Local Compression Properties of Double-Stranded DNA Based on a Dynamic Simulation

Abstract

Using a simple sphere-tip compression system, the local radial mechanical properties of DNA are systematically studied by changing the tip size. When the tip size decreases, the radial compression elastic properties under external loads become sensitive to the tip size and the local DNA conformation. A sudden force break appears in the compression-force curve when the tip size is less than or equal to 12 nm in diameter. The analysis of the hydrogen bonds and the base stacking interaction shows that a local unwinding process occurs. During the compression process, firstly the hydrogen bonds between complement base pairs are broken. With the compression accumulating, the local backbones in the compression center are unwound from the double helix conformation to a kind of parallel conformation. This local unwinding behavior deduced by external loads is helpful to understand the biological process and is important to DNA-based nanomechanical devices.