Nav: Home

It is easier for a DNA knot...

March 28, 2017

Anyone who has been on a sailing boat knows that tying a knot is the best way to secure a rope to a hook and prevent its slippage. The same applies to sewing threads where knots are introduced to prevent them slipping through two pieces of fabric. How, then, can long DNA filaments, which have convoluted and highly knotted structure, manage to pass through the tiny pores of various biological systems? This is the fascinating question addressed by Antonio Suma and Cristian Micheletti, researchers at the International School for Advanced Studies (SISSA) in Trieste who used computer simulations to investigate the options available to the genetic material in such situations. The study has just been published in PNAS, the journal of the National Academy of Sciences of the Unites States.

"Our computational study sheds light on the latest experimental breakthroughs on knotted DNA manipulation and adds interesting and unexpected elements" explains Micheletti. "We first observed how knotted DNA filaments pass through minuscule pores with diameter of about 10 nanometers (10 billionths of a meter). The behaviour observed in our simulations was in good agreement with the experimental measurements obtained by an international research team led by Cees Dekker, which were published only a few months ago in Nature Biotechnology. These advanced and sophisticated experiments marked a turning point for understanding DNA knotting. However, current experiments cannot "see" how DNA knots actually pass through the narrow pore". In fact, the phenomenon occurs over a tiny spatial scale, and therefore inaccessible to microscopes. This is precisely the reason why our group resorted to what the great German biophysicist Klaus Schulten called "the computational microscope", that is, computer simulations".

Suma and Micheletti explain: "The simulations revealed that the passage of the knot can occur in two distinct ways: one where the knot is tight, and the other where the knot is more delocalised. In both cases, the knot not only manages to pass through the pore, but it does so in a very brief time". Moreover, the knot usually passes in the final stages of the translocation, when most of the DNA strand has already passed. "But there is something more that is counterintuitive" state the authors, "the size of the knot, be it small or large, does not seem to affect much the pore obstruction time. The latter depends instead on the translocation speed, which, in turn, depends on the initial position of the knot along the filament". These results, say the researchers, ought to help the design of future experiments probing the spontaneous knotting of DNA, a still largely unexplored venue, especially regarding the size of DNA knots.

Advancing our current understanding of knots in biological molecules is important to clarify their implications in biological contexts as well as in applicative ones, such as DNA sequencing using nanopores. Suma and Micheletti hope that the promising directions suggested by their study can lead to a more detailed and accurate profiling of entanglement in DNA, RNA and proteins.
-end-


Scuola Internazionale Superiore di Studi Avanzati

Related Dna Articles:

Penn State DNA ladders: Inexpensive molecular rulers for DNA research
New license-free tools will allow researchers to estimate the size of DNA fragments for a fraction of the cost of currently available methods.
It is easier for a DNA knot...
How can long DNA filaments, which have convoluted and highly knotted structure, manage to pass through the tiny pores of biological systems?
How do metals interact with DNA?
Since a couple of decades, metal-containing drugs have been successfully used to fight against certain types of cancer.
Electrons use DNA like a wire for signaling DNA replication
A Caltech-led study has shown that the electrical wire-like behavior of DNA is involved in the molecule's replication.
Switched-on DNA
DNA, the stuff of life, may very well also pack quite the jolt for engineers trying to advance the development of tiny, low-cost electronic devices.
Researchers are first to see DNA 'blink'
Northwestern University biomedical engineers have developed imaging technology that is the first to see DNA 'blink,' or fluoresce.
Finding our way around DNA
A Salk team developed a tool that maps functional areas of the genome to better understand disease.
A 'strand' of DNA as never before
In a carefully designed polymer, researchers at the Institute of Physical Chemistry of the Polish Academy of Sciences have imprinted a sequence of a single strand of DNA.
Doubling down on DNA
The African clawed frog X. laevis genome contains two full sets of chromosomes from two extinct ancestors.
'Poring over' DNA
Church's team at Harvard's Wyss Institute for Biologically Inspired Engineering and the Harvard Medical School developed a new electronic DNA sequencing platform based on biologically engineered nanopores that could help overcome present limitations.

Related Dna Reading:

Blueprint: How DNA Makes Us Who We Are (The MIT Press)
by Robert Plomin (Author)

The Family Tree Guide to DNA Testing and Genetic Genealogy
by Blaine T. Bettinger (Author)

Move Your DNA: Restore Your Health Through Natural Movement Expanded Edition
by Katy Bowman (Author)

The Innovator's DNA: Mastering the Five Skills of Disruptive Innovators
by Jeff Dyer (Author), Hal Gregersen (Author), Clayton M. Christensen (Author)

Dinosaur DNA: A Nonfiction Companion to the Films (Jurassic World)
by Marilyn Easton (Author)

Native American DNA: Tribal Belonging and the False Promise of Genetic Science
by Kim TallBear (Author)

DNA: The Story of the Genetic Revolution
by James D. Watson (Author), Andrew Berry (Author), Kevin Davies (Author)

Cosmic Serpent: DNA and the Origins of Knowledge
by Jeremy Narby (Author)

The Adoptee's Guide to DNA Testing: How to Use Genetic Genealogy to Discover Your Long-Lost Family
by Tamar Weinberg (Author)

DNA Science: A First Course, Second Edition
by David Micklos (Author), Greg Freyer (Author)

Best Science Podcasts 2018

We have hand picked the best science podcasts for 2018. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Where Joy Hides
When we focus so much on achievement and success, it's easy to lose sight of joy. This hour, TED speakers search for joy in unexpected places, and explain why it's crucial to a fulfilling life. Speakers include inventor Simone Giertz, designer Ingrid Fetell Lee, journalist David Baron, and musician Meklit Hadero.
Now Playing: Science for the People

#500 500th Episode
This week we turn 500! To celebrate, we're taking the opportunity to go off format, talk about the journey through 500 episodes, and answer questions from our lovely listeners. Join hosts Bethany Brookshire and Rachelle Saunders as we talk through the show's history, how we've grown and changed, and what we love about the Science for the People. Here's to 500 more episodes!