Molecular Dynamics Simulation Of The Sieving Of DNA In Micro-nanometer Channel

We investigated DNA migration in realistic shape micro-nanometer channel using a coarse-grained hybrid molecular dynamics approach. The trapping effects of different DNA chain in channel have been analyzed. Results show that the micro-nanometer channel can efficiently separate different DNA in chain length. The probability density distributions of different DNA chains in channel are obviously different. The short chain DNA has a high distribution probability at the inlet of nanometer channel. The trapping effect is distinctly observed for the DNA in shorter chain length. There is no notable increase of the probability density in the inlet of nanometer channel for short chain DNA, but a higher probability density at the outlet of it for long chain DNA. Next, we investigated the impacts of the shape of micro-nanometer channel to the mobility of different DNA chains. We found that the mobility of long chain DNA is increase with the length of nanometer channel. But when we increase the depth of the nanometer channel, there are two different migration states that have been observed. We also investigated the relationship between the slope of the micrometer channel and DNA mobility. DNA mobilities are increasing with the slope of micrometer channel. In the end, we designed an asymmetrical micro-nanometer channel. The positive/opposite direction mobilities of DNA chains in this asymmetrical channel are obviously different. In the asymmetrical channel, a certain time asymmetrical pulsed-field has selectivity of certain DNA chain.