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 Protein Shake-Up
27.03.2015 | Oak Ridge National Laboratory

nachricht How did the chicken cross the sea?
27.03.2015 | Michigan State University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Experiment Provides the Best Look Yet at 'Warm Dense Matter' at Cores of Giant Planets

In an experiment at the Department of Energy's SLAC National Accelerator Laboratory, scientists precisely measured the temperature and structure of aluminum as...

Im Focus: Energy-autonomous and wireless monitoring protects marine gearboxes

The IPH presents a solution at HANNOVER MESSE 2015 to make ship traffic more reliable while decreasing the maintenance costs at the same time. In cooperation with project partners, the research institute from Hannover, Germany, has developed a sensor system which continuously monitors the condition of the marine gearbox, thus preventing breakdowns. Special feature: the monitoring system works wirelessly and energy-autonomously. The required electrical power is generated where it is needed – directly at the sensor.

As well as cars need to be certified regularly (in Germany by the TÜV – Technical Inspection Association), ships need to be inspected – if the powertrain stops...

Im Focus: 3-D satellite, GPS earthquake maps isolate impacts in real time

Method produced by UI researcher could improve reaction time to deadly, expensive quakes

When an earthquake hits, the faster first responders can get to an impacted area, the more likely infrastructure--and lives--can be saved.

Im Focus: Atlantic Ocean overturning found to slow down already today

The Atlantic overturning is one of Earth’s most important heat transport systems, pumping warm water northwards and cold water southwards. Also known as the Gulf Stream system, it is responsible for the mild climate in northwestern Europe. 

Scientists now found evidence for a slowdown of the overturning – multiple lines of observation suggest that in recent decades, the current system has been...

Im Focus: Robot inspects concrete garage floors and bridge roadways for damage

Because they are regularly subjected to heavy vehicle traffic, emissions, moisture and salt, above- and underground parking garages, as well as bridges, frequently experience large areas of corrosion. Most inspection systems to date have only been capable of inspecting smaller surface areas.

From April 13 to April 17 at the Hannover Messe (hall 2, exhibit booth C16), engineers from the Fraunhofer Institute for Nondestructive Testing IZFP will be...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

World Conference On Regenerative Medicine 2015: Registration And Abstract Submission Now Open

25.03.2015 | Event News

University presidents from all over the world meet in Hamburg

19.03.2015 | Event News

10. CeBiTec Symposium zum Big Data-Problem

17.03.2015 | Event News

 
Latest News

Two Most Destructive Termite Species Forming Superswarms in South Florida

27.03.2015 | Agricultural and Forestry Science

ORNL-Led Team Demonstrates Desalination with Nanoporous Graphene Membrane

27.03.2015 | Materials Sciences

Coorong Fish Hedge Their Bets for Survival

27.03.2015 | Ecology, The Environment and Conservation

VideoLinks
B2B-VideoLinks
More VideoLinks >>>