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A Molecular Ruler for Measuring Quantitative Distance Distributions

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  • Rebecca S Mathew-Fenn
  • Rhiju Das
  • Joshua A Silverman
  • Peter A Walker
  • Pehr A B Harbury

Abstract

We report a novel molecular ruler for measurement of distances and distance distributions with accurate external calibration. Using solution X-ray scattering we determine the scattering interference between two gold nanocrystal probes attached site-specifically to a macromolecule of interest. Fourier transformation of the interference pattern provides a model-independent probability distribution for the distances between the probe centers-of-mass. To test the approach, we measure end-to-end distances for a variety of DNA structures. We demonstrate that measurements with independently prepared samples and using different X-ray sources are highly reproducible, we demonstrate the quantitative accuracy of the first and second moments of the distance distributions, and we demonstrate that the technique recovers complex distribution shapes. Distances measured with the solution scattering-interference ruler match the corresponding crystallographic values, but differ from distances measured previously with alternate ruler techniques. The X-ray scattering interference ruler should be a powerful tool for relating crystal structures to solution structures and for studying molecular fluctuations.

Suggested Citation

  • Rebecca S Mathew-Fenn & Rhiju Das & Joshua A Silverman & Peter A Walker & Pehr A B Harbury, 2008. "A Molecular Ruler for Measuring Quantitative Distance Distributions," PLOS ONE, Public Library of Science, vol. 3(10), pages 1-9, October.
    • Handle: RePEc:plo:pone00:0003229
    DOI: 10.1371/journal.pone.0003229
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    References listed on IDEAS

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    1. Andrew P. Carter & William M. Clemons & Ditlev E. Brodersen & Robert J. Morgan-Warren & Brian T. Wimberly & V. Ramakrishnan, 2000. "Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics," Nature, Nature, vol. 407(6802), pages 340-348, September.
    2. Brian T. Wimberly & Ditlev E. Brodersen & William M. Clemons & Robert J. Morgan-Warren & Andrew P. Carter & Clemens Vonrhein & Thomas Hartsch & V. Ramakrishnan, 2000. "Structure of the 30S ribosomal subunit," Nature, Nature, vol. 407(6802), pages 327-339, September.
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