Topology-dependent hole transfer in G-quadruplex by molecular dynamics and density functional theory

Molecular electronics is one of the explored possibilities to fabricate computational devices beyond the limits of Moore's law. DNA-based molecular wires are particularly appealing in this context because of DNA’s nanoscale self-organization and high yield synthesis. G-quadruplex, a helical form of nucleic acids, is a fascinating alternative to duplex DNA with higher stiffness and electronic coupling. For the development of molecular wires, it is important to optimize electron transport along the wire axis. One powerful basis to do so is by manipulating the structure, based on known effects that electron transport strongly depends on the structural changes. Here, we investigate such effects, by a combination of classical simulations of the structure and dynamics and quantum calculations of electronic couplings. We find that this structure-function relationship is complex. A single helix shape parameter alone does not embody such complexity. Nay, it is a linear combination of different inter-base helix shape parameters that influences the charge transfer. The coefficients of this linear combination can be tuned to optimize charge transport. We provide an optimized combination of the shape parameters to maximize the structure-function correlation in G-quadruplex.