A DNA origami platform for single-pair Förster Resonance Energy Transfer investigation of DNA-DNA interactions and ligation.

DNA double-strand breaks (DSBs) pose an everyday threat to the conservation of genetic information and therefore life itself. Several pathways have evolved to repair these cytotoxic lesions by re-joining broken ends, among them the non-homologous end-joining (NHEJ) mechanism that utilizes a DNA ligase. Here, we use a custom-designed DNA origami nanostructure as a model system to specifically mimic a DNA DSB, enabling us to study the end-joining of two fluorescently-labeled DNA double-strands with the T4 DNA ligase on the single-molecule level. The ligation reaction is monitored by Förster Resonance Energy Transfer (FRET) experiments both in solution and on surface-anchored origamis. Due to the modularity of DNA nanotechnology, DNA double-strands with different complementary overhang lengths can be studied using the same DNA origami design. We show that the T4 DNA ligase repairs sticky ends more efficiently than blunt ends and that the ligation efficiency is both influenced by DNA sequence and the incubation conditions. Before ligation, dynamic fluctuations of the FRET signal are observed due to transient binding of the sticky overhangs. After ligation, the FRET signal becomes static. Thus, we can directly monitor the ligation reaction through the transition from dynamic to static FRET signals. Finally, we revert the ligation process using a restriction enzyme digestion and re-ligate the resulting blunt ends. The here presented DNA origami platform is thus suited to study complex multi-step reactions occurring over several cycles of enzymatic treatment.