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Yorodumi- EMDB-16221: Triple-stranded DNA as a structural element in DNA origami rod object -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16221 | |||||||||||||||
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Title | Triple-stranded DNA as a structural element in DNA origami rod object | |||||||||||||||
Map data | 10 helix bundle DNA origami object | |||||||||||||||
Sample |
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Keywords | DNA Origami / Triplex forming Oligo / Triplex / TFO / DNA | |||||||||||||||
Biological species | synthetic construct (others) / Phage M13mp18 (virus) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.27 Å | |||||||||||||||
Authors | Sachenbacher K / Khoshouei A / Honemann MN / Engelen W / Feigl E / Dietz H | |||||||||||||||
Funding support | European Union, Germany, Netherlands, 4 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16221.map.gz | 3.5 MB | EMDB map data format | |
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Header (meta data) | emd-16221-v30.xml emd-16221.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16221_fsc.xml | 7.1 KB | Display | FSC data file |
Images | emd_16221.png | 67.1 KB | ||
Others | emd_16221_half_map_1.map.gz emd_16221_half_map_2.map.gz | 23.4 MB 23.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16221 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16221 | HTTPS FTP |
-Validation report
Summary document | emd_16221_validation.pdf.gz | 601.7 KB | Display | EMDB validaton report |
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Full document | emd_16221_full_validation.pdf.gz | 601.2 KB | Display | |
Data in XML | emd_16221_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | emd_16221_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16221 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16221 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16221.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | 10 helix bundle DNA origami object | ||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: 10 helix bundle DNA origami object / half map 1
File | emd_16221_half_map_1.map | ||||||||||||
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Annotation | 10 helix bundle DNA origami object / half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 10 helix bundle DNA origami object / half map 2
File | emd_16221_half_map_2.map | ||||||||||||
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Annotation | 10 helix bundle DNA origami object / half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : DNA Nanostructure
Entire | Name: DNA Nanostructure |
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Components |
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-Supramolecule #1: DNA Nanostructure
Supramolecule | Name: DNA Nanostructure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: synthetic construct (others) |
-Supramolecule #2: Scaffold DNA single-strand
Supramolecule | Name: Scaffold DNA single-strand / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Phage M13mp18 (virus) |
-Supramolecule #3: staple oligonucleotides
Supramolecule | Name: staple oligonucleotides / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: synthetic construct (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 5 / Details: 5 mM MES, 5mM NaCl and 5 mM MgCl2 |
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |