Three Dimensional Dynamics and Fluctuations of DNA-Nanogold Dimers by Individual-Particle Electron Tomography

Abstract

Organic-inorganic hybridized nanocrystals have been proven as an important additional tool for addressing many emerging challenges biological and material sciences. Nanogold and quantum dot conjugates have been used extensively as biomolecular markers, while DNA base pairing has directed the self-assembly of discrete groupings and arrays of organic and inorganic nanocrystals in formation of a network solid for electronic devices and memory components. The control of DNA-mediated assembly depends crucially upon the ability to exposure three-dimensional (3D) structure of DNA-nanocrystals hybridized building blocks. Current techniques limit in structure determination of flexible and heterogeneous sample. Here, we employed the electron tomography and negative-staining techniques to investigate the 3D structure of DNA-nanogold dimers that were self-assembled from a mixture of an 84-base-pair double-stranded DNA (dsDNA) conjugated with two 5-nm nanogold particles. We reconstructed a total of 14 electron density maps at a resolution of ∼2 nm from each individual dsDNA-nanogold particle using the individual-particle electron tomography (IPET) reconstruction method. Using these 3D density maps as constrain, we projected a standard flexible DNA model onto the observed EM density maps and derived 14 conformations of dsDNA by molecular dynamics simulations. By aligning these structures from one distal end nanogold, the distribution showed the DNA fluctuation and flexibility between nanogolds, which providing a blueprint research for studying of DNA-mediated assembly of complex inorganic nanostructures.