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- EMDB-67284: Octahedral Symmetry of DNA Tesseract -

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Basic information

Entry
Database: EMDB / ID: EMD-67284
TitleOctahedral Symmetry of DNA Tesseract
Map data
Sample
  • Complex: DNA tesseract nanostructure
KeywordsDNA Tesseract / DNA Nanostructure / DNA
Biological speciesNot Applicable (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.16 Å
AuthorsShiu SCC
Funding support Hong Kong, 3 items
OrganizationGrant numberCountry
Other government17125920 Hong Kong
Other government17125221
Other government17127124
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Acoustically seeded fabrication of a DNA tesseract into a conductive wire.
Authors: Simon Chi-Chin Shiu / Marcello DeLuca / Wai Hin Chui / Pingping Zhang / Xiaoyong Mo / Ryan Ho Ping Siu / Erqian Dong / Sichao Qu / Calvin Chun Long Cheung / Andrew B Kinghorn / William L ...Authors: Simon Chi-Chin Shiu / Marcello DeLuca / Wai Hin Chui / Pingping Zhang / Xiaoyong Mo / Ryan Ho Ping Siu / Erqian Dong / Sichao Qu / Calvin Chun Long Cheung / Andrew B Kinghorn / William L Whitehouse / Jingyu Cui / Weisi He / Xue-Yan Wang / Jiahui Li / Areebah Gul Khan / Sophie H von Torklus / Tsz Fai Yu / Khuloud T Al-Jamal / Edmund C M Tse / Gaurav Arya / Nicholas Xuanlai Fang / Keda Zhou / Julian A Tanner /
Abstract: Assembly of DNA nanostructures to sub-millimetre scales is expected to have significant potential for applications in materials science and medicine. One approach to control nanostructure growth is ...Assembly of DNA nanostructures to sub-millimetre scales is expected to have significant potential for applications in materials science and medicine. One approach to control nanostructure growth is through using acoustic waves to create pressure nodes for clustering. Here, we report a facet-based underlying DNA nanostructure architecture with structural and stability characteristics ideal for acoustic patterning. The architecture comprises only 16 canonical DNA oligonucleotides which self-assemble to form a nested cube, inspired by the four-dimensional hypercube known as a "tesseract." Cryogenic electron microscopy (Cryo-EM) and atomic force microscopy (AFM) analysis revealed a fully formed tesseract structure with exceptional stiffness and a melting temperature of 84°C, significantly higher than other unmodified DNA nanostructures. The DNA tesseract nanostructures could be acoustically shaped into wires spanning over 500 µm, observed after deposition onto an interdigitated electrode (IDE). The wires were shown to be electrically conductive, highlighting unique prospects for application. Simplified bottom-up assembly of a small number of oligonucleotides into a relatively complex and structurally stable DNA nanostructure with characteristics ideal for modular assembly holds promise for applications across bioelectronics and other fields.
History
DepositionNov 25, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_67284.png

Downloads & links

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Map

FileDownload / File: emd_67284.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 400 pix.
= 382.28 Å		0.96 Å/pix.
x 400 pix.
= 382.28 Å		0.96 Å/pix.
x 400 pix.
= 382.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9557 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0445
Minimum - Maximum-0.031839613 - 0.12441342
Average (Standard dev.)0.0007036248 (±0.008328172)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 382.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : DNA tesseract nanostructure

EntireName: DNA tesseract nanostructure
Components
  • Complex: DNA tesseract nanostructure

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Supramolecule #1: DNA tesseract nanostructure

SupramoleculeName: DNA tesseract nanostructure / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Not Applicable (fungus)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 14.16 Å / Resolution method: OTHER / Software - Name: cryoSPARC / Number images used: 4745
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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