How DNA can take on the properties of sand or toothpaste

May 2, 2016, University of California - San Diego
DNA
DNA double helix. Credit: public domain

When does DNA behave like sand or toothpaste?

When the genetic material is so densely packed within a virus, it can behave like grains of sand or in a tube.

That's essentially what biophysicists at UC San Diego discovered when they began closely examining the physical properties of DNA jammed inside viruses.

"We found that under certain conditions, DNA behaves like toothpaste or sand, or like LEGO pieces when you try to put them back into the box and they don't seem to all fit," said Douglas Smith, a professor of physics at UC San Diego who headed a team that published its unusual discovery this week in the journal Nature Physics. "Strands of DNA not only contain genetic information, but can behave like 'granular' materials composed of randomly arranged particles (in this case, segments of the DNA string) that undergo what physicists call 'jamming' and 'unjamming' transitions, resulting in either solid-like or fluid-like behavior," he explained. "Sand pours out of a cup like a fluid, but comes to rest in a solid pile on the ground where the sand grains are jammed together. Toothpaste doesn't flow out of the tube until you squeeze it because it is contains tightly packed particles that are jammed but un-jam when you apply force so that the toothpaste can flow out.

Many viruses use a tiny "nanomotor" to pack DNA into their viral shells. But during this process, strands of DNA sometimes become jammed and the motor is unable to complete its job.

To better understand this process, Smith's team of researchers, which included molecular virologists at the University of Minnesota, cleverly applied the research of other physicists who characterized the processes of jamming (and un-jamming) a diverse set of materials consisting of randomly arranged particles—such as sand, pastes, foams and emulsions—to determine exactly what was happening to the viral DNA on a nanometer scale.

The researchers found to their surprise that DNA segments frequently become jammed within the virus when they are "sticky," or more attractive, a condition that physicists had previously predicted would make it easier to pack the DNA.

"On the contrary, we found that this condition inhibits packaging," said Smith. "We also found to our surprise that it is easier to pack the

DNA in conditions where segments of the DNA string repel each other. Our measurements suggest this is because when the DNA is sticky to itself, it becomes packed in a very disordered, or messy, way which causes the DNA segments to become jammed. Repulsive interactions appear to help the DNA pack in a more ordered state where it does not become jammed."

DNA packaging is an essential step in the life cycles of many kinds of viruses, including adenoviruses, pox viruses and herpes viruses that infect humans. So could this discovery be used to inhibit DNA packaging and keep dangerous viruses from replicating and infecting us?Possibly. The scientists found that addition of polyamines—small, positively charged molecules—causes viral DNA to become jammed and halt its packaging process.

"However, we did this in a test tube, not inside infected cells," said Smith. "For a chemical to be useful as a drug one also has to get it into cells and make sure that it doesn't interfere with normal healthy processes. But the basic idea of blocking viral assembly by causing the viral DNA to become jammed may be feasible. One could imagine that a special chemical could be developed that would specifically jam the viral DNA without affecting other processes in the cell. Such an approach would differ from ones currently used to combat viral infections, such as vaccines, which act by spurring one's immune system to attack by recognizing their exterior shell, as opposed to targeting the packaging of the DNA."

Explore further: Retroviral DNA needs time to find its home, but insertion happens in a blink

More information: Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging, Nature Physics, DOI: 10.1038/nphys3740

Related Stories

Relaxation helps pack DNA into a virus

May 26, 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 ...

HIV can develop resistance to CRISPR/Cas9

April 7, 2016

The CRISPR/Cas9 gene-editing platform may need a little bit more tweaking before it can be used as an effective antiviral, reports a study published April 7 in Cell Reports. Researchers who used CRISPR/Cas9 to mutate HIV-1 ...

'Key' to recognizing and immunizing herpes, common cold

April 4, 2016

Researchers at McMaster University have discovered a critical step in the immune system's recognition of DNA viruses. It's a key finding, they say, that could lead to vaccinations for herpes, the common cold or even cancer.

Smallpox vaccine virus helps scientist understand immunity

April 15, 2015

A virus that helped wipe out smallpox in the last century is now helping a University of Nebraska-Lincoln virologist better understand human immunity. This research may lead to better treatment of some viral diseases, including ...

Recommended for you

Physicists discover new class of pentaquarks

March 26, 2019

Tomasz Skwarnicki, professor of physics in the College of Arts and Sciences at Syracuse University, has uncovered new information about a class of particles called pentaquarks. His findings could lead to a new understanding ...

Coffee-based colloids for direct solar absorption

March 22, 2019

Solar energy is one of the most promising resources to help reduce fossil fuel consumption and mitigate greenhouse gas emissions to power a sustainable future. Devices presently in use to convert solar energy into thermal ...

Physicists reveal why matter dominates universe

March 21, 2019

Physicists in the College of Arts and Sciences at Syracuse University have confirmed that matter and antimatter decay differently for elementary particles containing charmed quarks.

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.