+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3408 | |||||||||
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Title | cryo-EM of nanoscale DNA assemblies | |||||||||
Map data | Reconstruction of DNA tetrahedron, 63-bp edge length | |||||||||
Sample |
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Keywords | Scaffolded DNA origami | |||||||||
Biological species | Enterobacteria phage M13 (virus) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 22.0 Å | |||||||||
Authors | Zhang K / Chiu W / Veneziano R / Ratanalert S / Zhang F / Yan H / Bathe M | |||||||||
Citation | Journal: Science / Year: 2016 Title: Designer nanoscale DNA assemblies programmed from the top down. Authors: Rémi Veneziano / Sakul Ratanalert / Kaiming Zhang / Fei Zhang / Hao Yan / Wah Chiu / Mark Bathe / Abstract: Scaffolded DNA origami is a versatile means of synthesizing complex molecular architectures. However, the approach is limited by the need to forward-design specific Watson-Crick base pairing manually ...Scaffolded DNA origami is a versatile means of synthesizing complex molecular architectures. However, the approach is limited by the need to forward-design specific Watson-Crick base pairing manually for any given target structure. Here, we report a general, top-down strategy to design nearly arbitrary DNA architectures autonomously based only on target shape. Objects are represented as closed surfaces rendered as polyhedral networks of parallel DNA duplexes, which enables complete DNA scaffold routing with a spanning tree algorithm. The asymmetric polymerase chain reaction is applied to produce stable, monodisperse assemblies with custom scaffold length and sequence that are verified structurally in three dimensions to be high fidelity by single-particle cryo-electron microscopy. Their long-term stability in serum and low-salt buffer confirms their utility for biological as well as nonbiological applications. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3408.map.gz | 36.7 MB | EMDB map data format | |
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Header (meta data) | emd-3408-v30.xml emd-3408.xml | 11.5 KB 11.5 KB | Display Display | EMDB header |
Images | EMD-3408.png | 138.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3408 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3408 | HTTPS FTP |
-Validation report
Summary document | emd_3408_validation.pdf.gz | 195 KB | Display | EMDB validaton report |
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Full document | emd_3408_full_validation.pdf.gz | 194.1 KB | Display | |
Data in XML | emd_3408_validation.xml.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3408 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3408 | HTTPS FTP |
-Related structure data
Related structure data | 3409C 3410C 3411C 3412C 3413C C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10066 (Title: Designer nanoscale DNA assemblies programmed from the top down Data size: 3.7 / Data #1: DNA tetrahedron [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3408.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of DNA tetrahedron, 63-bp edge length | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.51 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : DNA tetrahedron, 52-bp edge length
Entire | Name: DNA tetrahedron, 52-bp edge length |
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Components |
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-Supramolecule #1000: DNA tetrahedron, 52-bp edge length
Supramolecule | Name: DNA tetrahedron, 52-bp edge length / type: sample / ID: 1000 Details: Monodisperse and pure sample were prepared by overnight folding reaction and purified using centrifugal filter (MWCO 100KDa) Oligomeric state: monomer / Number unique components: 2 |
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Molecular weight | Experimental: 560 KDa / Theoretical: 560 KDa / Method: Calculation |
-Macromolecule #1: M13mp18 phage genome segment
