A novel enzymatic system for extracting sequencing-ready DNA in a single tube

Presented live on February 13, 2020

Speakers: Jo Stanton, PhD and David Saul, PhD

The DNA extraction process is often the rate-limiting step in next-generation sequencing workflows. In common extraction methods, sample is transferred between a variety of tubes and subjected to various wash steps. This process is not only slow and labor intensive but introduces opportunities for cross-contamination. In this webinar, the speakers discuss a novel method that enables extraction of sequencing-ready DNA from bacteria in a single tube. The PDQeX Nucleic Acid Extractor, developed by MicroGEM, combines thermostable enzymes with thermoresponsive plastics to enable DNA extraction without centrifugation or harsh solvents. The faster, gentler, cleaner protocol omits the need for wash steps, such that the resulting sample can be used directly in sequencing workflows without any further purification.

Bacterial DNA isolated via the PDQeX system is appropriate for whole genome sequencing including long-read sequencing of bacterial genomes, yielding high-resolution sequencing data to facilitate applications such as microbial Identification, building reference genomes, understanding the temporal and spatial dynamics of epidemics/pathogenesis, and monitoring horizontal gene transfer and antibiotic resistance.

In the webinar, David Saul and Jo Stanton will highlight the quality of DNA extracted using the rapid PDQeX protocol compared to competing methodologies. The particular advantages to using this enzyme-driven chemistry for sequencing projects will also be discussed. Finally, the speakers will share insights on compatibility of the PDQeX system with emerging sequencing technologies.


Hosted by:



Jo Stanton PhD

Senior Research Fellow, Department of Anatomy

University of Otago (New Zealand)


David Saul PhD

Chief Scientific Officer (enzymes and reagents)


Jo Stanton, PhD, uses nucleic acid-based technologies to explore a range of scientific interests related to infectious disease, reproduction, the microbiome, anthropology and forensics. Dr. Stanton leads a team of cross-disciplinary scientists from both academia and industry to develop rapid, accurate and cost-effective handheld molecular diagnostic devices and systems for in-field and point-of-care applications.

She is one of New Zealand's experts in high-throughput sequencing technologies, having established the first fully-operational New Zealand HTS Service based around the 454 Roche GS FLX. This service expanded to include the SOLiD platform from Life Technologies (CA, USA). She currently works with MinION technology from Oxford Nanopore (UK) and MicroGEM's (UK) PDQeX Nucleic Acid Extractor to adapt their use for point-of-care and in-field situations.

Dr. Stanton received a BSc (Honors) from the Australian National University (ACT, Australia) and a PhD from the University of Western Australia (WA, Australia).

David Saul, PhD, has research expertise that spans molecular genetics, microbiology, biotechnology, computational biology and forensic DNA analysis. His key research interest has been the development of biotechnical application of microorganisms living in extreme environments. With a focus on DNA detection and identification, Dr. Saul has generated a substantial body of intellectual property around processes and devices for simple, low-cost and competitive diagnostics.

Prior to co-founding ZyGem (now MicroGEM), Dr. Saul worked as a researcher and academic at the University of Auckland (New Zealand). He has worked in several fields relating to the molecular study of organisms and their genes. He graduated with a PhD in molecular genetics from The University of Sheffield (UK).