A rapid and high-yield method for nucleic acid extraction

We report a magnetic silica bead-based nucleic acid extraction method which is rapid (6 - 7 min) and efficient (extracts nearly all the nucleic acid in the sample). We call this method SHIFT-SP (Silica bead based HIgh yield Fast Tip based Sample Prep). Factors such as pH during binding of nucleic acid to bead, the mode of bead movement during binding, the duration of binding, pH, temperature and duration of elution affect the final yield of the method. We have compared the method developed here to commercially available bead and column-based methods. The commercially available bead-based method took about 40 minutes from lysed sample to extracted nucleic acid and had a similar DNA yield as SHIFT-SP. The commercially available column-based method took 25 minutes with half the DNA yield as SHIFT-SP. In addition to a favorable time and yield, all steps in this developed method are automation compatible. We demonstrated a similar efficiency and speed of extraction for both DNA and RNA and showed that the performance of SHIFT-SP was unaffected by DNA size. SHIFT-SP was also able to extract DNA from low concentrations of microbes from enriched whole blood, for downstream whole genome amplification and sequencing.