Salt contribution to the flexibility of single‐stranded nucleic acid of finite length

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/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 2+-dependent persistence length l p 's of ss nucleic acid are in accordance with the available experimental data, and through systematic calculations, we obtained the empirical formulas for l p as a function of [Na + ], [Mg 2+ ] and chain length.

Ion assisted structural collapse of a single stranded DNA: A molecular dynamics approach

“…According to the present work, the concentration of MgCl 2 at which the ss-DNA starts experiencing the effect of significant overcharging is 0.3 M (Fig. 11b) and this is consistent with the findings by Wang and co-workers [20].…”

“…Although the use of coarse-graining reduces the number of atoms and simplifies the system, it misses out chemical details which can only be captured in all atom simulation. As for example, the structural flexibility of the ss-DNA as a function of increased positive charge on the ion and its concentration was well addressed by Wang and co-workers [20] but further information about the base pair stacking both in the native as well as collapsed state of the DNA could not be extracted due to the coarse-grained formalism. An alternate atomistic molecular dynamics simulation would be computationally expensive but worth employing as it would be extremely useful in analyzing the conformational changes of the molecule and the preferential affinity of DNA bases and backbone for ions and the solvent.…”

Correlation Force Spectroscopy for Single Molecule Measurements

“…It was recently suggested that tethering a chain at one or both ends or vicinity of molecular tethers can cause variations in measured flexibility. Since tethering is a requirement in all mechanical SMFS, this issue needs attention and can be addressed for example with molecular simulations [139,140].…”

“…The force required to extend a polymer chain in the WLC model was given as equation (3.1) [49] [51,135], valence [133], and number of nucleotides [135,137]. Other recent attempts to measure p l of ssDNA include transient electric birefringence (TEB) [135], AFM imaging [138], and Monte Carlo simulation [139,140].…”

RNA structure prediction: Progress and perspective

“…Since RNAs are highly charged polyanionic polymers, the RNA structures are sensitive to temperature and ion conditions. [93][94][95][96] Is there a model that can predict the RNA structures at a given temperature and ionic temperatures with the mean errors 1.0℃ from extensive experimental data at extensive Na + concentrations [96] . Meanwhile, it can provide the ensemble of probable 3D structures of RNA hairpins at different temperature/salt conditions.…”