New DNA Preservation Technique – Leading the Way for Researchers Everywhere
Students and researchers at Northeastern’s Ocean Genome Legacy Center (OGL) recently published a paper about a new way to effectively preserve DNA, which has implications for many scientific research disciplines.
DNA preservation is important for an institution like OGL, which is a biorepository, meaning that it collects, catalogs, and stores material for research. People have been using ethanol to preserve biological materials i.e., food and beverages “since the Roman times,” according to Dr. Dan Distel, the executive director of the OGL. Formaldehyde is also used for preserving biological samples, though it is generally not useful for preserving DNA. A recent strategy, developed in the 1990s, is using DMSO-salt or DESS, which consists of dimethyl sulfoxide (DMSO), Ethylenediaminetetraacetic acid (EDTA), and sodium chloride. In 2020 however, OGL published a paper showing that EDTA was the active ingredient in DESS that is responsible for preserving the DNA. Using just EDTA is beneficial because one of the ingredients in DESS, DMSO, can be dangerous to use. Although DMSO is not toxic, if it is accidentally contaminated with a toxin, it will transport that toxin right through human skin and into the blood.
“If you use DMSO and you get it on your fingers, you can taste it immediately. It actually goes through your skin enters your blood and can carry any contaminating toxins right into your body,” Distel said.
Additionally, ethanol is extremely flammable and must be transported as a hazardous material, which makes it expensive and cumbersome to use for research in remote locations.
EDTA however is commonly used as a preservative in food and cosmetics, which means it is not flammable, not toxic, and not difficult to transport. In 2020, OGL’s paper proved that EDTA was an effective preservative, and in 2023 they proved that increasing pH level makes it an even more effective preservative.
DNA breaks down because of enzymes called nucleases, which need certain metal ions to function. EDTA traps those ions so that nucleases can’t use them and are therefore unable to break down the DNA.
Typically, the EDTA within DESS is prepared at a pH between 7.5 and 8. A pH of 7 is neutral whereas higher values are more basic, or less acidic. In this latest experiment, they increased the pH, i.e., decreased acidity, and measured how well DNA was preserved in EDTA that had pH levels of 8, 9, and 10. They preserved DNA from 5 species, sandworm, northern crayfish, Atlantic Spanish mackerel, quahog and American lobster. After a year in different pH solutions, DNA from the specimens was extracted and measured. They found that an increased pH resulted in recovery of DNA of increased molecular weight and higher quality.
At OGL, co-op students design and conduct their own experiment while also continuing the experiment of the previous co-op. For this paper, Mia DeSanctis, who worked at OGL from July to December 2019, designed the experiment and conducted research before handing it off to the next co-op student, Elizabeth Soranno. Soranno worked at the OGL from January to June of 2020, and her work in the lab was interrupted by COVID-19. Research technician Rosie Poulin however stayed at the lab and continued the work. She did the DNA extractions and Soranno focused instead on data analysis.
“We actually managed to keep progress going pretty well through COVID. But this research does take a long time,” Poulin said. “It’s really a credit to this whole crew but they’re able to keep it going and not lose the momentum.”
The long process paid off however, getting a paper published not only was an extraordinary accomplishment for undergraduate students, but it is also an impressive discovery that will help generations of future scientists.
OGL collections associate Hannah Appiah-Madson describes looking at the data and seeing the change as a “really fantastic moment.”
“That was such an exciting moment to see hypothesis exist, and then it plays out in the data just the way that we expected,” Appiah-Madson said.
Despite having published the paper, the work is not over yet. According to Ella Messner, who worked at OGL as a co-op from January to June of 2021, as soon as one question is answered, there are ten more that arise. In her time with OGL, she continued the experiment started by DeSanctis and developed her own experiment focused on combining EDTA and ethanol. What they have accomplished is really only a “starting point,” and to Messner, DNA preservation is a crucial and underdeveloped field.
“The ability to preserve DNA and preserve tissue is so important and I think a lot of people don’t think about that,” Messner said. “It’s a field that’s really underfunded.”
Ideally, their strategy of preserving DNA will catch on and be used by other researchers. DNA preservation is important for an array of scientific disciplines, including ecology research, forensics, health sciences, biology, epidemiology, geneticists, pharmacology, and more. For people dedicated to saving our planet, literally preserving its life for research purposes is key.
“Science moves slowly. Researchers are very cautious about adopting a new method. So we hope that people will start using this because it’s very effective,” Distel said.
Written by Renée Abbott, February 17th, 2023