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.

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.

The nanoassembly behavior of trivalent small molecule-DNA hybrids (SMDH3s) were investigated as a function of core geometry and supramolecular flexibility through a synergistic experimental-modeling study. While complementary SMDH3s possessing a highly flexible tetrahedral trivalent core primarily assemble into nanoscale caged dimers, the nanoassemblies of SMDH3 comonomers with rigid pyramidal and trigonal cores yields fewer caged dimers and more large-oligomer networks. Specifically, the rigid pyramidal SMDH3 comonomers tend to form smaller nanosized aggregates (dimer, tetramer, and hexamer) upon assembly, attributable to the small (<109 °) branch-core-branch angle of the pyramidal core. In contrast, the more-rigid trigonal planar SMDH3 comonomers have a larger (~120 °) branch-core-branch angle, which spaces their DNA arms farther apart, facilitating the formation of larger nanoassemblies (≥ nonamer). The population distributions of these nanoassemblies were successfully captured by coarse-grained molecular dynamics (CGMD) simulations over a broad range of DNA concentrations. CGMD simulations can also forecast the effect of incorporating Tn spacer units between the hydridizing DNA arms and the rigid organic cores to increase the overall flexibility of the SMDH3 comonomers. Such “decoupling” of the DNA arms from the organic core was found to result in preferential formation of nanoscale dimers up to an optimal spacer length, beyond which network formation takes over due to entropic factors. The excellent agreement between simulation and experimental results confirm the versatility of the CGMD model as a useful and reliable tool for elucidating the nanoassembly of SMDH-based building blocks.