Titre :

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

Auteur(s) :

Singh, Raghvendra Pratap [Auteur]
Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 [IEMN]
Blossey, Ralf [Auteur]
Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] [IRI]
Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 [UGSF]
Cleri, Fabrizio [Auteur]
Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 [IEMN]
Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] [IRI]

Titre de la revue :

Biophysical Journal

Nom court de la revue :

Biophys. J.

Numéro :

105

Pagination :

2820-2831

Date de publication :

2013-12-17

ISSN :

1542-0086

Mot(s)-clé(s) en anglais :

Molecular Sequence Data
DNA, Single-Stranded
Nanowires
Nucleotide Motifs
Base Sequence
Molecular Dynamics Simulation

Discipline(s) HAL :

Chimie/Chimie théorique et/ou physique

Résumé en anglais : [en]

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 ...
Lire la suite >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.Lire moins >

Langue :

Anglais

Audience :

Non spécifiée

Établissement(s) :

ISEN
Univ. Valenciennes
CNRS
Institut Catholique Lille
Centrale Lille
Université de Lille

Collections :

• Institut d'Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR 8520
• Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576

Équipe(s) de recherche :

Computational Molecular Systems Biology

Date de dépôt :

2020-02-12T15:11:14Z
2021-03-17T09:49:45Z