Passing Behavior of Oligonucleotides through a Stacked DNA Nanochannel with Featured Path Design

DNA nanotechnology has emerged as a useful tool for constructing artificial channels penetrating the lipid bilayer. In this work, we introduce a stacked DNA origami nanochannel device characterized by a width-variable pathway, consisting of narrow entrance and exit channels coupled with a wide, modifiable lumen. This design modulates the translocation behavior of oligonucleotides, revealing distinct stages of signal patterns in the recorded current traces. The observed prolonged dwell times indicate oligonucleotide retention, specifically due to the transition from the wide lumen to the narrower exit channel, while variations in current recovery between events suggested intermediate channel states between conducting and blocking. Further, by incorporating sequence-specific overhangs within the channel lumen, we achieved unique asymmetric current profiles during ATP aptamer translocation events. Featured stages also highlighted the aptamer binding dynamics and ATP-induced release. The distinguished oligonucleotide passing behaviors afforded by the stacked DNA origami channel with interior decoration demonstrated the strategic and profitable attempts at DNA nanochannel engineering for nanodevice development and applications.