Mg2+effects on the single-stranded DNA conformations and nanopore translocation dynamics

Mg2+ ion has shown novel merits in the control of the translocation of single-stranded DNAs (ssDNAs) though nanopores. To advance the understanding of the Mg2+ ion effects on the translocation, it is critical to study the conformational change of ssDNAs under the influence of the Mg2+ ions and how it affects the translocation dynamics. To this end, a combination of computational simulation and theoretical analysis is used to systematically and thoroughly study the Mg2+ ion concentration-dependent conformations and translocation dynamics of the ssDNAs with different lengths. The simulation model with originally developed energetic field is validated against previous experiments. Our simulation results reveal that the radius of gyration R-g and translocation time tau have the similar behaviors with the changes of ion concentration [Mg2+] and ssDNA length N. The newly reported half-empirical functions are used to predict the ion concentration and ssDNA length-dependent R-g and tau, which support the observations in simulations. Both simulation results and quantitative analyses show that for a ssDNA with fixed length N, tau is proportional to R-g at different ion concentrations. Moreover, the Flory exponent nu in the scaling law R-g -N nu varies from 0.51 at infinitely high ion concentration to 0.73 in the absence of ions, leading to the change of the scaling exponent alpha in the scaling law tau -N-alpha from 1.38 to 1.48 accordingly. On the contrary, the scaling exponent beta (=-0.94) in the scaling relationship tau -f(beta) with f as the driving force is independent of the ion concentrations.

Automated summary

The influence of Mg2+ ion concentration and ssDNA length on the conformation and transcription dynamics is studied, revealing similar behaviors of radius of gyration and translocation time with changes in ion concentration and length. Half-empirical functions are used to predict the effects, and changes in conformation and scaling exponent are observed under different ion concentrations.