Computer simulations show how two knots on a DNA strand can interchange their positions
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.
Schematic representation of the swapping event: one of the knots grows in size, while the other diffuses along the contour of the former.
ill./©: Peter Virnau, JGU
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 molecular dynamics simulations, 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 living organisms,” 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 base pairs have an increasing chance of knots, which is relevant for sequencing.
Benjamin Trefz, Jonathan Siebert, Peter Virnau
How molecular knots can pass through each other
Proceedings of the National Academy of Sciences, 19 May 2014
Dr. Peter Virnau
Condensed Matter Theory Group (KOMET)
Institute of Physics
Johannes Gutenberg University Mainz (JGU)
D 55099 Mainz, GERMANY
phone +49 6131 39-20493
fax +49 6131 39-20496
http://www.uni-mainz.de/presse/17448_ENG_HTML.php - press release
Petra Giegerich | idw - Informationsdienst Wissenschaft
About injured hearts that grow back - Heart regeneration mechanism in zebrafish revealed
10.02.2016 | Universität Ulm
Chemical cages: New technique advances synthetic biology
10.02.2016 | Arizona State University
Atomic clock experts from the Physikalisch-Technische Bundesanstalt (PTB) are the first research group in the world to have built an optical single-ion clock which attains an accuracy which had only been predicted theoretically so far. Their optical ytterbium clock achieved a relative systematic measurement uncertainty of 3 E-18. The results have been published in the current issue of the scientific journal "Physical Review Letters".
Atomic clock experts from the Physikalisch-Technische Bundesanstalt (PTB) are the first research group in the world to have built an optical single-ion clock...
The University of Würzburg has two new space projects in the pipeline which are concerned with the observation of planets and autonomous fault correction aboard satellites. The German Federal Ministry of Economic Affairs and Energy funds the projects with around 1.6 million euros.
Detecting tornadoes that sweep across Mars. Discovering meteors that fall to Earth. Investigating strange lightning that flashes from Earth's atmosphere into...
Physicists from Saarland University and the ESPCI in Paris have shown how liquids on solid surfaces can be made to slide over the surface a bit like a bobsleigh on ice. The key is to apply a coating at the boundary between the liquid and the surface that induces the liquid to slip. This results in an increase in the average flow velocity of the liquid and its throughput. This was demonstrated by studying the behaviour of droplets on surfaces with different coatings as they evolved into the equilibrium state. The results could prove useful in optimizing industrial processes, such as the extrusion of plastics.
The study has been published in the respected academic journal PNAS (Proceedings of the National Academy of Sciences of the United States of America).
Exceeding critical temperature limits in the Southern Ocean may cause the collapse of ice sheets and a sharp rise in sea levels
A future warming of the Southern Ocean caused by rising greenhouse gas concentrations in the atmosphere may severely disrupt the stability of the West...
Indications of light-induced lossless electricity transmission in fullerenes contribute to the search for superconducting materials for practical applications.
Superconductors have long been confined to niche applications, due to the fact that the highest temperature at which even the best of these materials becomes...
09.02.2016 | Event News
02.02.2016 | Event News
26.01.2016 | Event News
10.02.2016 | Life Sciences
10.02.2016 | Earth Sciences
10.02.2016 | Physics and Astronomy