PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons
E-Collection

Related Articles
Families in Gene Neighborhoods
June 2015
Expanding the Reach of SAD
April 2015
Greasing the Path for SFX
January 2015
Time-Resolved Crystallography with HATRX
December 2014
Structures Without Damage
August 2014
Error Prevention
July 2014
A Refined Refinement Strategy
May 2014
Membrane Proteome: Microcrystals Yield Big Data
April 2014
Optimizing Damage
February 2014
Getting Better at Low Resolution
January 2014
Building a Structural Library
November 2013
Drug Discovery: Identifying Dynamic Networks by CONTACT
October 2013
Microbiome: Solid-State NMR, Crystallized
September 2013
Fluorescence- and Chromatography-Based Protein Thermostability Assay
October 2012
Insert Here
October 2012
Native phasing
August 2012
Smaller may be better
April 2012
Metal mates
February 2012
Not so cool
December 2011
One from many
August 2011
Rosetta hone
July 2011
Solutions in the solution
June 2011
Beyond crystals, solutions, and powders
May 2011
Snapshot crystallography
March 2011
FERM-ly bound
February 2011
A new amphiphile for crystallizing membrane proteins
January 2011
'Super-resolution' large complexes
December 2010
Proteinase K and Digalacturonic Acid
September 2010
Some crystals like it hot
May 2010
Tips for crystallizing membrane proteins in lipidic mesophases
February 2010
Tackling the phase problem
November 2009
Crystallizing glycoproteins
September 2009
Crystals from recalcitrant proteins
August 2009
Tips for crystallizing membrane proteins
June 2009
Chaperone-assisted crystallography
March 2009
An “X-ray” ruler
January 2009
Methylation boosts protein crystallization
December 2008

Technology Topics Crystallography

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).

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health