Promotor: Prof.dr. T. Schmidt, Co-Promotor: Dr. ir. S.J.T. van Noort

The studies presented in the work show the potential of the integrative use of biophysical data in defining the structural basis of protein interactions.

In human cells, a meter-long DNA is condensed inside a micrometer-sized cell nucleus. Simultaneously, the genetic code must remain accessible for its replication and transcription to functional proteins.

PhD defence

DNA carries various forms of information. Out of these forms of information the most well-known is classical genetic information.

The genetic information of all living organisms is contained in their DNA. Cells modify the degree of DNA compaction by epigenetics, which largely determines what genes are read out and which genes are transcriptionally silent.

The way DNA folds, largely determines which genes are read out. John van Noort and his group have quantified how easily rolled-up DNA parts stack. This costs less energy than previously assumed. Publication in Biophysical Journal.

Nature uses a special class of histone proteins, histone variants, to modulate the properties of chromatin at defined genomic locations.

Our DNA molecules are packaged by proteins in compact structures. The aim of this project is to understand how modern gene editing techniques nevertheless get access to their target in the DNA.

Theoretical physicist Helmut Schiessel receives an NWO Projectruimte grant of 390,000 euro. He will use this budget to hire a postdoc and a PhD student to continue his research on flexibility of double stranded DNA.

Promotor: Prof.dr. T. Schmidt, Co-promotor: Dr. ir. S. J.T. van Noort

How do you fit two meters of DNA in a tiny compartment and at the same time are able to access the right parts of it at the right times?

Single-celled organisms have stiffer DNA than multicellular lifeforms like humans and rice. Theoretical physicists managed to simulate the folding in full genomes for the first time to reach this conclusion. Publication in Biophysical Journal on February 7.

Leiden theoretical physicists have proven that not only the genetic information in DNA determines who we are, but also DNA’s mechanics. Helmut Schiessel and his group simulated many DNA sequences and found a correlation between mechanical cues and the way DNA is folded. Publication in PLoS One.

PhD defence

The CIGR comprises research groups from the Institute of Biology Leiden (IBL), the Leiden Institute of Chemistry (LIC), the Leiden Academic Centre for Drug Research (LACDR) and the Leiden Institue of Physics (LION).

PhD defence

Throughout all domains of life, from bacteria and archaea to eukaryotes, genomes adopt well-organized three-dimensional structures that can change in space and time to accommodate preferred transcriptional programs for environmental adaptation, the maintenance of cellular identity and differentiation…

In an Advance Online Publication biophysicist John van Noort and others show using magnetic tweezers that DNA is folded in compliant helices of chromatin. This allows enzymes access to the DNA needed for gene expression. Van Noort's research group made the discovery in close partnership with researchers…

Leiden physicist Maarten Kruithof has discovered how our DNA is infallibly able to fold itself and to unfold again. In his dissertation he demonstrates how DNA is folded in a single long, very flexible spiral.

With the aid of physics and a minuscule magnet, researchers have discovered a new structure of telomeric DNA. Telomeres are sometimes seen as the key to living longer. They protect genes from damage but get a bit shorter each time a cell divides. If they become too short, the cell dies. The new discovery…

Relevant publications of the CIGR participants.

The genomic DNA of every organism is organized and compacted in order to fit inside the cell. This is achieved by the joint action of numerous architectural proteins that aid in folding the genome. Genome folding is tightly interconnected with transcription, with genes in certain regions being silenced,…

A group of single-celled organisms organises its DNA in a similar way to higher organisms such as plants, animals, and fungi. However, the way packaged DNA is read out differs between the two related groups, Bram Henneman discovered. PhD defence on 5 December.

‘It's where disciplines intersect that the most exciting scientific questions arise.' This was the message given by John van Noort, Professor of Biophysics, in his inaugural lecture. His own research is at the interface between biology and physics. Inaugural lecture 23 April.

Lecture

Lecture

Below thesis archives will be moved shortly (work in progress) to the Leiden Repository. Once this is done, theses submitted by MI students (from 2008 onwards) can be accessed via the Repository and will be removed from this site.