Nonequilibrium Thermodynamics of DNA Nanopore Unzipping

Hotter Is Not Faster for a Melting RNA Hairpin

We investigate the denaturation dynamics of nucleic acids through extensive molecular dynamics simulations of a coarse-grained RNA hairpin model. In apparent contradiction to Arrhenius' law, our findings reveal that the denaturation time of RNA hairpins is a nonmonotonous function of temperature for molecules longer than few persistence lengths, with an optimal temperature above the melting point, T_{m}, at which denaturation occurs fastest. This anomaly arises from the existence of two distinct pathways: "unidirectional" unzipping, progressing from one end to the other and favored near T_{m}, and "bidirectional" denaturation, where competing unzipping events initiate from both ends at higher temperatures. The two regimes manifest distinct scaling laws for the melting time vs length, L, and are separated by a crossover temperature T_{×}, with (T_{×}-T_{m})∼L^{-1}. The results highlight the significant role of the helical structure in the out-of-equilibrium dynamics of RNA and DNA denaturation and unveil multiple surprises in a decades-old problem.

RNA Translocation through Protein Nanopores: Interlude of the Molten RNA Globule

Direct translocation of RNA with secondary structures using single-molecule electrophoresis through protein nanopores shows significant fluctuations in the measured ionic current, in contrast to unstructured single-stranded RNA or DNA. We developed a multiscale model combining the oxRNA model for RNA with the 3-dimensional Poisson-Nernst-Planck formalism for electric fields within protein pores, aiming to map RNA conformations to ionic currents as RNA translocates through three protein nanopores: α-hemolysin, CsgG, and MspA. Our findings reveal three distinct stages of translocation (pseudoknot, melting, and molten globule) based on contact maps and current values. Two translocation modes emerge: fast and slow. In the fast mode, the speed is determined by the electric field, independent of pore geometry. In the slow mode, the molten globule stage is the rate-determining factor in slowing the translocation, instead of the previous paradigm of melting of the base pairs. Using these insights, we propose a neural network framework to identify and reconstruct RNA secondary structures from ionic current windows. We find that the electric field distribution, not the nanopore geometry, drives the molten globule stage. Our results explain the large current fluctuations. These results provide a fundamental understanding of the role of secondary and tertiary structures in the translocation of RNA in direct RNA translocation platforms based on single-molecule electrophoresis. This work offers design rules for new protein pores and real-time imaging of the secondary structures of RNA.

Coarse-grained modeling of DNA-RNA hybrids

We introduce oxNA, a new model for the simulation of DNA-RNA hybrids that is based on two previously developed coarse-grained models-oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes, including their structure, persistence length, and force-extension characteristics. By parameterizing the DNA-RNA hydrogen bonding interaction, we fit the model's thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model's applicability, we provide three examples of its use-calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop, and simulating RNA-scaffolded wireframe origami.