Quo Vadis: Cees Dekker

Speaker: Cees Dekker
Department: Bionanoscience, TU Delft
Location: TU Delft
Date: July 6, 2017
Author: Teun Huijben

As start of the summer Quo Vadis of the Bionanoscience Department, Cees Dekker was invited to give a talk. Literally translated from Latin, Quo Vadis means: ’Where are you going?’. In light of this title Cees decided to give a summarizing talk about covering all the exciting research happening in his lab and what he hopes to achieve in the next years.

Since Cees has the largest lab of the department, of lot of different topics are studied in his group. The different topics can be roughly divided into three categories: developing novel nanotechnologies, studies on chromosomal organization and developing the synthetic cell. Of each of these subject he highlights some interesting ongoing studies and his vision on the future.

The first topic Cees elaborates on are the novel nanotechnological techniques his group is developing. The most important technique is the solid state nanopore, which is a very small hole in a thin membrane. When a voltage is applied over the chip, an ionic current starts running and DNA can be dragged through the pore, because of its overall negative charge. While translocating the pore, the DNA blocks the ionic current partly and the decrease in current can be measured. The nanopore technique can be used in different studies. Firstly, it may enable sequencing of DNA optically, when the pore is used in combination with plasmonic structures. The gold plasmonic structures create a high-energetic field trapping the DNA in the pore. In combination with Raman spectroscopy, chemical structures of the DNA can be deduced from the emitted radiation.

Secondly, nanopores are also useful in studying nuclear pore complexes. By covering the inside of the pore with nuclear pore proteins, the transport of proteins can be mimicked through this artificial pore. The advantage is that it can be done in vitro, instead of in living cells. At last, they are also trying to sequence proteins using biological nanopores.

The second main part of Cees’ talk was about the study of chromosome organization. For multiple years, his group is interested in the higher structures of DNA and how that structure is determined. An important part of chromosome structures are supercoils, in which DNA is coiled up to store it in a compact way and suppress transcription. The main question is whether these supercoils (or plectonemes) are sequence dependent. His group developed a new technique to study the coiling, and indeed the position of the supercoils is dependent on the sequence of the DNA. Modeling of the DNA gave the insight that certain sequences have an intrinsic curvature, and the model predicted which sequence will increase the probability of having a supercoil, since the tip of the supercoils needs Experiments with these sequence indeed showed a higher probability of having a supercoil at that position. This shows that the intrinsic curvature of the DNA determines higher structures of the chromatin, so the DNA sequence not only codes for proteins, but also for its own structure.

The last part of his talk was about making a synthetic cell, the ultimate dream of Cees. The goal is to create a vesicle (liposome) with a working division mechanism inside. One idea is to use the bacterial MinE-MinD oscillating proteins to position a FtsZ-ring in the middle of the cell and actively contract this ring to divide the cell. This idea will need some years to become reality, so right now his group is studying the different components of this idea separately and hopefully the first ’synthetic’ cell will be there is a few years.

What I found particularly nice about this talk was that Cees summarized all the research that is currently done in his large lab. In this way the department got a better idea of all the things happening within this part of Bionanoscience. Besides that, Cees is a very enthusiastic speaker what makes if nice to listen to.

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