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- EMDB-16213: Triple-stranded DNA as a structural element in DNA origami large ... -

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Basic information

Entry
Database: EMDB / ID: EMD-16213
TitleTriple-stranded DNA as a structural element in DNA origami large cuboid object
Map datalarge cuboid DNA origami object
Sample
  • Complex: DNA Nanostructure
    • Complex: Scaffold DNA single-strand
    • Complex: staple oligonucleotides
KeywordsDNA Origami / Triplex forming Oligo / Triplex / TFO / DNA / DNA nanotechnology
Biological speciessynthetic construct (others) / Phage M13mp18 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.31 Å
AuthorsSachenbacher K / Khoshouei A / Honemann MN / Engelen W / Feigl E / Dietz H
Funding supportEuropean Union, Germany, Netherlands, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)101018465European Union
German Research Foundation (DFG) Germany
Netherlands Organisation for Scientific Research (NWO)019.182EN.037 Netherlands
European Union (EU)899619European Union
CitationJournal: ACS Nano / Year: 2023
Title: Triple-Stranded DNA As a Structural Element in DNA Origami.
Authors: Ken Sachenbacher / Ali Khoshouei / Maximilian Nicolas Honemann / Wouter Engelen / Elija Feigl / Hendrik Dietz /
Abstract: Molecular self-assembly with DNA origami offers an attractive route to fabricate arbitrary three-dimensional nanostructures. In DNA origami, B-form double-helical DNA domains (dsDNA) are commonly ...Molecular self-assembly with DNA origami offers an attractive route to fabricate arbitrary three-dimensional nanostructures. In DNA origami, B-form double-helical DNA domains (dsDNA) are commonly linked with covalent phosphodiester strand crossovers to build up three-dimensional objects. To expand the palette of structural motifs in DNA origami, here we describe hybrid duplex-triplex DNA motifs as pH-dependent building blocks in DNA origami. We investigate design rules for incorporating triplex forming oligonucleotides and noncanonical duplex-triplex crossovers in multilayer DNA origami objects. We use single-particle cryoelectron microscopy to elucidate the structural basis of triplex domains and of duplex-triplex crossovers. We find that duplex-triplex crossovers can complement and fully replace the canonical duplex-duplex crossovers within DNA origami objects, for example, to increase the crossover density for potentially greater rigidity and reduced interhelical spacing, and to create connections at sites where conventional crossovers may be undesirable. We also show the pH-induced formation of a DNA origami object stabilized entirely by triplex-mediated strand crossovers.
History
DepositionNov 23, 2022-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateJun 7, 2023-
Current statusJun 7, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16213.png

Downloads & links

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Map

FileDownload / File: emd_16213.map.gz / Format: CCP4 / Size: 303.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlarge cuboid DNA origami object
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.00505
Minimum - Maximum-0.0061122025 - 0.026872862
Average (Standard dev.)0.00062034576 (±0.0023846233)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions430430430
Spacing430430430
CellA=B=C: 365.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: large cuboid DNA origami object / half map 1

Fileemd_16213_half_map_1.map
Annotationlarge cuboid DNA origami object / half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: large cuboid DNA origami object / half map 2

Fileemd_16213_half_map_2.map
Annotationlarge cuboid DNA origami object / half map 2
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 Nanostructure

EntireName: DNA Nanostructure
Components
  • Complex: DNA Nanostructure
    • Complex: Scaffold DNA single-strand
    • Complex: staple oligonucleotides

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Supramolecule #1: DNA Nanostructure

SupramoleculeName: DNA Nanostructure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)

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Supramolecule #2: Scaffold DNA single-strand

SupramoleculeName: Scaffold DNA single-strand / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Phage M13mp18 (virus)

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Supramolecule #3: staple oligonucleotides

SupramoleculeName: staple oligonucleotides / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
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 / Details: 5 mM Tris, 1 mM EDTA, 5 mM NaCl and 5 mM MgCl2
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: de-novo generated initial model
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 151581
FSC plot (resolution estimation)

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