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Cees Dekker Lab

Department                             Bionanoscience

Principal investigator          Cees Dekker

E-mail address                       c.dekker@tudelft.nl

Website                                   https://ceesdekkerlab.nl/

 

For more projects, see https://ceesdekkerlab.nl/come-join-us/student-projects/.

Various projects on synthetic cell genome design, cell growth, and cell division

Suitable as a BEP? Yes

Suitable as a MEP? Yes

Suitable as an Academic Research Project? No

Techniques:

  • DNA nanotechnology
  • Advanced microscopy
  • Microfluidics
  • Algorithmic genome design
  • Single-molecule fluorescence microscopy

In our lab, we aim to uncover the fundamental principles of life by reverse-engineering a synthetic cell from the bottom up. Our research spans three complementary but distinct projects: genome design, cell growth, and cell division. In one line of work, we reconstitute and integrate division and growth proteins from diverse organisms and develop microfluidic and nucleic acid–based systems to control these processes in synthetic cells. In another, we focus on genome design, creating minimal DNA scaffolds devoid of functional elements and computationally “cleaning” coding sequences to remove unwanted features. To test our rationally designed sequences, we employ single molecule techniques to observe transcription and translation in real-time. Together, these efforts advance our goal of building a self-sustaining synthetic cell.

Further reading (click to link to article)

https://research.tudelft.nl/en/publications/dynamin-a-as-a-one-component-division-machinery-for-synthetic-cel/

Single-molecule microscopy of DNA loop extrusion

Suitable as a BEP? Yes

Suitable as a MEP? Yes

Suitable as an Academic Research Project? No

Techniques:

  • Single-molecule fluorescence microscopy
  • AFM
  • Python data analysis
  • magnetic tweezers
  • FRET

In our lab, we aim to understand how the genome is organized by the SMC family of protein complexes including cohesin and condensin. We employ single-molecule microscopy and complex data analysis to measure how these proteins enlarge loops of DNA at rapid speeds, though using very small forces. At the heart of this process called loop extrusion is a complex interplay between biochemistry and polymer physics. We are currently investigating what happens when an SMC complex meets something else on the DNA, be it another SMC, nucleosomes, transcribing RNA polymerases, etc. As our research is evolving rapidly, interested students best reach out to our team to find out what exciting new project is available.

Further reading (click to link to article)

doi.org/10.1126/science.aar7831

Nanopore protein sequencing

Suitable as a BEP? Yes

Suitable as a MEP? Yes

Suitable as an Academic Research Project? Yes

Techniques:

  • Protein biochemistry
  • complex data analysis and signal processing
  • DNA origami

A major advance in Nanobiology is nanopore DNA sequencing, which enables rapid and accurate reading of genomic material. While this technique can also be applied to RNA, proteins are the true effectors of the cell, making direct protein sequencing a key frontier. In our lab, we are developing nanopore sequencing of proteins and peptides. We modify nanopores to improve translocation efficiency and reading accuracy, for example through genetic engineering or by attaching DNA origami nanostructures. Alongside nanopore optimization, we advance instrumentation, biological applications, and data analysis to enable high-resolution protein sequencing. Interested students are encouraged to reach out, as multiple exciting projects are ongoing in this rapidly developing area.

Further reading (click to link to article)

doi.org/10.1021/acsnano.4c09872

Engineering biomimetic nuclear and peroxisome pore complexes

Suitable as a BEP? Yes

Suitable as a MEP? Yes

Suitable as an Academic Research Project? Yes

Techniques:

  • Advanced microscopy
  • DNA origami design

In this project, we attempt at reconstituting the selective transport of the nuclear pore complex and peroxisome pore complex using a bottom-up designed artificial pore. We design DNA origami rings that insert themselves into biological membranes and serve as a selective barrier by mimicking their flexible protein mesh. To test the properties of these structures, we insert these artificial pores into large vesicles or flat membranes and visualize the transport through them with advanced fluorescence microscopy (TIRF and confocal microscopy).

