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Keywords:

  • ss nucleic acid;
  • ions;
  • overcharging;
  • persistence length

Nucleic acids are negatively charged macromolecules and their structure properties are strongly coupled to metal ions in solutions. In this article, the salt effects on the flexibility of single-stranded (ss) nucleic acid chain ranging from 12 to 120 nucleotides are investigated systematically by the coarse-grained Monte Carlo simulations where the salt ions are considered explicitly and the ss chain is modeled with the virtual-bond structural model. Our calculations show that, the increase of ion concentration causes the structural collapse of ss chain and multivalent ions are much more efficient in causing such collapse, and both trivalent/small divalent ions can induce more compact state than a random relaxation state. We found that monovalent, divalent, and trivalent ions can all overcharge ss chain, and the dominating source for such overcharging changes from ion-exclusion-volume effect to ion Coulomb correlations. In addition, the predicted Na+ and Mg2+-dependent persistence length lp’s of ss nucleic acid are in accordance with the available experimental data, and through systematic calculations, we obtained the empirical formulas for lp as a function of [Na+], [Mg2+] and chain length. © 2012 Wiley Periodicals, Inc. Biopolymers 99: 370–381, 2013.