Individual-Particle Electron Tomography: A Method for Monitoring the 3D Structure of Low-Dimensional DNA-Based Nanodevice

Abstract

DNA base-pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of the three-dimensional (3D) structure of the DNA-nanocrystal hybridized building blocks. Existing techniques do not allow for the structural determination of these flexible and heterogeneous samples. Here, we employed cryo-electron microscopy (cryo-EM) and negative-staining (NS) techniques to investigate the morphology of DNA-nanogold conjugates that were self-assembled from a mixture of an 84-base-pair double-stranded DNA (dsDNA) conjugated with two 5-nm nanogold particles for potential substrates in plasmon coupling experiments. Using NS electron tomography and the individual-particle electron tomography (IPET) reconstruction method, we obtained 3D reconstructed 14 electron density maps at a resolution of ~2 nm from each individual dsDNA-nanogold particle. Using these 3D density maps as constraints, we derived 14 conformations of dsDNA by projected a standard flexible dsDNA model onto the observed EM density maps using Molecular Dynamics (MD) simulations. The variation of the conformations was largely consistent with the variation from liquid solution. Moreover, the IPET approach provides the most complete experimental determination of the flexibility and fluctuation range of these directed nanocrystal assemblies to date. The general features revealed by these experiments can be expected to occur in a broad range of DNA-assembled nanostructures.