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- EMDB-49953: Dimerized subunit pair: modular DNA origami subunit with top = 3 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-49953
TitleDimerized subunit pair: modular DNA origami subunit with top = 3 poly-T, bottom = 3 poly-T overhangs
Map dataPrimary electron density map.
Sample
  • Complex: Modular DNA origami building block for self-assembly: dimer
KeywordsDNA origami / synthetic construct / DNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 39.45 Å
AuthorsVidebaek TE / Wei W-S / Rogers WB / Fraden S
Funding support United States, 4 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-2011846 United States
National Science Foundation (NSF, United States)CMMI-2323969 United States
National Science Foundation (NSF, United States)ACI-2138259 United States
National Science Foundation (NSF, United States)ACI-2138286 United States
CitationJournal: ACS Nano / Year: 2025
Title: Economical and Versatile Subunit Design Principles for Self-Assembled DNA Origami Structures.
Authors: Wei-Shao Wei / Thomas E Videbæk / Daichi Hayakawa / Rupam Saha / Juanita Pombo / Gaurav Arya / W Benjamin Rogers / Seth Fraden /
Abstract: We describe a modular design approach for creating versatile DNA origami subunits that can target diverse self-assembled structures. The subunit consists of a constant "core module" with variable ...We describe a modular design approach for creating versatile DNA origami subunits that can target diverse self-assembled structures. The subunit consists of a constant "core module" with variable "bond modules" and "angle modules" added to its exterior, controlling interaction specificity, strength, and structural geometry. The design features flexible joints between subunits, implemented by using single-stranded angle modules, whose mechanical properties and possible conformations are characterized by cryogenic electron microscopy and coarse-grained molecular modeling. We demonstrate the design's versatility through the assembly of structures with different Gaussian curvature, including sheets, spherical shells, and tubes. Our findings suggest that incorporating a judicious amount of flexibility in the bonds provides error tolerance in design and fabrication while maintaining target fidelity. Furthermore, off-target assemblies potentially introduced by flexibility can be counterbalanced by increasing the number of distinct bonds. This approach enables precise targeting of specific structural binding angles across a broad range of configurations by eliminating unfavorable interactions.
History
DepositionApr 1, 2025-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49953.png

Downloads & links

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Map

FileDownload / File: emd_49953.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary electron density map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.64 Å/pix.
x 280 pix.
= 1577.94 Å		5.64 Å/pix.
x 280 pix.
= 1577.94 Å		5.64 Å/pix.
x 280 pix.
= 1577.94 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.6355 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.07214408 - 0.26111013
Average (Standard dev.)0.00036756476 (±0.01788505)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 1577.94 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: First half map of the structure.

Fileemd_49953_half_map_1.map
AnnotationFirst half map of the structure.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Second half map of the structure.

Fileemd_49953_half_map_2.map
AnnotationSecond half map of the structure.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Modular DNA origami building block for self-assembly: dimer

EntireName: Modular DNA origami building block for self-assembly: dimer
Components
  • Complex: Modular DNA origami building block for self-assembly: dimer

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Supramolecule #1: Modular DNA origami building block for self-assembly: dimer

SupramoleculeName: Modular DNA origami building block for self-assembly: dimer
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes
Molecular weightTheoretical: 10 MDa

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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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 601 / Average exposure time: 4.5 sec. / Average electron dose: 29.0 e/Å2 / Details: Camera used is the Gatan OneView Camera (4k x 4k).
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 0.8 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2776
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 39.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 2734
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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