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An “X-ray” ruler

PSI-SGKB [doi:10.1038/th_psisgkb.2008.23]
Technical Highlight - January 2009
Short description: X-ray scattering from gold-labelled, double-stranded DNA is a powerful technique for investigating nucleic acid structure.Science 322, 446-449 (2008)

Shown are DNA structures of normal geometry (center), and subject to compression (left) and extension (right), each by 10%. These images were generated using coordinates provided by R. Das (Stanford University).

In the past few years, traditional assumptions about how to model the flexibility of the DNA double helix have been thrown into doubt. But measuring structural fluctuations in the double helix has been incredibly challenging (See figure).

Now Matthew-Fenn et al. use a technique they recently developed to measure DNA length. They attached gold nanocrystals to the ends of DNA double helices ranging from 10 to 35 base pairs in length via a 3′ thiol linker. These nanocrystals are clusters of 75 gold atoms, and they are so electron dense they scatter X-rays very strongly.

Interference between the X-rays scattered from the DNA generates a scattering profile, which can then be Fourier transformed to give the mean distance between each cluster and a distribution showing the variation in center–center distances. This “X-ray ruler” gives an almost instantaneous distribution of distances.

This technique recorded an average rise per base pair that was very close to that of a standard B-form helix by X-ray crystallography. In addition, the width of the distribution indicated that a significant proportion of DNA molecules undergoes stretching, even without an external force applied. Surprisingly, in the absence of tension, this scattering technique shows that DNA is more pliable and more prone to stretch than when measured under tension using single-molecule, force-extension experiments.

The variation in distribution was quadratically related to helix length, which suggests that stretching is cooperative along the DNA. Such long-range stretching implies that DNA double helices transmit information over a least 20 base pairs through an allosteric change, which the authors term a “domino effect”.

This powerful technique will be useful for investigating nucleic acid structure more generally and will undoubtedly reveal more secrets of the double helix and other nucleic acid structures.

Maria Hodges

References

  1. Matthew-Fenn Rebecca S., Das Rhiju and Harbury Pehr A. B. Remeasuring the double helix.
    Science 322, 446-449 (2008).

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