Journal of Proteomics & Bioinformatics
Open Access
ISSN: 0974-276X
+44 1223 790975
ISSN: 0974-276X
+44 1223 790975
Lei Zhang, Dongsheng Lei, Jessica M Smith, Huimin Tong, Xing Zhang, Zhuoyang Lu, Paul Alivisatos and Gang Ren
Xi��?an Jiao tong University, China
The Molecular Foundry, USA
Lawrence Berkeley National Laboratory, USA
University of California, USA
Posters & Accepted Abstracts: J Proteomics Bioinform
DNA base-pairing has been used for many years to direct the arrangement of inorganic nano-crystals 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 electron tomography and negative-staining techniques to investigate the 3D structure 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. We reconstructed 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 a constraint, we projected a standard flexible DNA model onto the observed EM density maps and derived 14 conformations of dsDNA by molecular dynamics simulations. The variation of the conformations was consistent with the variation from liquid solution, but 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.
Email: zhangleio@mail.xjtu.edu.cn