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- EMDB-3413: cryo-EM of nanoscale DNA assemblies -

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Basic information

Entry
Database: EMDB / ID: EMD-3413
Titlecryo-EM of nanoscale DNA assemblies
Map dataReconstruction of a DNA nested cube
Sample
  • Sample: DNA nested cube, 73-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: 40.0 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 18, 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: 0.431
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.431
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3413.png

Downloads & links

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Map

FileDownload / File: emd_3413.map.gz / Format: CCP4 / Size: 210.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of a DNA nested cube
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.95 Å/pix.
x 384 pix.
= 1132.8 Å		2.95 Å/pix.
x 384 pix.
= 1132.8 Å		2.95 Å/pix.
x 384 pix.
= 1132.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.431 / Movie #1: 0.431
Minimum - Maximum-1.11901414 - 3.40679574
Average (Standard dev.)0.00494157 (±0.10736071)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 1132.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.952.952.95
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z1132.8001132.8001132.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-192-192-192
NC/NR/NS384384384
D min/max/mean-1.1193.4070.005

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Supplemental data

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Sample components

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Entire : DNA nested cube, 73-bp edge length

EntireName: DNA nested cube, 73-bp edge length
Components
  • Sample: DNA nested cube, 73-bp edge length
  • DNA: M13mp18 phage genome segment
  • DNA: Synthetic DNA oligonucleotides

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Supramolecule #1000: DNA nested cube, 73-bp edge length