Email of responsible supervisor: S.Wang-17@tudelft.nl

Further reading (click to link to article)

doi.org/10.1080/19491034.2025.2510106

(Example) projects submitted by lab in past years

(2024-2025) A ground-breaking adventure in the fascinating world of pattern formation

Supervisors: Eva Bertosin & Sabrina Meindlhumer, e.bertosin@tudelft.nl & s.meindlhumer@tudelft.nl

Pattern formation is a phenomenon that appears at all biological levels, from pattern-forming proteins used for cell division to the stripes on the animal fur. How do these pattern-forming systems work? To answer this question, we’re not just exploring, but actively creating these captivating phenomena using the power of DNA nanotechnology. Imagine crafting stunning patterns from the simplest of systems!

You will work in a multidisciplinary experimental environment and also in close collaboration with experts in the theory and modelling of pattern formation.

We are looking for an independent, creative, and passionate Master student (starting preferably in January 2024) ready to craft stunning and mesmerising patterns from scratch! Let your curiosity lead the way and join us on this exciting exploration!

Techniques

  • Designing DNA strands
  • Testing the system using fluorescence microscopy
  • Performing bulk fluorescence measurements
  • Understanding the relation between our artificial systems and biological ones

 

(2024-2025) Building a living cell from scratch using microfluidics

Supervisor: Bert van Herck, b.vanherck@tudelft.nl

Throughout the course of evolution life has developed a staggering complexity at the cellular level. To shed light on the fundamental blueprint of a cell and get a better understanding of the governing principles of cellular life, we are aiming to build a synthetic cell from the bottom-up using molecular building blocks (www.basyc.nl).

More specifically, we developed a microfluidic technology, Octanol-assisted Liposome Assembly (OLA), to produce cell-sized (5–20 µm) liposomes in our lab. These liposomes can be immobilized using microfluidic traps for further manipulations. In the past, we already succeeded in mimicking the form of rod-shaped bacteria by squeezing the liposomes into narrow confinements. Further, liposome growth was established by recruiting lipids from the external environment, and liposome division was induced by colliding them against well-defined microfluidic structures. Now the time has come to combine these modules into an integrated lab-on-a-chip system to establish a dynamic cycle of growing and dividing liposomes, mimicking a continuous life cycle of a living cell.

Techniques

  • Microfluidic setup
  • Basic light- and epifluorescence microscopy
  • On-chip production of synthetic cells

 

(2024-2025) Protein sequencing with nanopores

Supervisor: Justas Ritmejeris, j.ritmejeris@tudelft.nl

Nanopore technologies have been used by astronauts aboard the International Space Station and biologists travelling across the far reaches of the Earth to study DNA at the single-molecule level. However, analyzing the protein composition of cells at the single-molecule level, while an extremely valuable diagnostic tool, remains a difficult task. In this project we are taking important steps in developing nanopore technologies for proteomics.

Currently, we are exploring methods inspired by nanopore DNA sequencing. This approach involves attaching a small piece of protein (peptide) to a DNA strand to form a peptide-oligo conjugate (POC) which is pulled through a nanopore by a DNA motor enzyme. By measuring the ion current through the pore as the peptide moves through it, we can distinguish individual amino acids and detect important post-translational modifications! Our group has pioneered the proof-of-concept of this method, but engineering and data analysis breakthroughs are needed to push this technology to the next stage!

Techniques

  • Wet lab
  • Handling data sets

 

(2024-2025) The ring of power: Building a biomimetic nuclear pore complex with DNA origami

Supervisor: Eva Bertosin & Anders Barth, e.bertosin@tudelft.nl & a.barth@tudelft.nl

The nuclear pore complex (NPC) is a huge, ring-shaped protein system inserted into the nuclear membrane that allows only certain macromolecules to translocate into the nucleus. It is an incredibly complex system that we aim to study using a bottom-up approach.

Our goal is to build a NPC from scratch by combining different NPC proteins (nucleoporins) grafted inside a ring-like DNA origami structure. This approach gives us precise control over the stoichiometry and the positioning of individual proteins. We utilize this platform to study the arrangement and structural dynamics of the FG-nucleoporins in the pore on the single-molecule level.

Techniques

  • Designing, folding and assembling DNA origami rings
  • Protein functionalization of the DNA origami structure
  • Gel electrophoresis
  • Mass photometry
  • Fluorescence correlation spectroscopy
  • Fluorescence microscopy
  • Transmission electron microscopy