Local compression properties of double-stranded DNA based on a dynamic simulation

TL;DR

This study uses dynamic simulations to explore how local mechanical properties of double-stranded DNA vary with tip size during compression, revealing a local unwinding process relevant to biology and nanotechnology.

Contribution

It provides a systematic analysis of DNA's local compression properties with varying tip sizes, highlighting a local unwinding mechanism under external loads.

Findings

Compression force curve shows a sudden break at small tip sizes.

Local unwinding involves breaking hydrogen bonds and changing DNA conformation.

Results align with experimental data for 16 nm tips.

Abstract

The local mechanical properties of DNA are believed to play an important role in their biological functions and DNA-based nanomechanical devices. Using a simple sphere-tip compression system, the local radial mechanical properties of DNA are systematically studied by changing the tip size. The compression simulation results for the 16 nm diameter sphere tip are well consistent with the experimental results. With the diameter of the tip decreasing, the radial compressive elastic properties under external loads become sensitive to the tip size and the local DNA conformation. There appears a suddenly force break in the compression-force curve when the sphere size is less than or equal to 12 nm diameter. The analysis of the hydrogen bonds and base stacking interaction shows there is a local unwinding process occurs. During the local unwinding process, first the hydrogen bonds between complement base pairs are broken. With the compression aggregating, the local backbones in the compression center are unwound from the double helix conformation to a kind of parallel conformation. This local unwinding behavior deducing by external loads is helpful to understand the biological process, and important to DNA-based nanomechanical devices.