Enhancing DNA-Mediated Assemblies of Supramolecular Cage Dimers through Tuning Core Flexibility and DNA LengthA Combined Experimental–Modeling Study

Abstract

Two complementary small-molecule–DNA hybrid (SMDH) building blocks have been combined to form well-defined supramolecular cage dimers at DNA concentrations as high as 102 μM. This was made possible by combining a flexible small-molecule core and three DNA arms of moderate lengths (<20 base pairs). These results were successfully modeled by coarse-grained molecular dynamics simulations, which also revealed that the formation of ill-defined networks in the case of longer DNA arms can be significantly biased by the presence of deep kinetic traps. Notably, melting point studies revealed that cooperative melting behavior can be used as a means to distinguish the relative propensities for dimer versus network formation from complementary flexible three-DNA-arm SMDH (fSMDH₃) components: sharp, enhanced melting transitions were observed for assemblies that result mostly in cage dimers, while no cooperative melting behavior was observed for assemblies that form ill-defined networks