April 4 2021
We are excited to welcome Femke, Pieter, Louise, and Fulvio who will be doing their bachelor internship with us. We hope you have fun in our group!
January 4 2021
Welcome to our group Ruben! Ruben is joining us for his HAN internship.
September 1 2020
We have four new group members starting this month. Welcome Carmen, Annet, Quan and Lise!
April 14 2020
Maike was awarded an NWO XS to figure out how cell-to-cell differences in protein expression can be regulated.
February 21 2020
Interview Maike Hansen
Maike Hansen, Assistant Professor in the group of Biophysical Chemistry within the Institute for Molecules and Materials (IMM), started working at IMM in January 2020. Maike is the new Tenure Track employee and is starting her own group. Her research focusses on gene expression dynamics by employing techniques at the interface of computational modeling, cell-free biochemistry, and quantitative single-cell biology. ‘I am really looking forward to building up my own group and carrying out my passion to learn why extremely complex systems like cells function so reliably and accurately’, Hansen says.
Read the full interview here.
March 4 2019
Nature Nanotechnology paper for Tom de Greef
In a paper published today in Nature Nanotechnology, Scientists from the Eindhoven University of Technology (TU/e), Radboud University, University of Bristol and Microsoft Research describe a method to make DNA-based computers faster and to protect them from enzyme degradation. To do so, the authors designed computational circuits in which synthetic DNA is confined (‘compartmentalized’) within communities of semi-permeable capsules (‘proteinosomes’). This new approach brings DNA-based computers one step closer to practical applications in biosensing and therapeutics.
Desktop computers use a series of logic gates to transform electric inputs into outputs. In a similar manner, molecular computers made from DNA use programmable interactions between DNA strands to transform DNA inputs into outputs. DNA computers can be programmed to perform complex algorithms on molecular data without human intervention.
In a study published today in Nature Nanotechnology, a team led by Tom de Greef from TU/e and the Radboud University and by Stephen Mann from the University of Bristol’s present a new approach for DNA-based computers called ‘BIO-PC’ (Biomolecular Implementation Of Protocell Communication). This approach uses communities of semi-permeable capsules (‘proteinosomes’) which are assembled together via microfluidic trapping devices. These capsules contain a diversity of DNA logic gates that together can be used for molecular sensing and computation, with potential applications in in-vitro diagnostics and smart therapeutics.
Faster, modular, effective
DNA computers are inherently slow and poorly scalable because they operate in a ‘chemical soup’ where they rely on random diffusion to interact with each other and execute a computational step. De Greef: “With the introduction of compartmentalization, we increase the concentration of DNA gates inside the capsules and, thus, the computing speed. Also, compartmentalization increases the modularity and designability of the computational circuits and reduces the cross-talk between the DNA strands.”
Indestructable in biological environments
One of the long-standing goals of nanotechnology is to create autonomous molecular machines that can operate in harsh biological environments. “To date”, explains de Greef, “DNA-based computers still cannot be used in biological relevant environments as enzymes present in blood and serum would destroy the DNA strands responsible for computations.”In the approach proposed in this study, the encapsulation of DNA gates inside proteinosomes makes them less vulnerable to digestion by enzymes, thereby greatly increasing their lifetime in blood serum and opening the way to the development of real, cell-like autonomous systems operating in physiological conditions.
Living cells communicate by secreting diffusible signalling molecules that activate key molecular processes in neighboring cells. These intercellular communication is often bidirectional and includes both positive and negative regulatory interactions. De Greef: “With our BIO-PC platform, we mimicked intercellular communication occurring in living systems by using two communities of artificial cells. For example, we showed that, when an input DNA strand enters and activates the first community, the secreted signal activates the second community. The latter responds secreting an inhibitor which deactivates back the first community.”
New applications in biosensing and therapeutics
This new approach lays the groundwork for using protocell communication platforms to bring embedded molecular control circuits closer to practical applications in biosensing and therapeutics. Currently, researchers at the TU/e and Microsoft are testing the compartmentalized DNA circuits to detect and classify microRNA patterns of diseased and non-diseased patients.
‘DNA-based communication in populations of synthetic protocells’ by A. Joesaar et al. is published today in Nature Nanotechnology (DOI: 1038/s41565-019-0399-9).
Tom de Greef appointed as professor in Biophysical Chemistry
Tom de Greef has been appointed Professor of Biophysical chemistry, with a focus on Synthetic Biology, at the Radboud University Faculty of Science with effect from 1 December 2018.
The appointment is for one day per week. In addition, Tom de Greef will continue as associate professor of synthetic biology at Eindhoven University of Technology, where he will conduct research in the field of synthetic biology and DNA nanotechnology.
Tom de Greef (1980) has been educated at Eindhoven University of Technology. In 2004, he receved his Master's degree with honours in Biomedical Engineering and in 2009 he obtained his PhD on research into the growth mechanisms of supramolecular polymers and the development of new materials based on non-covalent interactions.
Tom de Greef has been working at the Eindhoven University of Technology since 2008. In 2013 he was a visiting scholar at Harvard. For his research he received an ERC Starting Grant (€ 1.9 million), an NWO VIDI, an NWO VENI grant and the Cram-Lehn-Pedersen prize, an award named after the winners of the Nobel Prize in Chemistry.
At Radboud University, Tom de Greef will continue his research in synthetic biology centered on RNA-based regulatory genetic circuits and further explore usage of DNA nanostructures to mimic and thereby better understand multivalent recognition, for example in immunology.