Tired of performing DNA extractions, bisulfite conversions, and PCR in three separate reactions? Is the sweet smell of phenol not helping you out with the opposite sex? Then, you’ll love DNA methylation analysis using methylation on beads (MOB)! Although it may sound like the stuff of infomercials, a team at Johns Hopkins University really found that performing MOB in a single tube was easy and it only took about half the time.
MOB attempts to address some big needs in the study of DNA methylation including reducing sample loss, and being able to efficiently handle several small clinical samples at once. A recent example of the type of research that could benefit from these improved methods is this study from EpiGenie reader Zdenko Herceg looking at predictive DNAm signatures in Hepatocellular Carcinoma (PLoS One, March 2010).
To perform MOB, cell lysates or patient samples are thrown together with silica superparamagnetic beads (SSBs) in a solution that helps DNA bind to the SSBs. The other cellular gunk is removed by putting a magnet near the tube (to keep the DNA and beads in there) and pouring off the liquid. Next comes the bisulfite conversion. Deamination and desulfonation steps are combined, eliminating many binding and washing steps. Finally, PCR buffer and reagents are squirted into the tube, and you are on your way to generating killier data.
The researchers analyzed all kinds of samples with MOB—fresh, frozen, and paraffin-embedded tissues (and even sputum), and got huge pre-PCR DNA yields. MOB even beat the old-school technique in a blind test analyzing methylation in real cancer samples.
Is MOB the DNA methylation version of The Snuggy? You be the judge: Clinical Chemistry, April 2010.