Relaxing DNA strands by using nano-channels

Graphic: Nano Channel

This is DNA in a nanochannel; © SISSA

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.

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: International School of Advanced Studies (SISSA)