Resolving DNA Conformations and Dynamics at the Graphene Interface by Graphene Energy Transfer

Abstract

The recent discovery that double-stranded DNA stands vertically on graphene has transformed graphene from a passive quenching surface into an active platform for axial single-molecule readout, opening opportunities in biosensing, molecular materials, and nanoscale devices. Here, we use graphene energy transfer with vertical nucleic acids (GETvNA) to resolve how partially single- and double-stranded DNA constructs interact with graphene at the molecular level. Single-molecule fluorescence lifetime measurements show that dsDNA adopts both vertical and parallel orientations on graphene and reveal rare 1–3 base-pair zipping and unzipping events. We further show that the ssDNA anchor length regulates dsDNA conformation by controlling the availability of graphene binding sites for exposed nucleotides, thereby modulating partial unzipping. Finally, we demonstrate programmable axial motion using DNA hybridization and strand-displacement reactions, realizing a single-molecule DNA nanoelevator with nanometer precision. These results establish GETvNA as a platform for probing molecular interfaces and engineering DNA-based nanodevices on graphene.