Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography

• Published in: Nature communications 2016-03, Vol.7 (1), p.11083-11083, Article 11083
• Main Authors: Zhang, Lei, Lei, Dongsheng, Smith, Jessica M., Zhang, Meng, Tong, Huimin, Zhang, Xing, Lu, Zhuoyang, Liu, Jiankang, Alivisatos, A. Paul, Ren, Gang
• Format: Article
• Language: English
• Subjects: 101/28; 38/47; 639/301/930/328/1259; 639/638/45/535/1258; 639/925/350/354; 82; Cryoelectron Microscopy; DNA - chemistry; Electron Microscope Tomography - methods; electron microscopy; Gold - chemistry; Humanities and Social Sciences; Imaging, Three-Dimensional; MATERIALS SCIENCE; multidisciplinary; nanoparticles; Nanoparticles - chemistry; Nanoparticles - ultrastructure; Negative Staining; Science; Science (multidisciplinary); Thermodynamics
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms11083

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 three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtain 14 density maps at ∼2-nm resolution. Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics. The control of DNA-mediated assembly depends on a precise understanding of the three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Here, the authors use cryo-electron microscopy and negative-staining techniques to investigate the morphology of DNA-nanogold conjugates.