SupramoleculeName: DNA nested cube, 73-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: 2.06 MDa / Theoretical: 2.06 MDa / 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: 1.03 MDa / Theoretical: 1.03 MDa
SequenceString: 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 TTATCAGCTA GAACGGTTGA ATATCATATT GATGGTGATT TGACTGTCTC CGGCCTTTCT CACCCTTTTG AATCTTTACC TACACATTAC TCAGGCATTG CATTTAAAAT ATATGAGGGT TCTAAAAATT TTTATCCTTG CGTTGAAATA AAGGCTTCTC CCGCAAAAGT ATTACAGGGT CATAATGTTT TTGGTACAAC CGATTTAGCT TTATGCTCTG AGGCTTTATT GCTTAATTTT GCTAATTCTT TGCCTTGCCT GTATGATTTA TTGGATGTTA ATGCTACTAC TATTAGTAGA ATTGATGCCA CCTTTTCAGC TCGCGCCCCA AATGAAAATA TAGCTAAACA GGTTATTGAC CATTTGCGAA ATGTATCTAA TGGTCAAACT AAATCTACTC GTTCGCAGAA TTGGGAATCA ACTGTTACAT GGAATGAAAC TTCCAGACAC CGTACTTTAG TTGCATATTT AAAACATGTT GAGCTACAGC ACCAGATTCA GCAATTAAGC TCTAAGCCAT CCGCAAAAAT GACCTCTTAT CAAAAGGAGC AATTAAAGGT ACTCTCTAAT CCTGACCTGT TGGAGTTTGC TTCCGGTCTG GTTCGCTTTG AAGCTCGAAT TAAAACGCGA TATTTGAAGT CTTTCGGGCT TCCTCTTAAT CTTTTTGATG CAATCCGCTT TGCTTCTGAC TATAATAGTC AGGGTAAAGA CCTGATTTTT GATTTATGGT CATTCTCGTT TTCTGAACTG TTTAAAGCAT TTGAGGGGGA TTCAATGAAT ATTTATGACG ATTCCGCAGT ATTGGACGCT ATCCAGTCTA AACATTTTAC TATTACCCCC TCTGGCAAAA CTTCTTTTGC AAAAGCCTCT CGCTATTTTG GTTTTTATCG TCGTCTGGTA AACGAGGGTT ATGATAGTGT TGCTCTTACT ATGCCTCGTA ATTCCTTTTG GCGTTATGTA TCTGCATTAG TTGAATGTGG TATTCCTAAA TCTCAACTGA TGAATCTTTC TACCTGTAAT AATGTTGTTC CGTTAGTTCG TTTTATTAAC GTAGATTTTT CTTCCCAACG TCCTGACTGG TATAATGAGC CAGTTCTTAA AATCGCATAA GGTAATTCAC AATGATTAAA GTTGAAATTA AACCATCTCA AGCCCAATTT ACTACTCGTT CTGGTGTTCT CGTCAGGGCA AGCCTTATTC ACTGAATGAG CAGCTTTGTT ACGTTGATTT GGGTAATGAA TATCCGGTTC TTGTCAAGAT TACTCTTGAT GAAGGTCAGC CAGCCTATGC GCCTGGTCTG TACACCGTTC ATCTGTCCTC TTTCAAAGTT GGTCAGTTCG GTTCCCTTAT GATTGACCGT CTGCGCCTCG TTCCGGCTAA GTAACATGGA GCAGGTCGCG GATTTCGACA CAATTTATCA GGCGATGATA CAAATCTCCG TTGTACTTTG TTTCGCGCTT GGTATAATCG CTGGGGGTCA AAGATGAGTG TTTTAGTGTA TTCTTTCGCC TCTTTCGTTT TAGGTTGGTG CCTTCGTAGT GGCATTACGT ATTTTACCCG TTTAATGGAA ACTTCCTCAT GAAAAAGTCT TTAGTCCTCA AAGCCTCTGT AGCCGTTGCT ACCCTCGTTC CGATGCTGTC TTTCGCTGCT GAGGGTGACG ATCCCGCAAA AGCGGCCTTT AACTCCCTGC AAGCCTCAGC GACCGAATAT ATCGGTTATG CGTGGGCGAT GGTTGTTGTC ATTGTCGGCG CAACTATCGG TATCAAGCTG TTTAAGAAAT TCACCTCGAA AGCAAGCTGA TAAACCGATA CAATTAAAGG CTCCTTTTGG AGCCTTTTTT TTTGGAGATT TTCAACGTGA AAAAATTATT ATTCGCAATT CCTTTAGTTG TTCCTTTCTA TTCTCACTCC GCTGAAACTG TTGAAAGTTG TTTAGCAAAA CCCCATACAG AAAATTCATT TACTAACGTC TGGAAAGACG ACAAAACTTT AGATCGTTAC GCTAACTATG AGGGTTGTCT GTGGAATGCT ACAGGCGTTG TAGTTTGTAC TGGTGACGAA ACTCAGTGTT ACGGTACATG GGTTCCTATT GGGCTTGCTA TCCCTGAAAA TGAGGGTGGT GGCTCTGAGG GTGGCGGTTC TGAGGGTGGC GGTTCTGAGG GTGGCGGTAC TAAACCTCCT GAGTACGGTG ATACACCTAT TCCGGGCTAT ACTTATATCA ACCCTCTCGA CGGCACTTAT CCGCCTGGTA CTGAGCAAAA CCCCGCTAAT CCTAATCCTT CTCTTGAGGA GTCTCAGCCT CTTAATACTT TCATGTTTCA GAATAATAGG TTCCGAAATA GGCAGGGGGC ATTAAC

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Macromolecule #2: Synthetic DNA oligonucleotides

