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

Lei Zhang, Dongsheng Lei, Jessica M. Smith, Meng Zhang, Huimin Tong, Xing Zhang, Zhuoyang Lu, Jiankang Liu, A. Paul Alivisatos and Gang Ren ()
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Lei Zhang: The Molecular Foundry, Lawrence Berkeley National Laboratory
Dongsheng Lei: The Molecular Foundry, Lawrence Berkeley National Laboratory
Jessica M. Smith: Lawrence Berkeley National Laboratory
Meng Zhang: The Molecular Foundry, Lawrence Berkeley National Laboratory
Huimin Tong: The Molecular Foundry, Lawrence Berkeley National Laboratory
Xing Zhang: The Molecular Foundry, Lawrence Berkeley National Laboratory
Zhuoyang Lu: The Molecular Foundry, Lawrence Berkeley National Laboratory
Jiankang Liu: Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Xi’an Jiaotong University
A. Paul Alivisatos: Lawrence Berkeley National Laboratory
Gang Ren: The Molecular Foundry, Lawrence Berkeley National Laboratory

Nature Communications, 2016, vol. 7, issue 1, 1-10

Abstract: 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 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.

Date: 2016
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DOI: 10.1038/ncomms11083

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