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- EMDB-13888: Antigen-Triggered Logic-Gating of DNA Nanodevices: T=1 DNA origam... -

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Basic information

Entry
Database: EMDB / ID: EMD-13888
TitleAntigen-Triggered Logic-Gating of DNA Nanodevices: T=1 DNA origami shell with two antidigoxigenin antibodies
Map data
Sample
  • Complex: T=1 DNA origami shell with two antidigoxigenin antibodies
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 22.7 Å
AuthorsEngelen W / Sigl C / Kadletz K / Willner EM / Dietz H
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: J Am Chem Soc / Year: 2021
Title: Antigen-Triggered Logic-Gating of DNA Nanodevices.
Authors: Wouter Engelen / Christian Sigl / Karoline Kadletz / Elena M Willner / Hendrik Dietz /
Abstract: Synthetic nanoscale devices that reconfigure dynamically in response to physiological stimuli could offer new avenues for diagnostics and therapy. Here, we report a strategy for controlling the state ...Synthetic nanoscale devices that reconfigure dynamically in response to physiological stimuli could offer new avenues for diagnostics and therapy. Here, we report a strategy for controlling the state of DNA nanodevices based on sensing antigens with IgG antibodies. To this end, we use IgG antibodies as structural elements to kinetically trap reconfigurable DNA origami structures in metastable states. Addition of soluble antigens displace the IgGs from the objects and triggers reconfiguration. We demonstrate this mechanism by antigen-triggered disassembly of DNA origami shells for two different IgGs and their cognate antigens, and we determined the corresponding dose response curves. We also describe the logic-gated actuation of DNA objects with combinations of antigens, as demonstrated with AND-type shells that disassemble only when two different antigens are detected simultaneously. We apply our system for the antigen-triggered release of molecular payload as exemplified by the release of virus particles that we loaded into the DNA origami shells. We expect our approach to be applicable in many types of DNA nanostructures and with many other IgG-antigen combinations.
History
DepositionNov 19, 2021-
Header (metadata) releaseOct 26, 2022-
Map releaseOct 26, 2022-
UpdateOct 26, 2022-
Current statusOct 26, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13888.png

Downloads & links

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Map

FileDownload / File: emd_13888.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.9 Å/pix.
x 500 pix.
= 1450. Å		2.9 Å/pix.
x 500 pix.
= 1450. Å		2.9 Å/pix.
x 500 pix.
= 1450. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00274
Minimum - Maximum-0.0171881 - 0.07227314
Average (Standard dev.)0.0047037518 (±0.012607684)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 1450.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : T=1 DNA origami shell with two antidigoxigenin antibodies

EntireName: T=1 DNA origami shell with two antidigoxigenin antibodies
Components
  • Complex: T=1 DNA origami shell with two antidigoxigenin antibodies

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Supramolecule #1: T=1 DNA origami shell with two antidigoxigenin antibodies

SupramoleculeName: T=1 DNA origami shell with two antidigoxigenin antibodies
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: synthetic construct (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 22.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 629
Initial angle assignmentType: OTHER
Details: maximum a posteriori (MAP), Regularized Likelihood OptimizatioN (Relion)
Final angle assignmentType: OTHER
Details: maximum a posteriori (MAP), Regularized Likelihood OptimizatioN (Relion)
FSC plot (resolution estimation)

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