Coupled dynamics of RNA folding and nanopore translocation

Abstract

The translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base pairs. Here, we study the interplay between the dynamics of translocation and base-pairing theoretically, using kinetic Monte Carlo simulations and analytical methods. We find that the transient formation of basepairs that do not occur in the ground state can significantly speed up translocation.

arXiv comment4 pages, 3 figures, to appear in Physical Review Letters

References in corpus (7)

• Polymer Translocation througha Pore in a Membrane
• Driven Polymer Translocation Through a Narrow Pore
• Unzipping Kinetics of Double-Stranded DNA in a Nanopore
• Anomalous Dynamics of Translocation
• Polymer Translocation Through a Long Nanopore
• Translocation of structured polynucleotides through nanopores
• Probing complex RNA structures by mechanical force

Cited by in corpus (13)

• Biased diffusion in confined media: Test of the Fick-Jacobs approximation and validity criteria
• Effective charge and free energy of DNA inside an ion channel
• Role of loop entropy in the force induced melting of DNA hairpin
• Theory for RNA folding, stretching, and melting including loops and salt
• Effect of Inhomogeneity in Translocation of Polymers through Nanopores
• Impact of loop statistics on the thermodynamics of RNA folding
• Topology Sorting and Characterization of Folded Polymers Using Nano-pores
• Electric-field-driven polymer entry into asymmetric nanoscale channels
• Translocation of polymers with folded configurations across nanopores
• Free Energy Barrier for Electric Field Driven Polymer Entry into Nanoscale Channels
• DNA-Graphene Interactions During Translocation Through Nanogaps
• Anomalous scaling in nanopore translocation of structured heteropolymers
• Amplitude and Frequency Spectrum of Thermal Fluctuations of A Translocating RNA Molecule