Scientists at the Osaka University in Japan have adapted cryo-electron microscopy(cryoEM) to view the 3D structure of a self-assembled DNA tetrahedron. The structure, which only has 20 base pair duplexes on a side, is the smallest self assembled 3D DNA configuration. The research team was able to use the cryoEM technique to differentiate between structurally very similar diastereomers of the compound, as portrayed in the image.
Michael Berger at Nanowerk reports:
According to the scientists, the resolution of cryoEM 3D image reconstruction can be increased by increasing the number of particle images to be averaged – a resolution better than 4 Å has already been reached by aligning and averaging about 10 000 particle images – but the achievable resolution is still dependent upon the particle size because the low contrast and low signal-to-noise ratio of raw cryoEM images make it difficult to select particles and accurately align raw images for averaging. This difficulty becomes extremely serious for particles smaller than a critical size of around 10 nm.
Naba and Turberfield explain that they "hypothesized that image noise in the solvent region surrounding the DNA tetrahedron molecule had lead to misclassification and misalignment of the particle images to some extent, resulting in the relatively poor resolution. We therefore applied a solvent flattening technique to reduce the noise in the solvent region and to improve the accuracy of image classification and alignment in the refinement cycle of single particle image analysis."
It turned out that the solvent flattening technique was very effective, possibly as a result of the presence of a large, solvent-filled space within the DNA tetrahedron as well as the significant noise reduction in the solvent region surrounding the particle and the resolution of the 3D density map was dramatically improved. The resolution of the 3D density map was dramatically improved to 12 Å – the helical twist of the DNA edges can now be seen clearly, and the exact positions of the B-DNA major grooves can be identified.
More from Nanowerk…
Abstract in Nano Letters: High-Resolution Structural Analysis of a DNA Nanostructure by cryoEM
Image: Comparison between the 3D density map and structural models of the two expected diastereomers. (a,b) Space-filling representation of atomic models of diastereomers with (a) the minor groove and (b) the major groove facing outward at the edge center. Arrows indicate the major grooves of the double helix, which are resolved in the density map. (c,d) Superposition of the model structures (a,b) and the density map obtained by cryoEM image reconstruction. Scale bar, 5 nm.