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- EMDB-7214: Single-Molecule 3D Image of DNA Origami Bennett Linkage by Indivi... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7214 | |||||||||||||||
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Title | Single-Molecule 3D Image of DNA Origami Bennett Linkage by Individual Particle Electron Tomography (No. 018) | |||||||||||||||
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Biological species | ![]() | |||||||||||||||
Method | electron tomography / cryo EM / negative staining / Resolution: 89.2 Å | |||||||||||||||
![]() | Lei D / Marras A / Liu J / Huang C / Zhou L / Castro C / Su H / Ren G | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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- ...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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 24.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.7 KB 11.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.9 KB | Display | ![]() |
Images | ![]() | 27 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.5 KB | Display | ![]() |
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Full document | ![]() | 77.6 KB | Display | |
Data in XML | ![]() | 495 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7155C ![]() 7156C ![]() 7157C ![]() 7158C ![]() 7159C ![]() 7160C ![]() 7161C ![]() 7162C ![]() 7163C ![]() 7164C ![]() 7165C ![]() 7166C ![]() 7167C ![]() 7168C ![]() 7169C ![]() 7170C ![]() 7171C ![]() 7172C ![]() 7173C ![]() 7174C ![]() 7175C ![]() 7176C ![]() 7177C ![]() 7178C ![]() 7179C ![]() 7180C ![]() 7181C ![]() 7182C ![]() 7183C ![]() 7184C ![]() 7185C ![]() 7186C ![]() 7187C ![]() 7188C ![]() 7189C ![]() 7190C ![]() 7191C ![]() 7192C ![]() 7193C ![]() 7194C ![]() 7195C ![]() 7196C ![]() 7197C ![]() 7198C ![]() 7199C ![]() 7200C ![]() 7201C ![]() 7202C ![]() 7203C ![]() 7204C ![]() 7205C ![]() 7206C ![]() 7207C ![]() 7208C ![]() 7209C ![]() 7210C ![]() 7211C ![]() 7212C ![]() 7213C ![]() 7215C ![]() 7216C ![]() 7217C ![]() 7218C ![]() 7219C ![]() 7220C ![]() 7221C ![]() 7222C ![]() 7223C ![]() 7224C ![]() 7225C ![]() 7226C ![]() 7227C ![]() 7228C ![]() 7229C ![]() 7230C ![]() 7231C ![]() 7232C ![]() 7233C ![]() 7234C ![]() 7235C ![]() 7236C ![]() 7237C ![]() 7238C ![]() 7239C ![]() 7240C ![]() 7241C ![]() 7242C ![]() 7243C ![]() 7244C ![]() 7245C ![]() 7246C ![]() 7247C ![]() 7248C ![]() 7249C ![]() 7250C ![]() 7251C ![]() 7252C ![]() 7253C ![]() 7254C ![]() 7255C ![]() 7256C ![]() 7257C ![]() 7258C ![]() 7259C ![]() 7260C ![]() 7261C ![]() 7262C ![]() 7263C ![]() 7264C ![]() 7265C ![]() 7266C ![]() 7267C ![]() 7268C ![]() 7269C ![]() 7270C ![]() 7271C ![]() 7272C ![]() 7273C ![]() 7274C ![]() 7275C ![]() 7276C ![]() 7277C ![]() 7278C ![]() 7279C ![]() 7280C ![]() 7281C ![]() 7282C ![]() 7283C ![]() 7284C ![]() 7285C C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : DNA origami Bennett linkage
Entire | Name: DNA origami Bennett linkage |
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Components |
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-Supramolecule #1: DNA origami Bennett linkage
Supramolecule | Name: DNA origami Bennett linkage / type: complex / ID: 1 / Parent: 0 |
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-Supramolecule #2: M13 phage genome segment
Supramolecule | Name: M13 phage genome segment / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Supramolecule #3: Synthetic DNA oligonucleotides
Supramolecule | Name: Synthetic DNA oligonucleotides / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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![]() | electron tomography |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Details: Tris-Borate-EDTA (TBE) buffer containing 11 mM MgCl2 |
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Staining | Type: NEGATIVE / Material: Uranyl Formate Details: The grid was washed twice by 1% (w/v) uranyl formate |
Grid | Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP |
Details | DNA origami Bennett linkage was diluted to ~2 nM with Tris-Borate-EDTA (TBE) buffer containing 11 mM MgCl2 |
Sectioning | Other: NO SECTIONING |
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Electron microscopy
Microscope | ZEISS LIBRA120PLUS |
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Specialist optics | Energy filter - Name: In-column Omega Filter |
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 1.55 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |