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

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

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

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

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

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

Charge Transport across DNA-Based Three-Way Junctions

DNA-based molecular electronics will require charges to be transported from one site within a 2D or 3D architecture to another. While this has been shown previously in linear, π-stacked DNA sequences, the dynamics and efficiency of charge transport across DNA three-way junction (3WJ) have yet to be determined. Here, we present an investigation of hole transport and trapping across a DNA-based three-way junction systems by a combination of femtosecond transient absorption spectroscopy and molecular dynamics simulations. Hole transport across the junction is proposed to be gated by conformational fluctuations in the ground state which bring the transiently populated hole carrier nucleobases into better aligned geometries on the nanosecond time scale, thus modulating the π–π electronic coupling along the base pair sequence