Supramolecular Interactions Modulate RNA:DNA Folding Observed via Nanopore Sensing

DNA and RNA nanotechnology enables the precise assembly of molecular architectures, with applications in bioengineering, supramolecular chemistry, and sensing. The material properties of these biopolymers can be adjusted covalently or, more simply, through non-covalent interactions with small molecules. Herein, we demonstrate the use of urea, an abundant and inexpensive small molecule, to modulate the stiffness of RNA:DNA hybrid nanostructures. Our results suggest that supramolecular interactions between urea and the A-form-like helix rigidify the hybrid polymers, as evidenced by both solid-state nanopore measurements and atomic force microscopy. Nanopore sensing reveals that preparing topologically-barcoded RNA:DNA hybrids in urea results in a 50% reduction in folded translocations. This decrease in folded events improves the proportion of useable data points, paving the way for the robust detection of low-abundance RNA analytes at the single-molecule level.