As nanotechnology progresses, it becomes increasingly important to know in detail the dynamics of the nanoworld (the world at the scale of a millionth of a millimeter). What happens, for example, when we try to drive a polyelectrolyte (a long chain of electrically charged molecules, such as DNA) through a nanopore if knots cause the translocation process to jam? It's not a pointless question, because now a new DNA sequencing method to electrochemically analyze every single strand by driving it through a nanopore, is being developed. Since those strands tend to tangle up if they are very long, Angelo Rosa of the International School for Advanced Studies and his colleagues set out to study the dynamics of this translocation theoretically, by carrying out a simulation.
The model chosen by the scientists has shown that jamming is not caused by the mere presence of the knot, but by the relationship between friction and the force applied to drive the molecule into the gap."The result is not so obvious if compared to what happens at a macro level," explained Cristian Micheletti, researcher at SISSA and one of the authors of the paper published in Physical Review Letters. "Knots introduce an effective friction that increases with the applied force and pulls the polymer to the other side of the nanopore. Translocation is only halted above a threshold force".
"According to what we observed in the simulation, to avoid obstruction of the pore and halt of the translocation, the force applied should be controlled, without pulling too much" explained Rosa.
This study is just a first step. For quantitative details on this process (what this threshold is and how the force should be measured out to maximize the effectiveness of this sequencing method) more in-depth examinations will be needed both at the theoretical (the model developed by Rosa, Di Ventra and Micheletti is mesoscopic, not atomistic) and at the experimental level.
More in detail…
Nanoporesequencing is an innovative technique, an alternative to more traditional methods such as PCA. This method involves separating the two nucleobase strands which make up the double helix of the DNA and analyzing them one by one. Each strand is driven through a nanopore as the electric variations in the translocation are recorded. That is an electrochemical method: alterations in the electric field give information on the chemical composition of the molecule driven through the pore and the composition is thus reconstructed. Up to now this method has yielded good results with short DNA fragments, while difficulties have been encountered for longer ones, because of the knots. That's why studies such as Rosa, Di Ventra and Micheletti's are an important step to increase its efficiency.
International School of Advanced Studies (SISSA): http://www.sissa.it
This press release was posted to serve as a topic for discussion. Please comment below. We try our best to only post press releases that are associated with peer reviewed scientific literature. Critical discussions of the research are appreciated. If you need help finding a link to the original article, please contact us on twitter or via e-mail.
With funding from the Defense Department, scientists have begun work on devices that would use electric pulses to realign a memory process gone awry
On Friday, the Food and Drug Administration released a vital set of numbers about the routine use of antibiotics …
Side order of veg with that mammoth leg? The Neanderthal diet was probably more varied than we think – using vegetables, herbs and different cooking techniques
An exoskeleton that enables movement and provides tactile feedback has helped eight paralysed people regain sensation and move previously paralysed muscles
A female western gray whale set a new record swimming from Russia to Mexico and back, a total of 13,988 miles, in 172 days
Scientists operating a remote-controlled vehicle about 2,000 feet below water get a rare glimpse of a sperm whale. CBSN's Vladimir Duthiers and Elaine Quijano report on the video.
According to the experts, "blinking is like a kitty kiss"
Genetic profiling of cancer cells can help guide treatment, but such profiles can be ambiguous. Results would be more accurate if all labs tested normal cells from each patient, too.
Researchers in Kenya uncover tools dated to 3.3 million years ago, long before the first humans, as we know them, walked the Earth.
Researchers are facing up to methodological flaws that plague functional magnetic resonance imaging, but the interpretative problems might be harder to solve