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

Abstract

The ion-dependence of the single-stranded DNA (ssDNA) conformational changes has attracted growing attentions because of the biological and technological importance. Although the single-species ion effects have been extensively explored, it...

Moving dynamics of a nanorobot with three DNA legs on nanopore-based tracks

“…77,78 In order to improve efficiency of the simulation, we use our recently developed coarse-grained (CG) model to describe the ssDNA chains. 79,80 The CG model employs three bead types, namely P (green), S (orange), and B (blue), which correspond to the atomic groups phosphate, sugar, and base thymine, respectively, within each nucleotide. The mass of each bead is equal to the total mass of its corresponding atomic group, and the bead radius is determined by considering the hydration effects.…”

“…† In brief, the volume excluded interaction U lj between two nonbonded beads, including the nanorobot beads and membrane beads, is described using a "12-6" Lennard-Jones potential; the three virtual bond-involved interactions U b , U a , and U d account for chain connectivity and angular rotation of the ssDNA legs; the electrostatic interaction U e is described by the Manning Counterion Condensation theory 81 that implicitly treats the ion effects. Especially, the energy parameters of the bondinvolved interactions are derived from the Boltzmann inversion 80 of the corresponding structural probability distributions, which can be statistically obtained from the experimentally measured ssDNA structures. The simulation results of the current CG model for the ssDNA structures have been validated against the experiment results.…”

“…The simulation results of the current CG model for the ssDNA structures have been validated against the experiment results. 79,80…”

Competition between Stacking and Divalent Cation-Mediated Electrostatic Interactions Determines the Conformations of Short DNA Sequences

“…Theoretical models, such as Poisson–Boltzmann (PB) equation, − simulations using Debye–Hückel (DH) theory, − or Manning condensation, have mimicked the influence of ions on NAs in monovalent salts. However, these models are not as successful in describing DNA interactions with divalent or multivalent cations, where ion–ion correlations are important.…”

Competition between stacking and divalent cation mediated electrostatic interactions determines the conformations of short DNA sequences

“…Theoretical models, such as, Poisson-Boltzmann (PB) equation [16][17][18][19], simulations using Debye-Hückel theory [20][21][22][23], or Manning condensation [24] have mimicked the influence of ions on NAs in monovalent salts. However, these models are not as successful in describing DNA interactions with divalent or multivalent cations, where ion-ion correlations are important.…”