Research: Hopping DNA supercoils

Artistic impression of the dynamics of DNA supercoils. A person manipulates a long DNA molecule. Loops in the DNA molecule are created by winding up the DNA. For the first time ever, the research by Van Loenhout, Grunt and Dekker revealed how these DNA loops dynamically move along the DNA strand.

If you take hold of a DNA molecule and twist it, this creates 'supercoils', which are a bit like those annoying loops and twists you get in earphone cables. Research carried out by TU Delft, The Netherlands, has found that in the DNA molecule these coils can make their way surprisingly quickly along the length of the DNA. This newly discovered 'hopping' mechanism - which takes places in a matter of milliseconds - could have important biological implications, because cells use the coils to bring specific pieces of DNA into contact with one another. The researchers from Cees Dekker's group at the Kavli Institute of Nanoscience in Delft will be publishing their results in Science this week.

Supercoiling

A DNA molecule in a cell is not simply a loose wire; it is completely wound up in a tangle of loops ('DNA supercoils'). These supercoils in a DNA molecule (see the illustration on the right) are similar to those annoying loops and twists you often get in earphone cables.

In living cells, the DNA supercoils form and unravel and move along the DNA molecule. They are vital to the regulation of DNA activity, in determining which genes are switched on or off for example. One of the ways in which cells use the supercoils is to bring pieces of DNA into contact with one another.

Dynamic

Static images of the DNA supercoils have been studied in detail in the past, but their dynamics remained unknown up till now. PhD student Marijn van Loenhout from the Kavli Institute of Nanoscience at Delft developed a new technique that enabled him to observe how the coils travel along a DNA molecule for the first time. The research was led by Professor Cees Dekker, head of the Bionanoscience Department.

The TU Delft team used magnetic tweezers to stretch out a small section of a DNA molecule and were then able to observe the movement of the DNA coils using fluorescence microscopy (see movies at the website). They succeeded in showing these movements in real time, at the level of the individual DNA molecule.

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Van Loenhout: "We have discovered that the coils can move slowly along the DNA via diffusion. But what we also saw - and this was totally unexpected - that they can 'hop' along relatively long distances (micrometres). In such a movement a loop disappears in one spot, while simultaneously another loop appears in another spot, much further away. This information enables us to test theories about the mechanics of DNA, testing how you tie a knot in DNA, as it were."

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Research: Hopping DNA supercoils