A molecular ruler for measuring quantitative distance distributions

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. Fourie...

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Bibliographic Details
Published in:PloS one 2008-10, Vol.3 (10), p.e3229-e3229
Main Authors: Mathew-Fenn, Rebecca S, Das, Rhiju, Silverman, Joshua A, Walker, Peter A, Harbury, Pehr A B
Format: Article
Language:English
Subjects:
Absorptiometry, Photon
Adenosine
Analysis
Aqueous solutions
Biochemistry
Biochemistry/Bioinorganic Chemistry
Biochemistry/Experimental Biophysical Methods
Biophysics
Biophysics/Experimental Biophysical Methods
Biophysics/RNA Structure
Biopolymers
Chemistry/Biochemistry
Circular Dichroism
Crystal structure
Crystallography
Deoxyribonucleic acid
DNA
DNA - chemistry
DNA probes
Entropy
Fourier transforms
Gold
Interference
Ligands
Measurement
Models, Molecular
Nanoparticles - chemistry
Nucleic Acid Conformation
Oligonucleotides - chemistry
Probability distribution
Probability distributions
Proteins
Scattering, Small Angle
Shape recognition
Temperature
X ray scattering
X ray sources
X-Rays
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0003229