Investigations of the cation binding to nucleotides by monitoring the hairpin-duplex equilibrium of a self-complementary sequence

Nucleotide folding accompanies cation binding that shields the electronegative potential of phosphate groups, and metal ions in the condensation layer predominantly associate diffusely with base-paired nucleotides. Although metal ions bound at specific sites have been well studied, information of diffusely bound cations, that usually have a weak binding affinity than those associating at specific sites, have not been thoroughly studied. We explored a convenient experimental system using a self-complementary nucleotide sequence for analyzing cationic ligands diffusely bound to DNA or RNA base pairs. To study the metal ion-nucleotide interaction under a non-homologous aqueous condition, solutions containing a large amount of PEG (polyethylene glycol) were examined. We found that PEG (e.g., 20 wt%) substantially influenced the metal ion binding to nucleotides, suggesting significances of the molecular environment on nucleotide-cation interactions.