Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Relaxation helps pack DNA into a virus

27.05.2014

Researchers at the University of California, San Diego have found that DNA packs more easily into the tight confines of a virus when given a chance to relax, they report in a pair of papers to be published in in the early edition of the Proceedings of the National Academy of Sciences the week of May 26 and the May 30 issue of Physical Review Letters.

DNA is a long, unwieldy molecule that tends to repel itself because it is negatively charged, yet it can spool tightly. Within the heads of viruses, DNA can be packed to near crystalline densities, crammed in by a molecular motor.


This image shows cross-sections of the empty prohead of the bacteriophage phi29 (left) and the fully assembled virus (right). A molecular motor transports the DNA (red) into the prohead through a portal. Higher resolution TIFF image available.

Credit: Jingua Tang and Timothy Baker, University of California, San Diego

"These are among the most powerful molecular motors we know of," says Douglas Smith, a professor of physics whose group studies them.

Within an infected cell, viruses assemble in a matter of minutes. Smith's group studies the process by isolating components of this system to watch single molecules in action.

... more about:
»DNA »Relaxation »equilibrium »knots »matter »viruses

They attach the empty head of a single virus, along with the molecular motor, to a microscopic bead that can be moved about using a laser. To another bead, they tether a molecule of viral DNA.

"It's like fishing," Smith says. "We dangle a DNA molecule in front of the viral motor. If we're lucky, the motor grabs the DNA and starts pulling it in."

Packaging proceeds in fits and starts, with slips and pauses along the way. These pauses increase, along with forces the motor counters, as the viral head becomes full.

Scientists who model this process have had to make assumptions about the state of the DNA within. An open question is whether the DNA is in its lowest energy state, that is at equilibrium, or in a disordered configuration.

"In confinement, it could be forming all kinds of knots and tangles," said Zachary Berndsen, a graduate student in biochemistry who works with Smith and is the lead author of the PNAS paper.

To figure this out, Berndsen stalled the motor by depriving it of chemical energy, and found that packaging rates picked up when the motor restarted. The longer the stall, the greater the acceleration.

DNA takes more than 10 minutes to fully relax inside the confines of a viral head where there's little wiggle room, the team found. That's 60,000 times as long as it takes unconfined DNA to relax.

"How fast this virus packages DNA is determined by physics more than chemistry," Smith said.

DNA's tendency to repel itself due to its negative charge may actually facilitate the relaxation. In related experiments, the researchers added spermidine, a positively charged molecule that causes DNA in solution to spool up.

"You might think the stickiness would enhance packing, but we find that the opposite is true," said Nicholas Keller, the lead author of this second report, published in Physical Review Letters.

Countering the negative charges, particularly to the point of making the DNA attractive to itself, actually hindered the packaging of DNA.

"The DNA can get trapped into conformations that just stop the motor," Keller said.

"We tend to think of DNA for its information content, but living systems must also accommodate the physical properties of such a long molecule," Berndsen said. "Viruses and cells have to deal with the forces involved."

Beyond a clearer understanding of how viruses operate, the approach offers a natural system that is a model for understanding and studying the physics of long polymers like DNA in confined spaces. The insights could also inform biotechnologies that enclose long polymers within minuscule channels and spheres in nanscale devices.

###

Shelley Grimes and Paul Jardine, microbiologists at the University of Minnesota co-authored both papers. Damian delToro, a graduate student in physics at UC San Diego, co-authored the paper published by Physical Review Letters.

The National Science Foundation and the National Institute of General Medical Sciences funded the work.

Doug Smith | Eurek Alert!
Further information:
http://www.ucsd.edu

Further reports about: DNA Relaxation equilibrium knots matter viruses

More articles from Life Sciences:

nachricht Surprising similarity in fly and mouse motion vision
30.07.2015 | Max Planck Institute of Neurobiology, Martinsried

nachricht Intracellular microlasers could allow precise labeling of a trillion individual cells
30.07.2015 | Massachusetts General Hospital

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: On the crest of the wave: Electronics on a time scale shorter than a cycle of light

Physicists from Regensburg and Marburg, Germany have succeeded in taking a slow-motion movie of speeding electrons in a solid driven by a strong light wave. In the process, they have unraveled a novel quantum phenomenon, which will be reported in the forthcoming edition of Nature.

The advent of ever faster electronics featuring clock rates up to the multiple-gigahertz range has revolutionized our day-to-day life. Researchers and...

Im Focus: Superfast fluorescence sets new speed record

Plasmonic device has speed and efficiency to serve optical computers

Researchers have developed an ultrafast light-emitting device that can flip on and off 90 billion times a second and could form the basis of optical computing.

Im Focus: Unlocking the rice immune system

Joint BioEnergy Institute study identifies bacterial protein that is key to protecting rice against bacterial blight

A bacterial signal that when recognized by rice plants enables the plants to resist a devastating blight disease has been identified by a multi-national team...

Im Focus: Smarter window materials can control light and energy

Researchers in the Cockrell School of Engineering at The University of Texas at Austin are one step closer to delivering smart windows with a new level of energy efficiency, engineering materials that allow windows to reveal light without transferring heat and, conversely, to block light while allowing heat transmission, as described in two new research papers.

By allowing indoor occupants to more precisely control the energy and sunlight passing through a window, the new materials could significantly reduce costs for...

Im Focus: Simulations lead to design of near-frictionless material

Argonne scientists used Mira to identify and improve a new mechanism for eliminating friction, which fed into the development of a hybrid material that exhibited superlubricity at the macroscale for the first time. Argonne Leadership Computing Facility (ALCF) researchers helped enable the groundbreaking simulations by overcoming a performance bottleneck that doubled the speed of the team's code.

While reviewing the simulation results of a promising new lubricant material, Argonne researcher Sanket Deshmukh stumbled upon a phenomenon that had never been...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

3rd Euro Bio-inspired - International Conference and Exhibition on Bio-inspired Materials

23.07.2015 | Event News

Clash of Realities – International Conference on the Art, Technology and Theory of Digital Games

10.07.2015 | Event News

World Conference on Regenerative Medicine in Leipzig: Last chance to submit abstracts until 2 July

25.06.2015 | Event News

 
Latest News

Roentgen prize goes to Dr Eleftherios Goulielmakis

30.07.2015 | Awards Funding

Intracellular microlasers could allow precise labeling of a trillion individual cells

30.07.2015 | Life Sciences

Real-time imaging of lung lesions during surgery helps localize tumors and improve precision

30.07.2015 | Health and Medicine

VideoLinks
B2B-VideoLinks
More VideoLinks >>>