Shen, Jia-Wei; Tang, Ting; Wei, Xiao-Hong; Zheng, Wei; Sun, Tian-Yang; Zhang, Zhisen; Liang, Lijun; Wang, Qi
On the loading mechanism of ssDNA into carbon nanotubes
RSC ADVANCES, 5:56896-56903, 2015

Understanding of the mechanism and dynamics of DNA loading into carbon nanotubes (CNTs) is very important for the promising applications of CNTs in DNA sequencing, drug delivery and gene delivery systems etc. In this work, the loading mechanism and dynamics of different ssDNA oligomers into single-walled carbon nanotubes (SWNTs) was investigated through molecular dynamics simulations, steered molecular dynamics simulation and binding free energy calculations. Our simulation results showed that the loading of different ssDNA oligomers into the zigzag SWNT is much easier than for the armchair SWNT. Confined in both zigzag and armchair type SWNTs, ssDNA oligomers have a helical structure and their bases adapt the orientation parallel to the interior wall. From detailed analysis of the interaction energy, potential of mean force (PMF) of the unloading process and nucleotide binding free energy, our results show that the chirality of SWNTs has a large effect on the binding strength of nucleotides, and hence affects the loading dynamics of ssDNA into SWNTs.

DOI:10.1039/c5ra01941a

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