DNA folded in compliant helix
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 from Cambridge.
DNA is compacted in a tight bead structure of connected protein packages. DNA and protein packged together form nucleosomes that in their turn fold into compact chromatin fibres. The big question is: if DNA is so compactly folded, how can enzymes access the DNA to enable gene expression? Leiden biophysicist John van Noort has resolved part of this question using magnetic tweezers: chromatin forms a flexible spiral that stretches by up to a third of its length following collisions with water molecules.
It was discovered thirty years ago that DNA is not loose in the cell nucleus, but folded in protein packages together with histones, proteins forming a nucleosome. The neighbouring nucleosomes attract one another and form fibres 30 nanometers in length. This we already knew. But what we did not know is how these structures are folded, and consequently how accessible the DNA is for enzymes.
Helix of nucleosomes
The nucleosomes are interspersed with bare pieces of DNA, which were always thought to be straight and rigid. Van Noort: ‘The traditional response to the question about the structure of chromatin is that if the DNA between the nucleosomes is rigid and straight, chromatin can do nothing other than form a kind of zigzag structure between two stacks. But we now know that this is not the case. The neighbouring nucleosomes are situated one on one, forming a stack, which subsequently folds into a helix. But for this to happen, the DNA between the nucleosomes has to be highly bent.
This is something that can't be seen with an electron microscope; the material is so tightly packed that you can't see through it; you can only see the outside. Van Noort: ‘What we did is to unravel the spiral using magnetic tweezers. We fix a small bead containing iron to one side of the molecule; the bead is 1000 times larger than the two nanometers of the DNA. On the other side we attach a microscope slide. You can't see DNA using an optical microscope, it's much too small, but you can see the bead. By pulling on the bead with a magnet, you also draw on the molecule. With an optical microscope you can determine the position of the bead to an accuracy of several nanometres. This way you can determine the length of the molecule.'
Gene expression due to weak spring
Van Noort: ‘We already knew that DNA is tightly compacted. How can an enzyme enter to free the DNA so that it can be read? What we have now discovered is that the spring is so weak that collisions with water molecules are sufficient to stretch it by almost a third. That's only possible because it is folded into a spiral.'
‘But what we have also learned from this experiment is that the nucleosomes stick to one another much more strongly than had been thought. And that's important because we know as a result that enzymes that have to free the DNA have to apply much more force than was realised. It sounds paradoxical: on the one hand there is the weak spiral, on the other the strongly adhering nucleosomes. But it is right; on the one hand DNA has to be well protected, but on the other hand it has to be capable of being read. We have identified a flexible structure which combines both characteristics.'
Mechanics of the genome
Biophysics is a relatively new field. Van Noort, who was awarded a Vidi subsidy by NWO in 2003, comments: 'We want to understand the mechanics of the genome. Ten years ago the first mechanical experiments were carried out on nucleosomes. A dozen or so articles have since appeared on this subject. But the force used in the experiments was so strong that the structure was destroyed, and it was only possible to measure the final steps in the unfolding. We work much more carefully, so that we can come much close to the natural course of affairs.'
The research groups from Leiden and Cambridge have recently been awarded a new subsidy by the Human Frontier Science Program to resolve the next step in the puzzle of the interaction between nucleosomes: the fact that the strong interaction can be modulated very easily by small chemical 'flags'. These changes are strongly correlated to the activity of genes.
‘Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber’,
Authors: Maarten Kruithof, Fan-Tso Chien, Andrew Routh, Colin Logie, Daniela Rhodes and John van Noort.
Advance Online Publication (AOP) on Nature Structural & Molecular Biology from Sunday 19 April, 19.00 hrs.
- Physics of Life Processes: Chromatin Dynamics
- Colliding protein beads reveal DNA (University Newsletter 2 February 2009)
(20 April 2009)