Folding Dynamics of Linear ssDNA–dsDNA Heterostructures through Solid-State Nanopores

Understanding the intricate details of the molecular mechanisms behind nanopore translocation is crucial to further the development of nanopores as single-molecule sensors. In this study, we assemble hybrid ss–dsDNA constructs with different effective persistence lengths to investigate their capture and folding behavior in solid-state nanopores. In general, we observe differences in event shapes for different flexible polymers with more flexible polymers leading to deeper, longer, and more complex events. We show that folding happens favorably in ssDNA segments along the heterogeneous polymer contour and can happen multiple times during the same event, blocking more current and generating more convoluted event shapes. By designing DNA heterostructures with various ss–dsDNA distributions, we further show that the propensity for folds at the ssDNA segments arises due to their higher flexibility allowing them to diffuse around the vicinity of a nanopore during the translocation process, as opposed to stiffer and nonrelaxed dsDNA segments through which the tension propagates during passage. These findings highlight the different translocation regimes of polymers of various rigidity, improving our understanding of the folding of polymers into nanopores which will ultimately be useful for the development of applications requiring single-file translocations, for example, for the decoding of barcoded nanostructured molecules for multiplexed biomarker detection or for molecular information storage schemes.