SCODA for DNA extraction from challenging samples

Can’t get DNA out of a difficult matrix? Before throwing your hands up in frustration, consider the new technique developed by Andre Marziali and colleagues at the University of British Columbia and the Michael Smith Genome Sciences Centre (both in Canada). The investigators apply a combination of rotating dipole and quadrupole electric fields in a gel—a method called synchronous coefficient of drag alteration (SCODA)—to produce a divergent velocity field that concentrates nucleic acids from complex samples.

Although column- and bead-based nucleic acid extraction methods are widely used, they fail when contaminants with chemical properties similar to nucleic acids coextract with the molecules or foul the capture matrix. Precipitation usually removes contaminants, but this step reduces yield, especially when the nucleic acid concentrations are low. For environmental samples that are full of interfering matter, this shortcoming is particularly vexing.

Marziali and colleagues tackled this problem by realizing that the nonlinear electrophoretic response of nucleic acids could be used as a physical parameter for separation. In addition, the velocity field pattern generated by SCODA concentrates biomolecules in regions of the conducting medium that is free of electrodes. By combining the two, the investigators could concentrate DNA directly from samples of interest while removing contaminants.

Marziali and colleagues demonstrated their approach by purifying DNA from the Athabasca oil sands, a sample that defied DNA extraction by other methods. By extracting and concentrating DNA from the sample, the investigators were able to generate the first metagenomics profile of the microflora present in the sands. (Proc. Natl. Acad. Sci. U.S.A. 2009, DOI 10.1073/pnas.0907402106)