The nanochannel that relaxes DNA

(Nanowerk News) A simple and effective way of unravelling the often tangled mass of DNA is to “thread” the strand into a nano-channel. A study carried out with the participation of the International School for Advanced Studies (SISSA) in Trieste used simulations to measure the characteristics that this channel should have in order to achieve maximum efficiency.
With the widespread use of methods for DNA analysis and manipulation, it’s certainly useful to find a way to unravel and relax the strands of this molecule that tends to form tangles spontaneously. One way is to use channels, or rather nano-channels, as Cristian Micheletti, SISSA research scientist, and Enzo Orlandini, of Padua University, did in a study just published in the journal Macro Letters ("Knotting and Unknotting Dynamics of DNA Strands in Nanochannels").
Model DNA chain inside a nanochannel that is 100nm wide. The spontaneous dynamical evolution of the DNA is accompanied by frequent knotting and entanglement at the chain ends.
The idea is to force the DNA into the channel so as to relax it completely. “But not just any channel will do,” explains Micheletti. “Depending on the diameter of the nano-channel, the strand extremities can arrange into hook-like structures that will end up forming a knot”.
“In our study we used simulation techniques to characterise the mechanisms leading to knot formation as a function of the diameter of the channel”, Micheletti continues.
The result? “Below 50 nanometres in diameter the tendency to form knots decreases dramatically”. Thanks to these observations it is possible to design channels having the ideal characteristics for achieving a nicely stretched out DNA strand, free of the entanglements that can hinder many methods for genetic analysis.
Source: Sissa Medialab
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