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. 2013 Jul;183(1):95-8.
doi: 10.1016/j.jsb.2013.04.008. Epub 2013 Apr 30.

The Challenge of Determining Handedness in Electron Tomography and the Use of DNA Origami Gold Nanoparticle Helices as Molecular Standards

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The Challenge of Determining Handedness in Electron Tomography and the Use of DNA Origami Gold Nanoparticle Helices as Molecular Standards

Ariane Briegel et al. J Struct Biol. .
Free PMC article

Abstract

The apparent handedness of an EM-tomography reconstruction depends on a number of conventions and can be confused in many ways. As the number of different hardware and software combinations being used for electron tomography continue to climb, and the reconstructions being produced reach higher and higher resolutions, the need to verify the hand of the results has increased. Here we enumerate various steps in a typical tomography experiment that affect handedness and show that DNA origami gold nanoparticle helices can be used as convenient and fail-safe handedness standards.

Keywords: DNA origami; Electron tomography; Handedness.

Figures

Figure 1
Figure 1. Schematic of DNA origami gold nanoparticle helices
Left or right handed nanohelices (diameter 34 nm, helical pitch 57 nm) consist of nine gold nanoparticles (diameter 10 nm) that are attached to the surface of DNA origami bundles (diameter 16 nm). With permission from (Kuzyk et al., 2012).
Figure 2
Figure 2. DNA origami gold nanoparticle helices as molecular handedness standards
Left-handed DNA origami gold nanoparticle helices (one example in red box) were mixed together with colloidal gold and Escherichia coli lysates, plunge-frozen, and imaged tomographically. An isosurface representation of the DNA origami gold nanoparticle helix with the attached 9 gold particles (yellow) and the modeled helix (white) is shown in the insets on the left (produced with 3dmod). Rotating the helix around the “x” (horizontal) axis reveals that the correct handedness has been maintained throughout the process (particle 1 is in the foreground and 9 is in the background). Bar: 200 nm.
Figure 3
Figure 3. Additional example reconstructions of DNA origami gold nanoparticle helices in vitreous ice and negative stain
A, overview image of negatively stained, left handed helices. B, C: Slices through cryotomograms of left handed nanohelices frozen in vitreous ice. D, E: Slices through tomograms of left handed helices in negative stain imaged with 2 different magnifications. Scale Bars B–E: 50 nm. 3D models of the complete helices are shown below, with bright blue rods connecting particles in the foreground, dim blue rods connecting particles in the background.

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