Polymer translocation, the process of pulling single filamentous molecules through narrow pores, has long been studied as an example of out-of-equilibrium statistical mechanics and for its relevance in DNA sequencing and biological processes. However, the case in which the polymer structure itself is deeply altered by translocation remains largely unexplored. Here, we address this phenomenon in two contexts involving nucleic acid filaments. First, we discuss DNA unzipping, where one of the two strands is pulled through a nanopore, while the other remains outside [1,2]. Next, we will extend considerations to xrRNAs, short and highly pseudoknotted RNAs that can withstand degradation by exonucleases. We use native-centric atomistic models and translocation simulations to elucidate the mechanistic basis of xrRNA resistance to degradation, demonstrating its dependence on the entangled architecture of xrRNA [3,4]. Finally, we will discuss recent results on the pore translocation of long DNAs, where experiments and simulations indicate that the torque imparted by the solvent flow induces the formation of plectonemes [5].
References
[1] A. Suma, V. Carnevale and C. Micheletti, "Nonequilibrium thermodynamics of DNA nanopore unzipping", Phys. Rev. Lett., (2023), 130 048101
[2] A. Suma and C. Micheletti, "Unzipping of knotted DNA via nanopore translocation", QRB Discovery 6 (2025) e4
[3] M. Becchi, P. Chiarantoni and C. Micheletti, RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration, J. Phys. Chem. B, 125, 1098-1196 (2021)
[4] M. Becchi, P. Chiarantoni and C. Micheletti "RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration", J. Phys. Chem. B, 125, 1098-1196 (2021)
[5] F. Zheng, A. Suma, C. Maffeo, K. Chen, M. Alawami, J. Sha, A. Aksimentiev, C. Micheletti, and U.F. Keyser, "Torsion-driven plectoneme formation during nanopore translocation of DNA polymers", Phys. Rev. X art. no. 023116(2025)