Sequence-Dependence of DX DNA Electronic Properties and Thermal Fluctuations

The Watson-Crick base-pairing of DNA has been exploited through sticky-end cohesion and branched junctions to create complex self-assemblying nanostructures. The double-crossover (DX) junction is a common motif in these structures. Interest in nanoelectronics has led to previous experimental studies of the DX structure as a nanoscale current splitter. Here, we build atomic-level models of both the original sequence and redesigned improved sequences. We produce 10 ns of molecular dynamics simulation snapshots for each sequence, which indicate a universally stable central core and fluctuating forks. We then use CNDO, a semi-empirical quantum mechanics method assuming zero differential overlap, to compute electronic structures for various segments of each system. Using the basic equation of Marcus theory, we find that our redesigned "Duke" sequence achieves a maximum cross-helical hopping rate fifty times greater than the original sequence. Our results form a foundation for atomic-level models of larger DNA nanostructures, and indicate that a careful consideration of three-dimensional geometry is crucial to sequence design in DNA nanotechnology.