Abstract
Alkli-earth metal ions play an important role in life activities. Molecular dynamics simulation method was used to compare the characteristics and differences of calcium ions and magnesium ions binding to dsDNA. The 12-mer DNA fragment (CGCGAATTCGCG) was dissolved in normal or less polarised water solvent containing calcium or magnesium ions. The results showed that compared with Mg2+,Ca2+ had a stronger tendency to compress and assemble DNA strands into compact structures. Through qualitative and quantitative analysis of ionic solvation and binding sites, we found that although the smaller magnesium ions are more likely to appear near the DNA backbone due to steric effect, the hydrated shell of DNA hinders the interaction between ions and DNA, weakening the neutralization of counterions on DNA chain. Thus, DNA presents a (A-B) mixed state in less polarised water solvent. Calcium ion has a more dynamic solvent shell and strong coordination with free oxygen atoms of phosphate, which limits the electrostatic repulsion to the backbones and is favorable to the formation of A-type DNA. Our simulation provides a simple explanation for the AFM experimental results observed at low ethanol concentration, i.e., the length of DNA strand in alkaline earth metal ions is Ca2+Mg2+. In addition, the competition between two coexisting divalent ions in solution is also discussed.
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