Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation.
نویسندگان
چکیده
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.
منابع مشابه
Planar Molecular Dynamics Simulation of Au Clusters in Pushing Process
Based on the fact the manipulation of fine nanoclusters calls for more precise modeling, the aim of this paper is to conduct an atomistic investigation for interaction analysis of particle-substrate system for pushing and positioning purposes. In the present research, 2D molecular dynamics simulations have been used to investigate such behaviors. Performing the planar simulations can provide a ...
متن کاملMolecular dynamics simulation of a binary mixture lubricant for use in hard disk interfaces
In Hard Disk Drives (HDD), it is necessary to decrease the Flying Height (FH) between the head and the disk (currently, FH is around 3-5 nm) so as to increase recording densities. Retaining the solid lubricant has become a difficult proposition owing to intermittent contact between the surfaces. ZTMD and Z are used as solid lubricant to lubricate these interfaces. In this paper, the behavior of...
متن کاملComparative Investigation of R213G Mutation in DNA-Binding Domain of P53 Protein via Molecular Dynamics Simulation
Introduction: P53 is a tumor suppressor protein with numerous missense mutations identified in its gene. These mutations are observed in a vast number of cancers. R213G is one of them which has a role in metastatic lung cancers. In this research, R213G was studied in comparison with the wild type via molecular dynamics simulation. Method: For the three-dimensional structure of the wild-type P53...
متن کاملDissipative Particle Dynamics simulation hydrated Nafion EW 1200 as fuel cell membrane in nanoscopic scale
The microphase separation of hydrated perfluorinated sulfonic acid membrane Nafion was investigated using Dissipative Particle Dynamics (DPD). The nafion as a polymer was modelled by connecting coarse grained beads which corresponds to the hydrophobic backbone of polytetrafluoroethylene and perfluorinated side chains terminated by hydrophilic end particles of sulfonic acid groups [1, 2]. Each f...
متن کاملMolecular dynamics simulation of a binary mixture lubricant for use in hard disk interfaces
In Hard Disk Drives (HDD), it is necessary to decrease the Flying Height (FH) between the head and the disk (currently, FH is around 3-5 nm) so as to increase recording densities. Retaining the solid lubricant has become a difficult proposition owing to intermittent contact between the surfaces. ZTMD and Z are used as solid lubricant to lubricate these interfaces. In this paper, the behavior of...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Biophysical journal
دوره 105 12 شماره
صفحات -
تاریخ انتشار 2013