Electron-Hole Transfer in G-Quadruplexes with Different Tetrad Stacking Geometries: A Combined QM and MD Study

Abstract

G-quadruplex nucleic acids represent a unique avenue for the building of electrically conductive wires. These four-stranded structures are formed through the stacking of multiple planar guanine assemblies termed G-tetrads. The diverse folding patterns of G-quadruplexes allow for several geometries to be adopted by stacked guanine bases within the core and at the dimeric interface of these structures. It is currently not clear how different G-tetrad stacking arrangements affect electron hole mobility through a G-quadruplex wire. Using a combined quantum mechanics and molecular dynamics approach, we demonstrate that the electron-hole transfer rates within the G-tetrad stacks vary greatly for different stacking geometries. We identify a distinguished structure that allows for strong electronic coupling and thus enhanced molecular electric conductance. We also demonstrate the importance of sampling a large number of geometries when considering the bulk properties of such systems. Hole hopping within single G-tetrads is slower by at least two orders of magnitude than between stacked guanines; therefore, hole jumping within individual tetrads should not affect the hole mobility in G-quadruplexes. The results of this study suggest engineering G-tetrads with continuous 5/6-ring stacking from an assembly of single guanosine analogs or through modification of the backbone in G-rich DNA sequences.