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Project

Electrochemical in-situ synthesized DNA probe arrays for spatial transcriptomics.

In this thesis, a novel method is developed to leverage state-of-the-art CMOS processing technology for high density electrochemical DNA microarray fabrication. DNA microarrays enable the analysis of thousands of genes at the same time, hence representing an eminent tool in genomic research. A DNA microarray consists of a substrate with a large collection of individual spots, so-called features, each containing DNA fragments with a distinct sequence of bases, called probes. Applications typically rely on the coupling of a target probe to a microarray probe via complementary base pairing, a natural mechanism that dictates mutual binding of specific bases. 

A number of methods have been developed for the fabrication of microarrays. These methods either rely on the immobilization of pre-synthesized probes, or on probe synthesis from scratch directly on the substrate. The techniques in this second group (i.e. de novo synthesis) can be further divided into three main categories: spotting or microprinting techniques, photolithographic methods using masks or micro-mirrors, and electrochemical techniques using multielectrode chips. 

An aggressive increase in feature density is required by novel DNA microarray applications, including next-generation data storage and spatial transcriptomics. In this dissertation, we have therefore developed a strategy to fabricate high density DNA microarrays by taking advantage of high resolution CMOS technology. The proposed method relies on a two-fold use of lithographically defined electrodes. On the one hand, electrochemical reduction is performed at the electrodes to achieve a suitable functionalization of the electrode surface. As such, the functionalized electrodes can act as solid support for on-chip DNA synthesis. On the other hand, the individually addressable electrodes are used to electrochemically induce DNA synthesis, enabling synthesis of a custom sequence on each electrode. High density synthesis requires precise containment of the electrochemical reaction products close to the activated electrodes. Therefore, finite element simulations were implemented to investigate different strategies for product diffusion confinement. Finally, a CMOS test array with switching matrix functionality was developed, as an important step towards a final CMOS-based device. 

Microelectronics-based DNA synthesis provides an excellent platform to push the density of microarrays used in applications such as synthetic biology and target enrichment for next-generation sequencing. To this end, we have demonstrated a method enabling electrochemical DNA synthesis on chip that benefits from advanced semiconductor processing techniques with lithographic resolutions.

Date:1 Oct 2013 →  12 May 2018
Keywords:CMOS addressable electrodes, electrografting, DNA synthesis
Disciplines:Biomaterials engineering, Biological system engineering, Biomechanical engineering, Other (bio)medical engineering, Environmental engineering and biotechnology, Industrial biotechnology, Other biotechnology, bio-engineering and biosystem engineering, Nanotechnology, Design theories and methods, Analytical chemistry, Physical chemistry
Project type:PhD project