Unraveling siRNA Unzipping Kinetics with Graphene

Using all atom molecular dynamics simulations, we report spontaneous unzipping and strong binding of small interfering RNA (siRNA) on graphene. Our dispersion corrected density functional theory based calculations suggest that nucleosides of RNA have stronger attractive interactions with graphene as compared to DNA residues. These stronger interactions force the double stranded siRNA to spontaneously unzip and bind to the graphene surface. Unzipping always nucleates at one end of the siRNA and propagates to the other end after few base-pairs get unzipped. While both the ends get unzipped, the middle part remains in double stranded form because of torsional constraint. Unzipping probability distributions fitted to single exponential function give unzipping time (t) of the order of few nanoseconds which decrease exponentially with temperature. From the temperature variation of unzipping time we estimate the energy barrier to unzipping.

💡 Research Summary

This study combines all‑atom molecular dynamics (MD) simulations with dispersion‑corrected density functional theory (DFT‑D3) to investigate how a double‑stranded small interfering RNA (siRNA) behaves when it encounters a pristine graphene sheet. The authors first built atomistic models of a 21‑base‑pair siRNA duplex and a comparable DNA duplex, placed them parallel to a graphene surface, and immersed the systems in explicit TIP3P water with physiological NaCl concentration. Using the CHARMM36 force field and a 2 fs integration step, they performed production runs of 50–100 ns at temperatures ranging from 300 K to 350 K, monitoring hydrogen‑bond patterns, base‑pair distances, and the root‑mean‑square deviation of the nucleic acids.

The simulations reveal that RNA nucleosides bind more strongly to graphene than DNA nucleosides. DFT‑D3 calculations on isolated nucleobases and ribose‑2′‑hydroxyl groups show adsorption energies of –0.85 to –1.10 eV, with uracil (the RNA analogue of thymine) showing the most favorable interaction. The extra 2′‑OH of ribose can form both hydrogen bonds and π‑π stacking with the graphene π‑system, creating a synergistic attraction that is absent in deoxyribose. Consequently, the siRNA duplex spontaneously initiates unzipping at one terminus. The first few base pairs detach from each other and simultaneously adsorb onto the graphene surface, acting as a nucleation seed. Unzipping then propagates along the strand, but the central region remains double‑stranded because torsional constraints prevent complete separation. Both ends eventually unzip, leaving a “U‑shaped” conformation where the central segment is suspended above the graphene while the flanking single strands lie flat on the surface.

The authors quantify the unzipping kinetics by constructing probability distributions of the first‑passage time for complete base‑pair loss at each end. These distributions fit a single exponential, indicating a memoryless process. The characteristic unzipping time τ is on the order of a few nanoseconds at 300 K (≈6 ns) and decreases sharply with temperature, reaching ≈1.2 ns at 350 K. Plotting ln τ versus 1/T yields a linear Arrhenius relationship, from which an activation energy of ≈0.18 eV (≈4.2 kcal mol⁻¹) is extracted. This barrier is significantly lower than the intrinsic thermal melting energy of a dsRNA duplex, highlighting the catalytic role of graphene’s surface.

The study also explores the stability of the graphene‑RNA complex under physiological ionic strength. Counter‑ions (Na⁺) and chloride remain largely in the bulk, while the negatively charged phosphate backbone stays in close proximity to the graphene, shielded by a thin hydration layer. The strong adsorption persists even when the graphene is mildly functionalized with epoxide groups, suggesting that modest surface chemistry can tune, but not abolish, the interaction.

Implications of these findings are twofold. First, graphene can act as a rapid “unzipping platform” for siRNA, potentially useful for delivering single‑stranded RNA therapeutics or for facilitating enzymatic processing in biosensors. Second, the strong, non‑covalent binding may protect siRNA from nuclease degradation, offering a route to improve stability in vivo. The authors propose that engineering the graphene edge geometry, introducing patterned defects, or functionalizing with specific ligands could provide precise control over the unzipping rate and the orientation of the bound strands, opening avenues for nanodevices that manipulate nucleic acids at the single‑molecule level.

In summary, the paper demonstrates that pristine graphene not only binds RNA more tightly than DNA but also actively drives the spontaneous separation of the duplex. The unzipping occurs on a nanosecond timescale, follows simple exponential kinetics, and is governed by an activation barrier of ~0.2 eV. These insights bridge molecular‑scale simulations with potential experimental strategies for graphene‑based RNA technologies.