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- EMDB-43592: PDI-containing spoke of a hexagonal wireframe DNA origami -

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Basic information

Entry
Database: EMDB / ID: EMD-43592
TitlePDI-containing spoke of a hexagonal wireframe DNA origami
Map dataEM map of PDI-containing spoke
Sample
  • Complex: PDI-containing DNA origami spoke
KeywordsDNA origami / DNA
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.8 Å
AuthorsHarris D / Parsons MF / Gorman J / Schlau-Cohen GS / Bathe M
Funding support United States, 6 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0019998 United States
Office of Naval Research (ONR)N00014-17-1-2609 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)P30-ES002109 United States
National Science Foundation (NSF, United States)CMMI-2240309 United States
Office of Naval Research (ONR)N00014-19-1-2344 United States
National Science Foundation (NSF, United States)NSF CCF-1956054 United States
CitationJournal: Chem / Year: 2024
Title: Sculpting photoproducts with DNA origami.
Authors: Jeffrey Gorman / Stephanie M Hart / Torsten John / Maria A Castellanos / Dvir Harris / Molly F Parsons / James L Banal / Adam P Willard / Gabriela S Schlau-Cohen / Mark Bathe /
Abstract: Natural light-harvesting systems spatially organize densely packed dyes in different configurations to either transport excitons or convert them into charge photoproducts, with high efficiency. In ...Natural light-harvesting systems spatially organize densely packed dyes in different configurations to either transport excitons or convert them into charge photoproducts, with high efficiency. In contrast, artificial photosystems like organic solar cells and light-emitting diodes lack this fine structural control, limiting their efficiency. Thus, biomimetic multi-dye systems are needed to organize dyes with the sub-nanometer spatial control required to sculpt resulting photoproducts. Here, we synthesize 11 distinct perylene diimide (PDI) dimers integrated into DNA origami nanostructures and identify dimer architectures that offer discrete control over exciton transport versus charge separation. The large structural-space and site-tunability of origami uniquely provides controlled PDI dimer packing to form distinct excimer photoproducts, which are sensitive to interdye configurations. In the future, this platform enables large-scale programmed assembly of dyes mimicking natural systems to sculpt distinct photophysical products needed for a broad range of optoelectronic devices, including solar energy converters and quantum information processors.
History
DepositionFeb 1, 2024-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43592.png

Downloads & links

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Map

FileDownload / File: emd_43592.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of PDI-containing spoke
Voxel sizeX=Y=Z: 4.34 Å
Density
Contour LevelBy AUTHOR: 1.62
Minimum - Maximum-0.79534775 - 9.290075
Average (Standard dev.)0.006367579 (±0.087393135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 1388.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half A EM map of PDI-containing spoke

Fileemd_43592_half_map_1.map
AnnotationHalf A EM map of PDI-containing spoke
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B EM map of PDI-containing spoke

Fileemd_43592_half_map_2.map
AnnotationHalf B EM map of PDI-containing spoke
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PDI-containing DNA origami spoke

EntireName: PDI-containing DNA origami spoke
Components
  • Complex: PDI-containing DNA origami spoke

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Supramolecule #1: PDI-containing DNA origami spoke

SupramoleculeName: PDI-containing DNA origami spoke / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli) / Strain: M13

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -2.0 µm / Nominal defocus min: -0.25 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 13.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5686
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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