MESA+ University of Twente
The BIOS Lab-on-a-chip group


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Name: Burcu Gumuscu


Room: Carré 2.431

Phone: 31-(0)53-289 4580

Function: Postdoctoral fellow

Tasks: Development of microfluidic devices for next generation sequencing, organ-on-chip, and desalination of water on the microscale.

Title of the Project

A patterned anisotropic nanofluidic sieving microchip for continuous flow separation of DNA and proteins

Project Description

Hydrogels are considered to be in the class of smart materials that find application in diagnostic, therapeutic, and fundamental science tools for miniaturized total analysis systems. The use of patterned hydrogels in closed fluidic microchips for different research fields depends crucially on the ease and accessibility of their fabrication technology. We developed two simple fabrication procedures to pattern hydrogel microarrays. First, intermittent illumination is applied on mechanically polished microchips for the photopatterning of hydrogels. Second, capillary pressure barriers are used for controlling the position of the liquid-air meniscus in microchip channels, allowing the subsequent patterning of hydrogels by photopolymerization and thermo-gelation.

As the first major application of hydrogels, we describe a novel method for concurrent continuous flow fractionation and purification of DNA fragments in a microfluidic device filled with agarose gel. We exploit the variation in the field-dependent mobility of DNA molecules with DNA length for the fractionation. Since this new mechanism can be applied using agarose gel, it provides a low-cost, robust, and versatile separation matrix.

We propose and demonstrate an in vitro microfluidic cell culture platform that consists of periodic 3D hydrogel structures as the second major application of hydrogels. The microchip enables culturing of human intestine cells, which spontaneously grow into 3D structures on the 3rd day of cell culturing. On the 8th day of culture, Caco-2 cells are co-cultured with intestinal bacteria E.coli, which adhered to the cells without affecting the cell viability. Different compartment geometries lead to a difference in the proliferation and cell spread profile of Caco-2 cells.

Microelectrodialysis is explored as the last major application of hydrogels in this thesis. Parallel streams of concentrated and ion-depleted water are formed in continuous flow when a potential difference is applied across the microchip containing alternating rows of patterned cation- and anion-selective hydrogels. The device could remove approximately 75% of the 1 mM sodium chloride salt introduced via the inlet streams. Secondly, the microchip enables ion transport visualization in the ion selective hydrogels and microchannels.

Educational Activities

IEEE 201400096

Lab on a Chip Module 10 2015-201500054-1B


Students interested in an assignment are always welcome to ask for more information.


Burcu Gumuscu received her bachelor degree in biology from Hacettepe University, Turkey in 2010. In her bachelor years, she worked on molecular genetics of Bietti’s crystalline dystrophy and detection of surfactant producing microorganisms. She pursued her education in Bilkent University Institute of Materials Science and Nanotechnology, where she received the M.Sc. degree on the biodegradation of 2,4,6-trinitrotoluene by biological agents in 2012. She finalized her Ph.D. studies at BIOS lab-on-a chip group in 2016. During her Ph.D., she developed microfluidic devices for next generation sequencing, organ-on-chip, and desalination of water on the microscale. Burcu is now working as a postdoctoral fellow at BIOS lab-on-a chip group.