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- EMDB-26848: Geometrically programmed DNA origami colloid for self-assembly of... -

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Basic information

Entry
Database: EMDB / ID: EMD-26848
TitleGeometrically programmed DNA origami colloid for self-assembly of tubules: X-particle
Map dataDNA origami particle for tubule self-assembly
Sample
  • Complex: Geometrically programmed DNA origami colloid for self-assembly of tubules: X-particle
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 23.5 Å
AuthorsHayakawa D / Videbaek TE / Hall DM / Fang H / Sigl C / Feigl E / Dietz H / Fraden S / Hagan MF / Grason GM / Rogers WB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-2011846 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Geometrically programmed self-limited assembly of tubules using DNA origami colloids.
Authors: Daichi Hayakawa / Thomas E Videbaek / Douglas M Hall / Huang Fang / Christian Sigl / Elija Feigl / Hendrik Dietz / Seth Fraden / Michael F Hagan / Gregory M Grason / W Benjamin Rogers /
Abstract: Self-assembly is one of the most promising strategies for making functional materials at the nanoscale, yet new design principles for making self-limiting architectures, rather than spatially ...Self-assembly is one of the most promising strategies for making functional materials at the nanoscale, yet new design principles for making self-limiting architectures, rather than spatially unlimited periodic lattice structures, are needed. To address this challenge, we explore the tradeoffs between addressable assembly and self-closing assembly of a specific class of self-limiting structures: cylindrical tubules. We make triangular subunits using DNA origami that have specific, valence-limited interactions and designed binding angles, and we study their assembly into tubules that have a self-limited width that is much larger than the size of an individual subunit. In the simplest case, the tubules are assembled from a single component by geometrically programming the dihedral angles between neighboring subunits. We show that the tubules can reach many micrometers in length and that their average width can be prescribed through the dihedral angles. We find that there is a distribution in the width and the chirality of the tubules, which we rationalize by developing a model that considers the finite bending rigidity of the assembled structure as well as the mechanism of self-closure. Finally, we demonstrate that the distributions of tubules can be further sculpted by increasing the number of subunit species, thereby increasing the assembly complexity, and demonstrate that using two subunit species successfully reduces the number of available end states by half. These results help to shed light on the roles of assembly complexity and geometry in self-limited assembly and could be extended to other self-limiting architectures, such as shells, toroids, or triply periodic frameworks.
History
DepositionMay 4, 2022-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateNov 2, 2022-
Current statusNov 2, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26848.png

Downloads & links

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Map

FileDownload / File: emd_26848.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDNA origami particle for tubule self-assembly
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.87 Å/pix.
x 360 pix.
= 1033.2 Å		2.87 Å/pix.
x 360 pix.
= 1033.2 Å		2.87 Å/pix.
x 360 pix.
= 1033.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0194
Minimum - Maximum-0.02880955 - 0.107629195
Average (Standard dev.)0.00024291621 (±0.007924173)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 1033.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map (1) from Refine 3D (RELION)

Fileemd_26848_half_map_1.map
AnnotationHalf map (1) from Refine 3D (RELION)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map (2) from Refine 3D (RELION)

Fileemd_26848_half_map_2.map
AnnotationHalf map (2) from Refine 3D (RELION)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Geometrically programmed DNA origami colloid for self-assembly of...

EntireName: Geometrically programmed DNA origami colloid for self-assembly of tubules: X-particle
Components
  • Complex: Geometrically programmed DNA origami colloid for self-assembly of tubules: X-particle

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Supramolecule #1: Geometrically programmed DNA origami colloid for self-assembly of...

SupramoleculeName: Geometrically programmed DNA origami colloid for self-assembly of tubules: X-particle
type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: 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
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 4.0 sec. / Average electron dose: 31.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 150.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 39000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 23.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3075
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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