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- EMDB-3410: cryo-EM of nanoscale DNA assemblies -

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Basic information

Entry
Database: EMDB / ID: EMD-3410
Titlecryo-EM of nanoscale DNA assemblies
Map dataReconstruction of a DNA octahedron object
Sample
  • Sample: DNA octahedron, 52-bp edge length
  • DNA: M13mp18 phage genome segment
  • DNA: Synthetic DNA oligonucleotides
KeywordsScaffolded DNA origami
Biological speciesEnterobacteria phage M13 (virus) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsZhang K / Chiu W / Veneziano R / Ratanalert S / Zhang F / Yan H / Bathe M
CitationJournal: 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
DepositionApr 14, 2016-
Header (metadata) releaseMay 4, 2016-
Map releaseJun 15, 2016-
UpdateJul 13, 2016-
Current statusJul 13, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3410.png

Downloads & links

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Map

FileDownload / File: emd_3410.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of a DNA octahedron object
Voxel sizeX=Y=Z: 2.51 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-0.76278681 - 3.5113132
Average (Standard dev.)0.02427775 (±0.20358118)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 642.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.512.512.51
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z642.560642.560642.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-0.7633.5110.024

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Supplemental data

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Sample components

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Entire : DNA octahedron, 52-bp edge length

EntireName: DNA octahedron, 52-bp edge length
Components
  • Sample: DNA octahedron, 52-bp edge length
  • DNA: M13mp18 phage genome segment
  • DNA: Synthetic DNA oligonucleotides

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Supramolecule #1000: DNA octahedron, 52-bp edge length

SupramoleculeName: DNA octahedron, 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
Molecular weightExperimental: 940 KDa / Theoretical: 940 KDa / Method: Calculation

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Macromolecule #1: M13mp18 phage genome segment

MacromoleculeName: M13mp18 phage genome segment / type: dna / ID: 1 / Name.synonym: Scaffold strand / Details: amplified using assymetric PCR / Classification: DNA / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Enterobacteria phage M13 (virus) / Strain: M13mp18 / synonym: M13 phage
Molecular weightExperimental: 520 KDa / Theoretical: 520 KDa
SequenceString: GCGACGATTT ACAGAAGCAA GGTTATTCAC TCACATATAT TGATTTATGT ACTGTTTCCA TTAAAAAAGG TAATTCAAAT GAAATTGTTA AATGTAATTA ATTTTGTTTT CTTGATGTTT GTTTCATCAT CTTCTTTTGC TCAGGTAATT GAAATGAATA ATTCGCCTCT ...String:
GCGACGATTT ACAGAAGCAA GGTTATTCAC TCACATATAT TGATTTATGT ACTGTTTCCA TTAAAAAAGG TAATTCAAAT GAAATTGTTA AATGTAATTA ATTTTGTTTT CTTGATGTTT GTTTCATCAT CTTCTTTTGC TCAGGTAATT GAAATGAATA ATTCGCCTCT GCGCGATTTT GTAACTTGGT ATTCAAAGCA ATCAGGCGAA TCCGTTATTG TTTCTCCCGA TGTAAAAGGT ACTGTTACTG TATATTCATC TGACGTTAAA CCTGAAAATC TACGCAATTT CTTTATTTCT GTTTTACGTG CTAATAATTT TGATATGGTT GGTTCAATTC CTTCCATAAT TCAGAAGTAT AATCCAAACA ATCAGGATTA TATTGATGAA TTGCCATCAT CTGATAATCA GGAATATGAT GATAATTCCG CTCCTTCTGG TGGTTTCTTT GTTCCGCAAA ATGATAATGT TACTCAAACT TTTAAAATTA ATAACGTTCG GGCAAAGGAT TTAATACGAG TTGTCGAATT GTTTGTAAAG TCTAATACTT CTAAATCCTC AAATGTATTA TCTATTGACG GCTCTAATCT ATTAGTTGTT AGTGCACCTA AAGATATTTT AGATAACCTT CCTCAATTCC TTTCTACTGT TGATTTGCCA ACTGACCAGA TATTGATTGA GGGTTTGATA TTTGAGGTTC AGCAAGGTGA TGCTTTAGAT TTTTCATTTG CTGCTGGCTC TCAGCGTGGC ACTGTTGCAG GCGGTGTTAA TACTGACCGC CTCACCTCTG TTTTATCTTC TGCTGGTGGT TCGTTCGGTA TTTTTAATGG CGATGTTTTA GGGCTATCAG TTCGCGCATT AAAGACTAAT AGCCATTCAA AAATATTGTC TGTGCCACGT ATTCTTACGC TTTCAGGTCA GAAGGGTTCT ATCTCTGTTG GCCAGAATGT CCCTTTTATT ACTGGTCGTG TGACTGGTGA ATCTGCCAAT GTAAATAATC CATTTCAGAC GATTGAGCGT CAAAATGTAG GTATTTCCAT GAGCGTTTTT CCTGTTGCAA TGGCTGGCGG TAATATTGTT CTGGATATTA CCAGCAAGGC CGATAGTTTG AGTTCTTCTA CTCAGGCAAG TGATGTTATT ACTAATCAAA GAAGTATTGC TACAACGGTT AATTTGCGTG ATGGACAGAC TCTTTTACTC GGTGGCCTCA CTGATTATAA AAACACTTCT CAAGATTCTG GCGTACCGTT CCTGTCTAAA ATCCCTTTAA TCGGCCTCCT GTTTAGCTCC CGCTCTGATT CCAACGAGGA AAGCACGTTA TACGTGCTCG TCAAAGCAAC CATAGTACGC GCCCTGTAGC GGCGCATTAA GCGCGGCGGG TGTGGTGGTT ACGCGCAGCG TGACCGCTAC ACTTGCCAGC GCCCTAGCGC CCGCTCCTTT CGCTTTCTTC CCTTCCTTTC TCGCCACGTT CGCCGGCTTT CCCCGTCAAG CTCTAAATCG GGGGCTCCCT TTAGGGTTCC GATTTAGTGC TTTACGGCAC CTCGACCCCA AAAAACTTGA TTTGGGTGAT GGTTCACGTA GTGGGCCATC GCCCTGATAG ACGGTTTTTC GCCCTT

