Mechanically bent DNA molecules as sensing amplifiers for probing interactions of DNA with metal ions and small organic molecules

A fascinating concept in physics is that many properties of a system are governed by its Hamiltonian, while an interesting direction rising from this concept is to perturb the energy landscape to modulate and/or bias chemical and biochemical systems and reactions by mechanical means. Here, we present our development of this concept of exploiting mechanical energies/forces to amplify the interactions between DNA and inorganic salts or small organic molecules. Due to the central role of DNA, these interactions are essential in various fundamental cellular processes in living systems and involved in many DNA-damage related diseases. Strategies to improve the sensitivity of the existing techniques for studying DNA interactions with other molecules is always appreciated in situations where the interactions are too weak. We developed a method based on perturbing energy landscapes using mechanical energy stored in the bent DNA molecules. With the bent DNA molecules, these interactions were easily visualized and quantified in gel electrophoresis, which were difficult to measure without bending. In addition, the strength of the interactions of DNA with the various salts/molecules were quantified using the modified Hill equation.