Molecular Dynamics Simulations of DNA Translocation through a biological Nanopore
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Experimental and simulation studies of nucleic acid transport through nanosized channels, both biological and synthetic, has become a rapidly growing research area over the last decade. While the utilization of the alpha-hemolysin channel as a sequencing device is soon to be realized, other biological nanochannels may hold advantages that are yet unknown. Motivated by this, the first reported molecular dynamics simulations of DNA translocation through a connexon 26 channel were accomplished, for single-strandeed DNA with a length of 24 nucleotides and with a sequence containing only adenine, cytosine, guanine or thymine bases. Transmembrane voltages between 40 mV and 8.4 V were applied for up to ~2 ns, and the minimum voltage needed for translocation was found to be at 2.4 V. Higher voltages led to shorter translocation times in most cases. Non-translocation or slow translocation events were normally the result of a high degree of foldedness at the entrance of the “funnel” region, the narrowest part of the connexon channel. Distinct differences were seen between the bases, in particular through slower translocations for the purines than for the pyrimidines. Comparison with published literature of alpha-hemolysin translocation found that some of the results were on the same order of magnitude for translocation through connexon channels subject to constraints. It was concluded that to characterize the translocation mechanisms, further investigations should be carried out; both by the use of experiments as well as more simulation studies.