Like most websites The Analytical Scientist uses cookies. In order to deliver a personalized, responsive service and to improve the site, we remember and store information about how you use it. Learn more.
Fields & Applications Genomics & DNA Analysis

Go With the Flow

The problem

Standard gel electrophoresis has been intensively used for DNA fractionation in various genotyping and sequencing applications, and has the advantages of great simplicity, versatility, and reproducibility. However, it suffers from long processing times – many hours or even days; for instance, a typical pulsed-field gel electrophoresis (PFGE) device takes 25 hours to perform fractionation of 5–120 kbp DNA. Given trends towards second-generation sequencing, replacing standard gel electrophoresis with microchip-based systems is an attractive option to minimize processing time and optimize DNA fractionation. We set out to develop a new method to improve sample throughput and recovery compared with current technology.


The development of DNA electrophoresis, using both slab gels and capillaries, enabled the first-generation DNA sequencing and genotyping technologies required for the Human Genome Project. However, only minimal sample numbers could be separated and identified, at very high cost. In recent years, efforts have been directed towards reducing the cost and analysis time of DNA genotyping in second- and later-generation sequencing tools. To achieve this, sample preparation methods, such as electrophoresis, must be optimized to increase the throughput and efficiency of the analyses via user-friendly, portable and functional platforms. In some devices, traditional DNA separation gels have been replaced by microfabricated post arrays for separation of genomic-length DNA. However, defect-free fabrication of 3D nanostructures, such as nanopost arrays and crystalline nanoarrays, is extremely challenging. 2D nanostructures are easier to manufacture, but intrinsically yield low sample throughput. An ideal sieving matrix should have simple design and fabrication steps, yet provide high-resolution, high-throughput separation. And that’s why we opted for gel-based devices. People had originally considered continuous flow separation in such devices impossible, but we showed that it could work.

Read the full article now

Log in or register to read this article in full and gain access to The Analytical Scientist’s entire content archive. It’s FREE and always will be!


Or register now - it’s free and always will be!

You will benefit from:

  • Unlimited access to ALL articles
  • News, interviews & opinions from leading industry experts
  • Receive print (and PDF) copies of The Analytical Scientist magazine

Or Login via Social Media

By clicking on any of the above social media links, you are agreeing to our Privacy Notice.

About the Author

Burcu Gumuscu

Burcu Gumuscu is based BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, the Netherlands.


Send me the latest from The Analytical Scientist.

Sign up now

Related Articles

Fields & Applications Environmental

Analyzing Life, the Universe, and Everything

| Jonathan James, Dirk Schulze-Makuch, Sam Kounaves

Fields & Applications Forensics

Stories of the Dead

| Matthew Hallam, Lana Brockbals, Pier Paolo Petrone, Cristina Barrocas Dias

Fields & Applications Clinical

In the News...

| Jonathan James

Register to The Analytical Scientist

Register to access our FREE online portfolio, request the magazine in print and manage your preferences.

You will benefit from:

  • Unlimited access to ALL articles
  • News, interviews & opinions from leading industry experts
  • Receive print (and PDF) copies of The Analytical Scientist magazine