Conformation driven conductance modulation in single-stranded RNA (ssRNA)

Abstract

The structural attributes of RNA, especially co-transcriptional folding, have enabled RNA origami to construct complex 3D architectures, serving as a platform to build RNA-based nanodevices. However, the potential of RNA in molecular electronics is largely unexplored, mainly due to its inherent conformational fluctuations. Although this variability poses challenges for a precise understanding of the conductance properties of RNA, it also offers opportunities for tuning RNA-based molecular devices by exploiting their dynamic nature. Accordingly, our objectives in this paper are twofold: (i) how do conformational fluctuations impact the charge transport properties of single stranded RNA (ssRNA), and (ii) how can these fluctuations be controlled? Toward that end, we first established a benchmark for ssRNA instability compared to double stranded RNA (dsRNA) based on molecular dynamics. Subsequently, we explore quantum transport across 123 distinct conformations, which show that the average conductance of ssRNA is 1.7 × 10⁻³ G₀, but with a high standard deviation of around 5.2 × 10⁻³ G₀. We demonstrate that the conductance of ssRNA is influenced primarily by backbone bending and nucleotide positioning. Specifically, while backbone bending tends to result in higher conductance at reduced end-to-end phosphorus distances, nucleotide positioning introduces significant stochasticity. To mitigate this variability, we also demonstrate that increasing the salt concentration can stabilize ssRNA, presenting a viable strategy for minimizing conductance fluctuations. Our findings reveal that if ssRNA conductance can be switched between folded and unfolded states, it can offer two distinct conductance modes. We anticipate the programmability of ssRNA folding and durability, coupled with its conductivity, can be leveraged for advancing molecular electronics.