Macromolecule | Name: M13mp18 phage genome segment / type: dna / ID: 1 / Name.synonym: Scaffold strand / Details: amplified using assymetric PCR / Classification: DNA / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: Enterobacteria phage M13 (virus) / Strain: M13mp18 / synonym: M13 phage |
Molecular weight | Experimental: 310 KDa / Theoretical: 310 KDa |
Sequence | String: GTCTCGCTGG TGAAAAGAAA AACCACCCTG GCGCCCAATA CGCAAACCGC CTCTCCCCGC GCGTTGGCCG ATTCATTAAT GCAGCTGGCA CGACAGGTTT CCCGACTGGA AAGCGGGCAG TGAGCGCAAC GCAATTAATG TGAGTTAGCT CACTCATTAG GCACCCCAGG ...String: GTCTCGCTGG TGAAAAGAAA AACCACCCTG GCGCCCAATA CGCAAACCGC CTCTCCCCGC GCGTTGGCCG ATTCATTAAT GCAGCTGGCA CGACAGGTTT CCCGACTGGA AAGCGGGCAG TGAGCGCAAC GCAATTAATG TGAGTTAGCT CACTCATTAG GCACCCCAGG CTTTACACTT TATGCTTCCG GCTCGTATGT TGTGTGGAAT TGTGAGCGGA TAACAATTTC ACACAGGAAA CAGCTATGAC CATGATTACG AATTCGAGCT CGGTACCCGG GGATCCTCTA GAGTCGACCT GCAGGCATGC AAGCTTGGCA CTGGCCGTCG TTTTACAACG TCGTGACTGG GAAAACCCTG GCGTTACCCA ACTTAATCGC CTTGCAGCAC ATCCCCCTTT CGCCAGCTGG CGTAATAGCG AAGAGGCCCG CACCGATCGC CCTTCCCAAC AGTTGCGCAG CCTGAATGGC GAATGGCGCT TTGCCTGGTT TCCGGCACCA GAAGCGGTGC CGGAAAGCTG GCTGGAGTGC GATCTTCCTG AGGCCGATAC GGTCGTCGTC CCCTCAAACT GGCAGATGCA CGGTTACGAT GCGCCCATCT ACACCAACGT AACCTATCCC ATTACGGTCA ATCCGCCGTT TGTTCCCACG GAGAATCCGA CGGGTTGTTA CTCGCTCACA TTTAATGTTG ATGAAAGCTG GCTACAGGAA GGCCAGACGC GAATTATTTT TGATGGCGTT CCTATTGGTT AAAAAATGAG CTGATTTAAC AAAAATTTAA CGCGAATTTT AACAAAATAT TAACGTTTAC AATTTAAATA TTTGCTTATA CAATCTTCCT GTTTTTGGGG CTTTTCTGAT TATCAACCGG GGTACATATG ATTGACATGC TAGTTTTACG ATTACCGTTC ATCGATTCTC TTGTTTGCTC CAGACTCTCA GGCAATGACC TGATAGCCTT TGTAGATCTC TCAAAAATAG CTACCCTCTC CGGCATTAAT |
-Macromolecule #2: Synthetic DNA oligonucleotides
Macromolecule | Name: Synthetic DNA oligonucleotides / type: dna / ID: 2 / Name.synonym: Staple strand Details: TCCGTGGGAACTTTTTAAACGGCGGAGCGATTAAGTTTTTTTGGGTAACGCCGTAGCCAGCTTTTTTTTCATCAACAT CCATCAAAAATTGTAAAACGACGGCCAGTGCCAATAGGAACG TGGCCTTCCTAGGGTTTTCCCAGTCACGACGTAATTCGCGTC ...Details: TCCGTGGGAACTTTTTAAACGGCGGAGCGATTAAGTTTTTTTGGGTAACGCCGTAGCCAGCTTTTTTTTCATCAACAT CCATCAAAAATTGTAAAACGACGGCCAGTGCCAATAGGAACG TGGCCTTCCTAGGGTTTTCCCAGTCACGACGTAATTCGCGTC CAAGCTTGCATTTTTTGCCTGCAGGTAATTCGTAATCTTTTTATGGTCATAGTAAATCAGCTCTTTTTATTTTTTAAC CTAACTCACATTTTTTTAATTGCGTTTGAATCGGCCATTTTTACGCGCGGGGAACATACGAGCTTTTTCGGAAGCATA GTGAAATTGTCGCCAGGGTGGTTATTTTTGTCTGTTTCCTGT AATTCCACACAGAGGCGGTTTGCGTATTGGGTATCCGCTCAC GCTGCGCAGGCAAAGCGCCATTCGCCGGGTAC CGAGCTCGCGACTCTAGAGGATCCCCATTCAG ACTGTTGGGACCGGAAACCA TCGTGCCACCCGCTTTCCAGTCGGACAACCCG TCGGATTCTAAATGTGAGCGAGTAGAAACCTG GCTGCATTAAGCGCTCACTG GGGATAGGTTGAAAGGGGGATGTGCTGCAAGTTGACCGTAAT GATGGGCGCATTCGCTATTACGCCAGCTGGCACGTTGGTGTA AGGGCGATCGGTTTTTTGCGGGCCTCTCGTAACCGTGTTTTTCATCTGCCAGTTTCCGGCACCTTTTTGCTTCTGGTG GATCGCACCGACGACCGTATCGGCGTGCCTAA TGAGTGAGAAGTGTAAAGCCTGGGCTCAGGAA TCCAGCCAGCTTTGAGGGGA Classification: DNA / Structure: SINGLE STRANDED / Synthetic?: Yes |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Experimental: 250 KDa / Theoretical: 250 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.56 mg/mL |
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Buffer | pH: 8 / Details: 40 mM Tris-HCl, 20 mM acetic acid, 2 mM EDTA |
Grid | Details: Quantifoil 200 mesh grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 1.5 second before plunging |
-Electron microscopy
Microscope | JEOL 2200FS |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 80,000 times magnification |
Specialist optics | Energy filter - Name: JEOL |
Details | 5k * 4k |
Date | Sep 17, 2015 |
Image recording | Category: CCD / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Number real images: 91 / Average electron dose: 63 e/Å2 Details: Every image is the average of 60 frames recorded by the direct electron detecto |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 25000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Details | The particles were selected manually using EMAN2 |
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CTF correction | Details: each particle |
Final reconstruction | Applied symmetry - Point group: T (tetrahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 2183 |