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

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.
Authors:
 [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.
Publication Date:
Grant/Contract Number:
AC02-05CH11231; DMR-1344290; R01GM104427
Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); National Science Foundation (NSF); National Institutes of Health (NIH)
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; cryoelectron microscopy; electron microscopy; nanoparticles
OSTI Identifier:
1379251

Zhang, Lei, Lei, Dongsheng, Smith, Jessica M., Zhang, Meng, Tong, Huimin, Zhang, Xing, Lu, Zhuoyang, Liu, Jiankang, Alivisatos, A. Paul, and Ren, Gang. Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography. United States: N. p., Web. doi:10.1038/ncomms11083.
Zhang, Lei, Lei, Dongsheng, Smith, Jessica M., Zhang, Meng, Tong, Huimin, Zhang, Xing, Lu, Zhuoyang, Liu, Jiankang, Alivisatos, A. Paul, & Ren, Gang. Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography. United States. doi:10.1038/ncomms11083.
Zhang, Lei, Lei, Dongsheng, Smith, Jessica M., Zhang, Meng, Tong, Huimin, Zhang, Xing, Lu, Zhuoyang, Liu, Jiankang, Alivisatos, A. Paul, and Ren, Gang. 2016. "Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography". United States. doi:10.1038/ncomms11083. https://www.osti.gov/servlets/purl/1379251.
@article{osti_1379251,
title = {Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography},
author = {Zhang, Lei and Lei, Dongsheng and Smith, Jessica M. and Zhang, Meng and Tong, Huimin and Zhang, Xing and Lu, Zhuoyang and Liu, Jiankang and Alivisatos, A. Paul and Ren, Gang},
abstractNote = {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.},
doi = {10.1038/ncomms11083},
journal = {Nature Communications},
number = ,
volume = 7,
place = {United States},
year = {2016},
month = {3}
}