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

Mutual effects between single-stranded DNA conformation and Na+–Mg2+ion competition in mixed salt solutions

“…Therefore, our simulation results, while ignoring hydration effects, should still be reliable. 84 The model-matched CG potentials include volume-excluded interaction (U lj ), virtual bond interaction (U b ), bond-bond angle potential (U a ), dihedral potential (U d ), and bead P-bead P electrostatic interaction (U e ):…”

“…The simulation results using the potential parameters agree well with the experiment results. 84 The last term in eqn (1), U e , is the electrostatic interaction between the P beads and the ion atmosphere, in which the ions can be classified into excess ions that are attracted by ssDNA from outside and background ions that are already there. The ion atmosphere has a neutralizing/screening effect on the ssDNA charge, reducing the electrostatic repulsion.…”

“…Here R N g denotes the intrinsic radius of gyration for ssDNA without electrostatic interactions between the phosphate beads, i.e., at an infinitely high ion concentration, and R 0 g is the contribution of ion-involved electrostatic repulsion to R g . In pure NaCl or MgCl 2 solution, R g can be expressed as follows: 16,84…”

“…14 Details relating to eqn (18) and the parameters therein are described in Section S3 in the ESI, † and further details can be found in our previous simulation studies. 84 In unstructured ssDNA-mixed ion systems, due to complicated Na + -Mg 2+ competition, which depends not only on the ion concentrations but also the ssDNA conformation, the radius of gyration of ssDNA should also be related to the ion concentrations and ssDNA conformation, as follows:…”

“…To balance the computational efficiency and prediction accuracy, a coarse-grained ssDNA model, MCC theory and the Monte Carlo TBI (MCTBI) model are integrated in this paper to study the conformational properties of unstructured ssDNA in mixed Na + /Mg 2+ ion solutions. Specifically, the ssDNA is described using a pseudo-atom CG (PACG) model, 84 which uses three pseudo-atoms (beads of P, S, and B) to represent the three atomic groups (phosphate, sugar, and base) of a nucleotide. The model-matched CG potentials are obtained via a ''topdown'' approach.…”