title: Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation.
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 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 deformations with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as well 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.
authors.affiliation: Institut d'Electronique Microelectronique et Nanotechnologie (IEMN UMR Cnrs 8520), University of Lille I, Villeneuve d'Ascq, France; Interdisciplinary Research Institute (IRI USR Cnrs 3078), University of Lille I, Villeneuve d'Ascq, France.
authors.forename: Raghvendra Pratap
authors.initials: RP
authors.lastname: Singh
authors.affiliation: Interdisciplinary Research Institute (IRI USR Cnrs 3078), University of Lille I, Villeneuve d'Ascq, France.
authors.forename: Ralf
authors.initials: R
authors.lastname: Blossey
authors.affiliation: Interdisciplinary Research Institute (IRI USR Cnrs 3078), University of Lille I, Villeneuve d'Ascq, France. Electronic address: fabrizio.cleri@univ-lille1.fr.
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Cleri
mesh_terms: D001483:Base Sequence; D004277:DNA, Single-Stranded / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D053770:Nanowires / Q000737:chemistry*; D059372:Nucleotide Motifs
chemical_list: D004277:DNA, Single-Stranded