer) and the oligomer composition of the solutions, nanoassemblies of different complexity can be generated. Our results show a subtle dependence of the melting behavior on the supramolecular arrangement of the DNA-based assemblies.