Rapid extraction of DNA suitable for NGS workflows from bacterial cultures using the PDQeX

Background: PDQeX is a novel, single-step DNA extraction method that purifies nucleic acid from sample in under 30 min. Materials & Methods: Six bacterial suspensions from species with different cell morphologies and growth optima were made. DNA from half the suspension was purified using PDQeX and the other half using a conventional column purification method. Sequencing and analyses using Ion PGM were performed, blinded to extraction method and species. Results: Genomes extracted with either method sequenced successfully. No significant sequence distribution biases were evident between PDQeX and column purification. Surveyed community preference suggested comparable performance between the two extraction methods. Conclusion: DNA prepared using the PDQeX performs as well for whole-genome sequencing as DNA purified using a conventional method, albeit much more rapidly. METHOD SUMMARY We introduce the PDQeX: a new, rapid, single-step method for DNA extraction that is compatible with high-throughput sequencing. Sample is added to the thermoresponsive PDQeX extractor tube with a cocktail of thermostable enzymes. Upon incubation and heating the extracted DNA is expelled into a collection tube ready for use in downstream applications in under 30 min.