DNA-carbon nanotube hybrids (DNA-CN) are novel nanoscale materials that consist of single-wall carbon nanotubes (SWCN) coated with a self-assembled monolayer of single-stranded DNA (ssDNA). Recent experiments on DNA-CN have shown that this material offers a remarkable set of technologically useful properties such as facilitation of SWCN sorting, chemical sensing, and detection of DNA hybridization. Despite the importance of DNA-CN, a detailed understanding of its microscopic structure and physical properties is lacking. To address this, we have performed classical all-atom molecular dynamics (MD) simulations exploring the self-assembly mechanisms, structure, and energetic properties of this nanomaterial. MD reveals that SWCN induces ssDNA to undergo a spontaneous conformational change that enables the hybrid to self-assemble via the pi-pi stacking interaction between ssDNA bases and SWCN sidewall. ssDNA is observed to spontaneously wrap about SWCN into compact right- or left-handed helices within a few nanoseconds. Helical wrapping is driven by electrostatic and torsional interactions within the sugar-phosphate backbone that result in ssDNA wrapping from the 3' end to the 5' end.
The DNA-carbon nanotube hybrid (DNA-CN) consists of a single-wall carbon nanotube (SWCN) coated with a self-assembled monolayer of single-stranded DNA (ssDNA). Recent experiments have demonstrated that this nanomaterial is ideal for numerous nanotechnological applications. Despite this importance, the structure of this material remains poorly understood. Molecular dynamics (MD) simulations have provided information about the self-assembly mechanisms and ssDNA conformations that characterize DNA-CN. However, MD simulations of biopolymers at low temperatures (T approximately 300 K) result in kinetic trapping that limits conformational sampling. Here, we present results of a large-scale replica exchange molecular dynamics (REMD) simulation that provides extensive sampling of the entire ensemble of oligonucleotide conformations in a (GT)(7)-SWCN hybrid. We calculate the free energy landscape and find minima corresponding to six distinct conformations, with a nonhelical loop structure as the global minimum. The hybrid contains significant structural disorder, with desorbed bases as an important structural feature. These results expand our understanding of DNA-CN and indicate the relevance of REMD for explorations of the physical properties of organic-inorganic multifunctional nanomaterials.
Modified DNA bases are widespread in biology. 5-Methylcytosine (mC) is a predominant epigenetic marker in higher eukaryotes involved in gene regulation, development, aging, cancer, and disease. Recently, 5-hydroxymethylcytosine (hmC) was identified in mammalian brain tissue and stem cells. However, most of the currently available assays cannot distinguish mC from hmC in DNA fragments. We investigate here the physical properties of DNA with modified cytosines, in efforts to develop a physical tool that distinguishes mC from hmC in DNA fragments. Molecular dynamics simulations reveal that polar cytosine modifications affect internal base pair dynamics, while experimental evidence suggest a correlation between the modified cytosine’s polarity, DNA flexibility, and duplex stability. Based on these physical differences, solid-state nanopores can rapidly discriminate among DNA fragments with mC or hmC modification by sampling a few hundred molecules in the solution. Further, the relative proportion of hmC in the sample can be determined from the electronic signature of the intact DNA fragment.
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