EMDB-7186: Single-Molecule 3D Image of DNA Origami Bennett Linkage by Indivi...

Basic information

• Entry: Database: EMDB / ID: EMD-7186
• Title: Single-Molecule 3D Image of DNA Origami Bennett Linkage by Individual Particle Electron Tomography (No. 129)
• Map data: primary map

Sample

• Complex: DNA origami Bennett linkage
  • Complex: M13 phage genome segment
  • Complex: Synthetic DNA oligonucleotides

• Biological species: Escherichia virus M13 / synthetic construct (others)
• Method: electron tomography / cryo EM / negative staining / Resolution: 84.8 Å
• Authors: Lei D / Marras A / Liu J / Huang C / Zhou L / Castro C / Su H / Ren G

Funding support

United States, 4 items

Organization	Grant number	Country
National Science Foundation (NSF, United States)	DMR-1344290	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01GM104427	United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	R01HL115153	United States
Department of Energy (DOE, United States)	DE-AC02-05CH11231	United States

• Citation: Journal: Nat Commun / Year: 2018; Title: Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography.; Authors: Dongsheng Lei / Alexander E Marras / Jianfang Liu / Chao-Min Huang / Lifeng Zhou / Carlos E Castro / Hai-Jun Su / Gang Ren / ; Abstract: Scaffolded DNA origami has proven to be a powerful and efficient technique to fabricate functional nanomachines by programming the folding of a single-stranded DNA template strand into three-dimensional (3D) nanostructures, designed to be precisely motion-controlled. Although two-dimensional (2D) imaging of DNA nanomachines using transmission electron microscopy and atomic force microscopy suggested these nanomachines are dynamic in 3D, geometric analysis based on 2D imaging was insufficient to uncover the exact motion in 3D. Here we use the individual-particle electron tomography method and reconstruct 129 density maps from 129 individual DNA origami Bennett linkage mechanisms at ~ 6-14 nm resolution. The statistical analyses of these conformations lead to understanding the 3D structural dynamics of Bennett linkage mechanisms. Moreover, our effort provides experimental verification of a theoretical kinematics model of DNA origami, which can be used as feedback to improve the design and control of motion via optimized DNA sequences and routing.

History

Deposition	Dec 6, 2017	-
Header (metadata) release	Feb 7, 2018	-
Map release	Feb 21, 2018	-
Update	Dec 25, 2019	-
Current status	Dec 25, 2019	Processing site: RCSB / Status: Released