Solid-State MoS2 Nanopore Membranes for Discriminating among the Lengths of RNA Tails on a Double-Stranded DNA: A New Simulation-Based Differentiating Algorithm

A robust and reliable detection scheme of RNA tails grown on a double-stranded DNA (dsDNA) can pave the way to a denser encoding of DNA-based storage systems that use the punch card mechanism. Here, we develop a systematic algorithmic approach based on signal processing to detect the presence of RNA tails on dsDNA as well as to differentiate the tail lengths from the transverse conductance signal of MoS2 membrane nanopores. Combining all-atom molecular dynamics simulations with electronic transport modeling, we suggest a method to detect RNA tails with lengths of 10, 15, and 20 nucleotides separated by 10 base pairs. Modified dwell times obtained by using normalized DNA velocity provide an easy and intuitive way to distinguish the lengths of the RNA tails. We show that this technique can be extended for multiple tails, separation distances, and substrate DNA lengths.