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- EMDB-17606: DNA-origami turbine with right-handed chirality -

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Basic information

Entry
Database: EMDB / ID: EMD-17606
TitleDNA-origami turbine with right-handed chirality
Map dataDNA-origami turbine with right-handed chirality
Sample
  • Complex: DNA Origami
    • Complex: scaffold DNA single strand
    • Complex: staple oligonucleotides
KeywordsDNA-origami / DNA nanoturbine / nanorobotics / nanomachine / rotary motor / hydrodynamic flows / DNA
Biological speciesInovirus M13 / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
AuthorsShi X / Pumm A-K / Maffeo C / Kohler F / Feigl E / Zhao W / Verschueren D / Golestanian R / Aksimentiev A / Dietz H / Dekker C
Funding supportEuropean Union, Netherlands, Germany, United States, 7 items
OrganizationGrant numberCountry
European Research Council (ERC)883684European Union
Netherlands Organisation for Scientific Research (NWO)BaSyC Netherlands
Other governmentNanoFront Netherlands
European Research Council (ERC)724261European Union
German Research Foundation (DFG)Gottfried-Wilhelm-Leibniz Program Germany
German Research Foundation (DFG)SFB863 111166240 TPA9 Germany
National Science Foundation (NSF, United States)DMR-1827346 United States
CitationJournal: Nat Nanotechnol / Year: 2024
Title: A DNA turbine powered by a transmembrane potential across a nanopore.
Authors: Xin Shi / Anna-Katharina Pumm / Christopher Maffeo / Fabian Kohler / Elija Feigl / Wenxuan Zhao / Daniel Verschueren / Ramin Golestanian / Aleksei Aksimentiev / Hendrik Dietz / Cees Dekker /
Abstract: Rotary motors play key roles in energy transduction, from macroscale windmills to nanoscale turbines such as ATP synthase in cells. Despite our abilities to construct engines at many scales, ...Rotary motors play key roles in energy transduction, from macroscale windmills to nanoscale turbines such as ATP synthase in cells. Despite our abilities to construct engines at many scales, developing functional synthetic turbines at the nanoscale has remained challenging. Here, we experimentally demonstrate rationally designed nanoscale DNA origami turbines with three chiral blades. These DNA nanoturbines are 24-27 nm in height and diameter and can utilize transmembrane electrochemical potentials across nanopores to drive DNA bundles into sustained unidirectional rotations of up to 10 revolutions s. The rotation direction is set by the designed chirality of the turbine. All-atom molecular dynamics simulations show how hydrodynamic flows drive this turbine. At high salt concentrations, the rotation direction of turbines with the same chirality is reversed, which is explained by a change in the anisotropy of the electrophoretic mobility. Our artificial turbines operate autonomously in physiological conditions, converting energy from naturally abundant electrochemical potentials into mechanical work. The results open new possibilities for engineering active robotics at the nanoscale.
History
DepositionJun 12, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17606.png

Downloads & links

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Map

FileDownload / File: emd_17606.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDNA-origami turbine with right-handed chirality
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.28 Å/pix.
x 400 pix.
= 912. Å		2.28 Å/pix.
x 400 pix.
= 912. Å		2.28 Å/pix.
x 400 pix.
= 912. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.28 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.046
Minimum - Maximum-0.02980631 - 0.15295106
Average (Standard dev.)0.00029922748 (±0.004409884)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 912.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: DNA-origami turbine with right-handed chirality unfiltered half map 2

Fileemd_17606_half_map_1.map
AnnotationDNA-origami turbine with right-handed chirality unfiltered half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: DNA-origami turbine with right-handed chirality unfiltered half map 1

Fileemd_17606_half_map_2.map
AnnotationDNA-origami turbine with right-handed chirality unfiltered half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DNA Origami

EntireName: DNA Origami
Components
  • Complex: DNA Origami
    • Complex: scaffold DNA single strand
    • Complex: staple oligonucleotides

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Supramolecule #1: DNA Origami

SupramoleculeName: DNA Origami / type: complex / ID: 1 / Parent: 0

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Supramolecule #2: scaffold DNA single strand

SupramoleculeName: scaffold DNA single strand / type: complex / ID: 2 / Parent: 1 / Details: m13mp18-derived, 8064 bases
Source (natural)Organism: Inovirus M13

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Supramolecule #3: staple oligonucleotides

SupramoleculeName: staple oligonucleotides / type: complex / ID: 3 / Parent: 1 / Details: chemically synthesized
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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: NONE / Details: De novo 3D Initial Model created in Relion
Final reconstructionApplied symmetry - Point group: C10 (10 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0beta) / Number images used: 97054
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0beta) / Details: Regularized Likelihood Optimization (Relion)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0beta) / Details: Regularized Likelihood Optimization (Relion)
FSC plot (resolution estimation)

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