Nucleic acid nanoparticles (NANPs), composed of short oligonucleotides assembled into specific architectures, are emerging as a programmable platform for the regulated drug delivery of various therapeutic agents. Here, we use a nanopore "clamp" to investigate the mechanical properties of six-stranded RNA and DNA-based NANPs with the connectivity of a cube of sizes below 10 nm. When electrophoretically forced through solid-state nanopores that are smaller than the cubes, deformation of the NANPs generates prolonged electrical signatures whose durations depend on the mechanical deformability of the structures. All-atom MD simulations further reveal differences in the mechanical flexibility of DNA, RNA, modified RNA, and hybrid DNA/RNA cubes, supporting these findings at the molecular level. While DNA cubes deform and translocate through the pore, analogous RNA cubes are too stiff and cannot squeeze through at a comparable voltage, despite having the same sequence and overall shape as the DNA cubes. Further, we find that hybrid RNA/DNA cubes exhibit intermediate mechanical deformability to pure DNA or RNA cubes, indicating an additive effect of the RNA content on nanocube stiffness. Finally, different chemical modifications introduced to the strands can be used to fine-tune the mechanical properties of the NANPs.
Keywords: MD simulations; flexibility; nucleic acid nanoparticles; solid-state nanopore; translocation.