title: Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography.
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.
authors.affiliation: The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.|Department of Applied Physics, School of Science, Xi'an Jiaotong University, Xi'an 710049, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Dongsheng
authors.initials: D
authors.lastname: Lei
authors.affiliation: Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.|Department of Chemistry, University of California, Berkeley, California 94720, USA.|Department of Materials Science, University of California, Berkeley, California 94720, USA.
authors.forename: Jessica M
authors.initials: JM
authors.lastname: Smith
authors.affiliation: The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Meng
authors.initials: M
authors.lastname: Zhang
authors.affiliation: The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Huimin
authors.initials: H
authors.lastname: Tong
authors.affiliation: The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.|Department of Applied Physics, School of Science, Xi'an Jiaotong University, Xi'an 710049, China.
authors.forename: Xing
authors.initials: X
authors.lastname: Zhang
authors.affiliation: The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.|Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, China.|School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.|Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
authors.forename: Zhuoyang
authors.initials: Z
authors.lastname: Lu
authors.affiliation: Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, China.|School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.|Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
authors.forename: Jiankang
authors.initials: J
authors.lastname: Liu
authors.affiliation: Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.|Department of Chemistry, University of California, Berkeley, California 94720, USA.|Department of Materials Science, University of California, Berkeley, California 94720, USA.|Kavli Energy NanoScience Institute, University of California, Berkeley, California 94720, USA.
authors.forename: A Paul
authors.initials: AP
authors.lastname: Alivisatos
authors.affiliation: The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Gang
authors.initials: G
authors.lastname: Ren
mesh_terms: D020285:Cryoelectron Microscopy; D004247:DNA / Q000737:chemistry*; D055032:Electron Microscope Tomography / Q000379:methods*; D006046:Gold / Q000737:chemistry*; D021621:Imaging, Three-Dimensional; D053758:Nanoparticles / Q000737:chemistry* / Q000648:ultrastructure; D016624:Negative Staining; D013816:Thermodynamics
chemical_list: D006046:Gold; D004247:DNA