NEW YORK (GenomeWeb News) – Researchers from the University of British Columbia and the Michael Smith Genome Sciences Centre in Vancouver have published a proof-of-principle study demonstrating the use of their electric field-based method for extracting DNA from contaminated material.
The team isolated DNA representing more than 200 different kinds of bacteria in oil sand samples that had previously been resistant to DNA extraction by conventional methods. The research is scheduled to appear online this week in the Proceedings of the National Academy of Sciences.
DNA extraction typically relies on cell lysis followed by extraction based on the chemical properties of the nucleic acid. But while this approach can be fairly cheap and straight forward, the authors explained, it has limitations when it comes to getting nucleic acids from contaminated samples or in cases where the samples contain very small amounts of DNA.
By taking into account the physical properties of the DNA molecule, such as charge, stiffness, and aspect ratio, senior author Andre Marziali, director of engineering physics at the University of British Columbia, told GenomeWeb Daily News, the researchers were able to develop a technique that exploits these properties.
They found that by using rotating electric fields they could actually move DNA in a non-linear way to concentrate it into the middle of an agarose gel, Marziali said. Contaminants, meanwhile, can be washed out of the sample using electrophoresis.
The UBC spinout company Boreal Genomics is commercializing nucleic acid extraction and purification systems based on this approach.
Earlier this year, GWDN sister publication In Sequence reported that Boreal Genomics' Synchronous Coefficient of Drag Alteration, or SCODA, was capable of isolating DNA from metagenomic oil sand samples — results that Marziali and his team have published in the new paper.
The oil sand that they tested was collected from the Athabasca Oil Sands in Alberta, Canada. Such samples contain heavy oil, water, sand, and clay, the researchers explained. After removing the oil, they put the samples through a lysis treatment and then into a SCODA injection chamber, "sand and all," Marziali said.
The team then made fosmid libraries from the DNA that had been extracted from the samples and sequenced them using an Applied Biosystems 3730xl sytem.
When they compared the sequences with GenBank databases, the researchers found matches to more than 200 different bacteria. Though they conceded that the results represent just one sample, which was collected through non-sterile drilling, the team argued that the identities of at least some of the microbes — such as bacteria that can degrade hydrocarbon or reduce metal — seem to be consistent with the oil sand environment.
In general, the team believes their approach has potential applications for everything from forensics to genomics and clinical applications. For instance, Marziali said that they have used the non-linear electrophoresis approach in experiments working with the Royal Canadian Mounted Police. Using mock samples provided by the RCMP, the team found that they could get DNA that could not be isolated using other techniques.
At the moment, Marziali said Boreal Genomics is concentrating much of its effort on the genomics market, though they are still collaborating with a UBC forensics lab to apply the electric field technology to recover DNA from challenging samples.
He noted that the team is also in the process of tweaking the extraction method so that DNA can be isolated in a sequence-specific way — an advance that could be used for DNA detection as well as extraction.
The SCODA instrument operates on a single channel machine, though Marziali said that he and his colleagues plan to develop an instrument that can extract several DNA samples at once. "We are envisioning a multi-channel machine as well," he said.
As reported in In Sequence, Boreal Genomics also featured a newer instrument, called Aurora, at the Lab Automation meeting earlier this year, which boasts faster nucleic acid extraction times, among other improvements.