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Welcome to the Nynke Dekker Lab

Our lab focuses on probing and explaining protein dynamics using integrative approaches that build on quantitative biophysics and state-of-the-art biochemistry. At present, we predominantly concentrate on DNA replication in eukaryotic systems (including also the chromatin context), but we have also examined bacterial and viral systems, the latter in the context of RNA replication and viral capsid mechanics. We typically perform our studies in vitro, using purified components, which allows us to build up and control the environment. 

Together with the other Biophysics groups at Oxford, we are part of the Department of Physics. Our labs are housed in the newly built Dorothy Crowfoot Hodgins building, which houses the interdisciplinary Kavli Institute for Nanoscience Discovery and the Department of Biochemistry.

Our work

In our group, we aim at understanding the molecular processes that underlie DNA replication and virology, with the particular goal of gaining spatiotemporal insight into their dynamics. More concretely, we are interested in understanding how individual molecules interact in space and time, so as to jointly perform challenging tasks extremely efficiently and accurately.

Our approach combines the development and use of cutting-edge single-molecule biophysics tools (e.g. single-molecule fluorescence and single-molecule force spectroscopy such as optical and magnetic tweezers, or a combination of both), which allow us to visualize and track individual molecules, with in-house purification of key proteins and advanced biochemical assays. This integrative approach allows us to switch between rapid ensemble assays and focused single-molecule biophysics experiments that target questions regarding the dynamics of proteins.

While the primary aim of our research is to provide fundamental mechanistic insight into DNA replication and virology, also biomedically relevant clues can be obtained using our approaches. For instance, we can study how eukaryotic genomes deal with not only replication of the genome but also with the replication of epigenetic information, or how mutations in a viral genome are triggered by drug compounds.

JOB OPENINGS

We have two openings at present:

(1) for a postdoctoral fellow: the scientist will use in vitro biochemical reconstitutions to characterize the interaction between key players in chromatin assembly during DNA replication, and their activity, which are established in the Mattiroli Lab. In collaboration with the Dekker lab, the fellow will use single-molecule imaging to unravel the kinetic parameters of these mechanisms. Deadline: 14th March 2025. Preferred start date is 1st April 2025.

(2) for a senior scientist with experience in single-molecule biophysics and strong affinity with instrumentation. This is one of the core positions in our lab geared towards the longer term. You will lead the development of the next generation of instruments and experiments in single-molecule biological physics. Deadline: February 14th. Preferred start date is summer or fall of 2025.

 

Separately to this, Oxford Biophysics is recruiting new Fellows (assistant professors) with an application deadline of February 15th. See the description here.

Enquiries can be directed towards Prof. Nynke Dekker.

Find application links and read more here!