DNA i-motif provides steel-like tough ends to chromosomes
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DNA i-motif provides steel-like tough ends to chromosomes Raghvendra P. Singh1,2 , Ralf Blossey2 and Fabrizio Cleri1 1
Institut d’Electronique Microelectronique et Nanotechnologie (IEMN Cnrs - UMR 8520), University of Lille I Sciences and Technology, 59652 Villeneuve d’Ascq, France
2
Interdisciplinary Research Institute (IRI Cnrs - USR 3078), University of Lille I Sciences and Technology, 59655 Villeneuve d’Ascq, France
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 NMR 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, i-motif nanowires share similarities with structural proteins, as far as their tensile stiffness, but are closer to nucleic acids and flexible proteins, as far as their bending rigidity is concerned. Curiously enough, their tensile strength makes such DNA fragments tough as mild steel or a nickel alloy. 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. INTRODUCTION The DNA i-motif is one of the recently identified, non-standard DNA structures, which do not follow the standard Watson–Crick association rule [1-6]. In-vitro, under acidic pH conditions, the i-motif exists as a tetrameric structure, formed by four intercalated DNA strands, held together by protonated cytosine-cytosine, or C•C+, pairs. However, i–motif tetramers have also been observed in vivo, most notably in the terminal part of the human genes, or telomere, where rather long (50-210 bases) asymmetric G-rich and C-rich single-stranded portions of DNA are found [5,6]. Besides their possible role in the genome, still awaiting a full clarification, such DNA nanowires can be also attractive in the domain of bio-inspired materials for nanotechnologies [7-10]. Notably, various kinds of biomimetic nanowires have been already obtained from B-DNA, proteins, and even from viral particles. Electrical, optical, plasmonic features have been added to such wires by metallization, wherein metals have been “coated” or “moulded” onto the outer or inner surfaces of these biomolecular templates [11,12]. The i–motif could as well be a good candidate for nano-templating, being easily be manipulated and apparently stable over quite long time scales. However, while its molecular structure is rather well assessed, a thorough mechanical characterization of such bionanowire is still lacking. In a
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