How knots can swap positions on a DNA strand

July 3, 2014
One of the knots grows in size, while the other diffuses along the contour of the former. Credit: Peter Virnau, JGU

Physicists of Johannes Gutenberg University Mainz (JGU) and the Graduate School of Excellence "Materials Science in Mainz" (MAINZ) have been able with the aid of computer simulations to confirm and explain a mechanism by which two knots on a DNA strand can interchange their positions.

For this, one of the knots grows in size while the other diffuses along the contour of the former. Since there is only a small free energy barrier to swap, a significant number of crossing events have been observed in , i.e., there is a high probability of such interchange of positions.

"We assume that this swapping of positions on a DNA strand may also happen in ," explained Dr. Peter Virnau of the JGU Institute of Physics, who performed the computer simulation together with his colleagues Benjamin Trefz and Jonathan Siebert.

The scientists expect that the mechanism may play an important role in future technologies such as nanopore sequencing, where long DNA strands are sequenced by being pulled though pores. Long DNA strands of more than 100,000 have an increasing chance of knots, which is relevant for sequencing.

Explore further: Pull with caution: A DNA strand should be driven gently through a nanopore

More information: Benjamin Trefz, Jonathan Siebert, Peter Virnau, How molecular knots can pass through each other , Proceedings of the National Academy of Sciences, 19 May 2014 . DOI: 10.1073/pnas.1319376111

Related Stories

Oxford Nanopore unveils portable genome sequencer – MinION

February 17, 2014

( —U.K. based Oxford Nanopore Technologies has made good on a promise made two years ago to produce an inexpensive genome sequencer that is based on nanopore technology. David Jaffe, with the Broad Institute reported ...

Recommended for you

A new form of real gold, almost as light as air

November 25, 2015

Researchers at ETH Zurich have created a new type of foam made of real gold. It is the lightest form ever produced of the precious metal: a thousand times lighter than its conventional form and yet it is nearly impossible ...

New 'self-healing' gel makes electronics more flexible

November 25, 2015

Researchers in the Cockrell School of Engineering at The University of Texas at Austin have developed a first-of-its-kind self-healing gel that repairs and connects electronic circuits, creating opportunities to advance the ...

Getting under the skin of a medieval mystery

November 23, 2015

A simple PVC eraser has helped an international team of scientists led by bioarchaeologists at the University of York to resolve the mystery surrounding the tissue-thin parchment used by medieval scribes to produce the first ...

Atom-sized craters make a catalyst much more active

November 24, 2015

Bombarding and stretching an important industrial catalyst opens up tiny holes on its surface where atoms can attach and react, greatly increasing its activity as a promoter of chemical reactions, according to a study by ...


Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.