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Preserving DNA in biological samples has long posed a challenge for researchers, but the process may be about to get a lot easier.

Researchers and students at Northeastern's Ocean Genome Legacy Center (OGL) have developed what they claim is a breakthrough in DNA recovery from frozen tissues. And they shared the discovery in a recent in PLOS One.

The Northeastern team found that using a common food additive called EDTA did a better job of preserving the DNA of biological specimens than traditional methods such as immersion in ethanol.

"We discovered that EDTA is very effective at preserving DNA in tissue samples, which was something that no one had actually demonstrated before," says Dan Distel, the project's principal investigator and director of OGL.

"EDTA is safer and more effective than ethanol, and much more convenient than working with frozen tissues," Distel says.

The team recently received patent approval to protect their discovery.

An unexpected discovery

The discovery came about when Distel and students were working with frozen fish samples, including samples they received from the state of Connecticut's Department of Energy & Environmental Protection.

The researchers extracted DNA directly from frozen tissues and from frozen tissue samples that were thawed in either EDTA or ethanol before DNA extraction.

What they found was that the quality and quantity of DNA recovered from the EDTA-thawed samples were superior to that recovered from either frozen or ethanol-thawed tissues.

"Freezing at ultra-cold temperatures is considered the gold standard for preserving DNA in tissue," says Distel.

"The problem is you have to thaw the material to extract the DNA, and it turns out that a very brief period of thawing, even for a matter of seconds, is enough to allow degradation of DNA in the tissue," he says.

Some of the frozen samples yielded so little high-quality DNA that lab members Hannah Appiah-Madson and Rosie Falco Poulin first flagged them as poor quality samples that were already degraded before they were frozen, Distel says.

But when students thawed samples from the same fish in EDTA, they obtained large amounts of high-quality DNA. "The effect was highly statistically significant," Distel says.

It was almost as if the DNA had been magically resurrected, he says. "That is when we realized that the original samples were fine. Instead, the damage was occurring during DNA extraction. However, when EDTA was present, it kept the DNA safe."

A chelating agent

The major players in DNA degradation are enzymes called DNases, which are found in most tissues. Short for ethylenediaminetetraacetic acid, EDTA is a chelating agent that works by scooping up the metal ions that these enzymes use to attack DNA, Distel says.

"It grabs those ions out of solution and binds them really tightly so the enzymes can't break down the DNA," he says.

In addition to using DNA extraction for sequencing genomes, scientists use it to detect viruses and bacteria in the environment, study forensic evidence and develop new drugs, among other things.

EDTA does not have the challenges of ethanol, which is flammable and must be shipped as a hazardous material, or of keeping specimens frozen.

"Maintaining a cold chain from a remote field collection site to a freezer at Northeastern—that's a pretty difficult task and very expensive to do," Distel says.

Undergraduate discoveries

What makes the EDTA discovery story a bit unusual is that the work in this paper, and two previous publications from Distel's lab, rely heavily on the work of undergraduate co-op students.

"You're not going to win a Nobel Prize for the newest preservative," Distel says. "But we realized that for undergraduate students, the research is ideal. They're not under any pressure to publish, but getting their name on publications is really a feather in their caps."

"Undergraduate students are the first authors on all three papers," he says.

It was undergraduates, for instance, that helped determine that EDTA is the in a commonly used preservative known as DMSO-salt, Distel says.

They also were involved in the discovery that increasing the pH of the EDTA solution significantly .

Fifth year student Molly Johnson says setting up a multi-year experiment to examine the effect of different chemicals, including EDTA, on DNA preservation as a co-op student further cemented her plans to study marine science in graduate school.

"It was very exciting to know I was working on novel research and contributing to a product that could make marine species sampling more accessible for international researchers," she says.

Preserving the ocean's legacy

Whether they know it or not, scientists exchanging marine samples with Northeastern's Ocean Genome Legacy Center have been using the preservative discovered by Distel's lab for years.

"We have a preservative that we distribute with our sample kits in pre-filled tubes that researchers mail back to us. We call it 'OGL Fix,' but it's EDTA," Distel says. "At OGL, we are always looking for better ways to preserve DNA in tissue," he says, " and we publish all our discoveries so that anyone can use them."