Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation

TL;DR

This study uses molecular dynamics simulations to analyze the structure and mechanical properties of DNA i-motif nanowires, revealing their potential for nanotechnology applications due to their unique mechanical characteristics.

Contribution

The paper provides the first detailed dynamic and mechanical characterization of long DNA i-motif nanowires, including their tensile and bending properties, based on molecular simulations.

Findings

i-motif nanowires have tensile stiffness similar to structural proteins

They exhibit bending rigidity comparable to nucleic acids and flexible proteins

The tensile toughness is close to that of metals

Abstract

We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual stacked C*C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression and bending deformation with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as wel as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to that of a metal. Besides their yet to be clarified biological significance, i-motif nanowires may qualify as interesting candidates for nanotechnology templates, due to such outstanding mechanical properties.