Mechanical-energy-based amplifiers for probing interactions of DNA with metal ions

Abstract

We report our development of a simple and cost-effective method to amplify and probe the interactions of DNA with metal ions, which are important for various fundamental processes in living systems. This method is based on perturbing energy landscapes using mechanical energy stored in bent DNA molecules. In this proof-of-principle study, the mechanical-energy-based amplifiers were applied to examine the interactions between DNA and ${\mathrm{Mg}}^{2+}$ ions or ${\mathrm{Ag}}^{+}$ ions. We demonstrated that interactions between DNA and ${\mathrm{Mg}}^{2+}$ or ${\mathrm{Ag}}^{+}$ ions, which are not detectable using gel electrophoresis without amplification, can be easily measured using our molecular amplifiers. In addition, we showed that quantitative details about the DNA-metal interactions can be estimated using our method. Our method is simple, sensitive, and cost-effective. We expect that the developed method will be useful for various applications.