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

Journal Article · · Nature Communications
DOI:https://doi.org/10.1038/ncomms11083· OSTI ID:1379251
 [1];  [2];  [3];  [2];  [2];  [1];  [4];  [5];  [6];  [2]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Foundry; Xi'an Jiaotong Univ. (China). Dept. of Applied Physics
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Foundry
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Science Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry, Dept. of Materials Science
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Foundry; Xi'an Jiaotong Univ. (China). School of Life Science and Technology, Frontier Inst. of Science and Technology
  5. Xi'an Jiaotong Univ. (China). School of Life Science and Technology, Frontier Inst. of Science and Technology
  6. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Science Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry, Dept. of Materials Science, Kavli Energy NanoScience Inst.
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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.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF); National Institutes of Health (NIH)
Grant/Contract Number:
AC02-05CH11231; DMR-1344290; R01GM104427
OSTI ID:
1379251
Journal Information:
Nature Communications, Vol. 7; ISSN 2041-1723
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 31 works
Citation information provided by
Web of Science

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Cited By (13)

Designing Melittin‐Graphene Hybrid Complexes for Enhanced Antibacterial Activity journal March 2019
Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography journal February 2018
Active DNA unwinding and transport by a membrane-adapted helicase nanopore journal November 2019
Single-Molecule 3D Images of “Hole-Hole” IgG1 Homodimers by Individual-Particle Electron Tomography journal June 2019
Super tough magnetic hydrogels for remotely triggered shape morphing journal January 2018
Dynamic DNA nanotechnology: toward functional nanoscale devices journal January 2020
Bio-macromolecular dynamic structures and functions, illustrated with DNA, antibody, and lipoprotein journal February 2018
Gold nanocrystal labels provide a sequence–to–3D structure map in SAXS reconstructions journal May 2018
IgG Antibody 3D Structures and Dynamics journal April 2018
Assessing the mechanisms of cholesteryl ester transfer protein inhibitors journal December 2017
Intracellular localization of nanoparticle dimers by chirality reversal journal November 2017
An Algorithm for Enhancing the Image Contrast of Electron Tomography journal November 2018
Polyhedral 3D structure of human plasma very low density lipoproteins by individual particle cryo-electron tomography 1 journal August 2016

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36 MATERIALS SCIENCE
cryoelectron microscopy
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