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ERDC environmental experts awarded patent for improving soil contamination testing

Dr. Jed Eberly, a former research microbiologist with the U.S. Army Engineer Research and Development Center’s Environmental Laboratory, led a team in the invention of “DNA-Based Testing for Environmental Contamination,” a process that earned a patent in February 2020.

Dr. Jed Eberly, a former research microbiologist with the U.S. Army Engineer Research and Development Center’s Environmental Laboratory, led a team in the invention of “DNA-Based Testing for Environmental Contamination,” a process that earned a patent in February 2020. Eberly currently serves as an assistant professor in Agronomy and Soil Microbiology for Montana State University’s Department of Research Centers and as the associate editor of the Agronomy Journal. (U.S. Army Corps of Engineers photo by Heather Fryer)

A team from the U.S. Army Engineer Research and Development Center’s Environmental Laboratory invented “DNA-Based Testing for Environmental Contamination,” a process that earned a patent in February 2020.

A schematic of DNA aptamers incorporated into an electrochemical sensor device. A team from the U.S. Army Engineer Research and Development Center’s Environmental Laboratory invented “DNA-Based Testing for Environmental Contamination,” a process that earned a patent in February 2020. The invention provides synthetic DNA aptamers that bind a target explosive to allow detection of that explosive. (U.S. Army Corps of Engineers photo)

VICKSBURG, Miss. - Testing soil for contaminants on military bases rather than sending samples to a laboratory has produced speedier, cost-saving results for researchers at the U.S. Army Engineer Research and Development Center’s (ERDC) Environment Laboratory (EL). The team received a U.S. Patent this year for their innovative process “DNA-Based Testing for Environmental Contamination.”

Led by Dr. Jed Eberly, a former microbiologist for EL’s Environmental Processes Branch, and including Dr. Karl Indest, a senior research microbiologist and Environmental Microbiology Branch team leader, and Matt Carr, a research assistant, the team was awarded the patent in February 2020.

“Since World War II, an explosive known as C-4 has been widely used for military and civilian operations,” said Eberly, who left the EL after seven years and currently serves as an assistant professor in Agronomy and Soil Microbiology for Montana State University’s Department of Research Centers and as the associate editor of the Agronomy Journal. “C-4 contains an environmental contaminant known as hexahydro-1, 3-5-trinitro-1, 3, 5-triazine or RDX. RDX can migrate through soil and contaminate underlying groundwater aquifers and may be harmful to humans at relatively low levels.” 

Protection priorities

“The EPA has identified more than thirty RDX contaminated sites on its list of national clean-up priorities,” Eberly said, explaining the need for new technologies for rapidly testing the presence of RDX contamination.

He notes several problems in testing for the presence of RDX and Nitrotriazolone (NTO), a high explosive developed in the weapons program, to determine the potential need for reporting and remediation.

“RDX and NTO concentrations are discrete particles that are irregularly dispersed throughout the soil,” Eberly said. “The concentration of samples from adjacent areas may vary considerably.

“Current RDX and NTO testing methods are intended to provide data about precise quantities of these residual explosives using highly sensitive, off-site instrumentation to separately test each sample. This type of high-sensitivity off-site testing is not appropriate for wide-scale environmental remediation projects.”                                           

He added that the lack of rapid testing prevents immediate reporting under the National Toxic Substance Incidents Program (NTSIP), which collects and combines information from many resources to protect people from harm caused by spills and leaks of toxic substances, and it often does not yield the necessary type of data for evaluating dispersal patterns over potentially contaminated sites.                                   

Eberly said, “For the purposes of remediation, it is important for site managers to be able to determine the presence or absence of contaminants over a dispersed area. Current high-sensitivity testing methods performed off-site are costly and prone to delay, because they cannot be performed at the site.”

How the invention works

“Our patent describes the screening and isolation of short synthetic pieces of the nucleic acid DNA sequences, known as aptamers, that bind specifically to the explosive RDX. In addition, the patent describes how these reagents could be interfaced with a relevant detection system/platform,” Eberly said, referring to reagents as a substance or mixture for use in chemical analysis or other reactions.

“Aptamer research is a rapidly developing field and similar technology had been described in the peer-reviewed literature for other targets. However, there are few reports of aptamers for detecting explosives. There was a perceived need for more research in this field which motivated this work,” he said.

He added that previous research led to the development of RNA aptamers that functioned in the bacterium E. coli as a fluorescent reporter for detecting RDX. This work led to the patent US 20170 107515A1 entitled “Rapid In Situ Testing For Environmental Contamination.”

“While this microbial based detection system was effective, there was a need for a more stable DNA aptamer that could potentially function in an electrochemical based sensor platform,” Eberly said.

As the patent application states, the present invention provides synthetic DNA aptamers that bind a target explosive to allow detection of that explosive. In various embodiments, the synthetic DNA aptamers may include one or more aptamers selected from the group consisting of SEQ ID 1-6.

The various synthetic DNA aptamers are sensitive to different explosives and provide an inexpensive, in situ means for testing for explosive, which may be used for both soil and water samples. This testing may include an assay method using the synthetic DNA aptamers or a biosensor linked to the synthetic DNA aptamers.

“Currently, more development is needed to evaluate performance in an electrochemical sensor platform before it will be ready for use in the field. However, this patent could provide the basis for a cost-effective rapid assay for testing of explosives contamination in the environment,” said Eberly.     

The EL team developed the DNA aptamers for RDX and NTO in 2016 at their laboratory in Vicksburg, Mississippi. They will be recognized later this year with a plaque presentation ceremony by the ERDC’s Office of Research and Technology Transfer which processes patents for the center.


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