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Macromolecule #2: Synthetic DNA oligonucleotides

MacromoleculeName: Synthetic DNA oligonucleotides / type: dna / ID: 2 / Name.synonym: Staple strand
Details: TAGAGCCGTCATTTTTATAGATAATACTGGCCAACAGTTTTTAGATAGAACC CCAGTAATAATTTAGAAGTATTAGACTTTACCAGTCACACGA AAGGGACATTCATTTGAGGA TTAATGGAAACTTTTTAGTACATAAAAATAACGGATTTTTTTCGCCTGATTG ...Details: TAGAGCCGTCATTTTTATAGATAATACTGGCCAACAGTTTTTAGATAGAACC CCAGTAATAATTTAGAAGTATTAGACTTTACCAGTCACACGA AAGGGACATTCATTTGAGGA TTAATGGAAACTTTTTAGTACATAAAAATAACGGATTTTTTTCGCCTGATTG CCTTTTACATTGAGTGAATAACCAAAGGGATCAGTAACAGTA CGGGAGAAACTCAATATATG TTTAGACAGGATTTTTACGGTACGCCTATTTACATTGTTTTTGCAGATTCAC AAGTGTTTTTGCTCAATCGTCTGAAATGGATAGAATCTTGAG ATAATCAGTGACATTTTGAC AAACAATTCGATTTTTCAACTCGTATGTTTAACGTCATTTTTGATGAATATA CCCGAACGTTAGAAATTGCGTAGATTTTCAGTAAATCCTTTG ATTAATTTTAACAGAAATAA CACAGACAATATTTTTTTTTTGAATGATTGAGGAAGGTTTTTTTATCTAAAA CAAATCAACATTTAATGCGCGAACTGATAGCTGGTCAGTTGG GTAGAAAGGAGCTATTAGTC AGGCGAATTATTTTTTTCATTTCAATTCAAGAAAACATTTTTAAATTAATTA AACAAACATACCTGAGCAAAAGAAACAGTGC CACGCTGATTAACACCGCCTGCAGATGATGA CCTAAAACATCTTTTTGCCATTAAAAACAGAGGTGAGTTTTTGCGGTCAGTA CAAACTATATCACTTGCCTGAGTACCAGCAG AAGATAAAATACCGAACGAACCAGAAGAACT GAGCCAGCAGCTTTTTAAATGAAAAAATCAAACCCTCTTTTTAATCAATATC AATATAATATTATCAGATGATGGCTGCTGAA CCTCAAATTCTAAAGCATCACCTAATTCATC CGGCCTTGCTGTTTTTGTAATATCCAAAAACGCTCATTTTTTGGAAATACCT CAACAGGAGAACAATATTACCGCCCGTAAGA ATACGTGGCTTCTGACCTGAAAGAGCCATTG AAAGTTTGAGTTTTTTAACATTATCAGGAATTATCATTTTTTCATATTCCTG GAAGGAGCTTTTGCGGAACAAAGATAACAAC TAATAGATTATCTTTAGGTGCACAACCACCA AGGCCACCGAGTTTTTTAAAAGAGTCACTTCTTTGATTTTTTTAGTAATAAC GTAGCAATTGTCCATCACGCAAATTTTGAAT TACCTTTTCATTTAACAATTTCATAACCGTT CCTGATTGTTTTTTTTGGATTATACTTCAAAATTATTTTTTTAGCACGTAAA CAACCATATCTGAATTATGGAAGGTACAAAA TCGCGCAGCTTTGAATACCAAGTAATTGAAC
Classification: DNA / Structure: SINGLE STRANDED / Synthetic?: Yes
Source (natural)Organism: synthetic construct (others)
Molecular weightExperimental: 420 KDa / Theoretical: 420 KDa

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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

Concentration1 mg/mL
BufferpH: 8 / Details: 40 mM Tris-HCl, 20 mM acetic acid, 2 mM EDTA
GridDetails: glow-discharged 200-mesh R1.2/1.3 Quantifoil grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 1.5 second before plunging

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 25000
Specialist opticsEnergy filter - Name: JEOL
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 80,000 times magnification
Details5k * 4k
DateSep 19, 2015
Image recordingCategory: CCD / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Number real images: 100 / Average electron dose: 63 e/Å2
Details: Every image is the average of 60 frames recorded by the direct electron detecto

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Image processing

CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: O (octahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 2678
DetailsThe particles were selected manually using EMAN2

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