Salt Contribution to the Flexibility of Single-stranded Nucleic Acid of Finite Length

TL;DR

This study uses simulations to explore how different salt ions influence the flexibility and structural properties of single-stranded nucleic acids, revealing ion-specific effects on chain collapse, overcharging, and persistence length.

Contribution

It provides a systematic analysis of salt effects on ss nucleic acid flexibility, including empirical formulas for persistence length based on ion type and chain length.

Findings

Multivalent ions induce more efficient chain collapse.

All ion types can cause overcharging of ss chains.

Persistence length depends on ion concentration and type.

Abstract

Nucleic acids are negatively charged macromolecules and their structure properties are strongly coupled to metal ions in solutions. In this paper, 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 trivalent and small divalent ions can both 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 Mg dependent persistence length lp 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, Mg and chain length.