MacromoleculeName: Synthetic DNA oligonucleotides / type: dna / ID: 2 / Name.synonym: Staple strand
Details: AAGTTTTGCCAACGACGTTGTA GCTTTTTTTTCCGGCACCGCAACGCCAGGGTTTTTTTTTCCCAGTCGAGGGG TGTGCTTTTTTGCAAGGCGAGAAACCAGGCATTTTTAAGCGCCATTGCTGCG TTCTGGTGCCGTTAAGTTGGGT TCGGATTCTCCAGATCGCACTC ...Details: AAGTTTTGCCAACGACGTTGTA GCTTTTTTTTCCGGCACCGCAACGCCAGGGTTTTTTTTTCCCAGTCGAGGGG TGTGCTTTTTTGCAAGGCGAGAAACCAGGCATTTTTAAGCGCCATTGCTGCG TTCTGGTGCCGTTAAGTTGGGT TCGGATTCTCCAGATCGCACTC GTGCATTTTTTCTGCCAGTTACGACAGTATCTTTTTGGCCTCAGGAGTGGGA TGAGGTAGATTAACGAGGGACG TCGGGTTTTTAAACCTGTCGTAATGAATCGGTTTTTCCAACGCGCGGTTTGC TGGGCCTGCATTGCCAGGCATC ACAGATTTTTTGAACGGTGTCATAGGCTGGCTTTTTTGACCTTCATCTTGAC ACTGCCAGGCGACAGACCCGCT GACCATTTTTTTAGATACATCAATAACCTGTTTTTTTTAGCTATATAAGTAC CCAACAATGGTTTCGCATTTGA CGGCCTTTTTAGTGCCAAGCAAAGCCTGGGGTTTTTTGCCTAATGATAGCAT ACATATTTTTCGAGCCGGAACAGGTCGACTCTTTTTTAGAGGATCCAGCTCG TTGCATGCCTGGCATAAAGTGT TTTGCTTTTTGGGATCGTCAACATTCAACTATTTTTATGCAGATACTCGTTT TAAAATTTTTCGAACTAACGCTTTGAGGACTTTTTTAAAGACTTTTGGGCTT GAAAGACAGCCAGTTGAGATTTAGGAATACCCCCTCAGCAGC GGTAGCAACGATTACAGGTAGAAAGATTCATATCGGAACGAG GCTACAGAGGGAACAACATT CAAAGCGAAATATCGCGTTTTAATGTCAGGAC GTTGGGAACTGGCTCATTATACCATCGAGCTT GAAAAATCTAATTTTAAGAA ACCAGACCGGAAAGACTTCA TGACCTTTTTATAAATCAAACCATCAATATGTTTTTATATTCAACCCCTTCC TGCAATTTTTTGCCTGAGTAAAAAGATTAAGTTTTTAGGAAGCCCGAAGCAA TACCCTGACTAGGCCGGAGACAGTCAAATCAAATCAGGTCTT AAGCAAAGCGAAAGATTCAAAAGGGTGAGAAATTATAGTCAG GATTGCATCAATGTGTAGGT GTAATTTTTTACTTTTGCGGTGTAGCTCAACTTTTTATGTTTTAAAGGCGCG TTTTTGCGGAATTTTTAGAACCCTCATATATATAAGAGGTCA TTAATTGCTGTATTTCAACGCAAGGATAAAATGGCTTAGAGC AATATAATGCGAGAAGCCTT CTATCTTTTTAGGTCATTGCCATGTCAATCATTTTTTATGTACCCCTAAATT TTGTACCACCTCAGAGCATAAAGCTCGATGAA CGGTAATCGGAGCAAACAAGAGAATAAATCGG GTAAAACTAGCTGAGAGTCT AAAACATTATAGCAATAAAG CCTAATTTTTAACGAAAGAGCGCGAAACAAATTTTTGTACAACGGATTACTT CCCAGCGAACACTAAAACACTCATTTAAACAG CTTGATACTTTCGAGGTGAATTTCCTTTGACC CGATAGTTGCATCAGCTTGC TTATACCAAGGCAAAAGAAT AGGCTTGCCCTACGTAATGCCACTACGAAGGTTCAGTGAATA ACCAGAACGAGTTTCCATTAAACGGGTAAAATGACGAGAAAC GTAGTAAATTTCATGAGGAA AATGATTTTTCAACAACCATCTTTCAACAGTTTTTTTTCAGCGGAGAAGGAA CGTTAGTAAAGAGGCTTGCAGGGAGTTAAAGGTCTTTCCAGA TATGGGATTTTAACCGATATATTCGGTCGCTTGAATTTTCTG TGCTAAACAACGCCCACGCA TCCACTTTTTAGACAGCCCTAGCGAGAGGCTTTTTTTTTGCAAAAGAAACGA ACCAGTTTTTACGACGATAAGTAACGATCTATTTTTAAGTTTTGTCGCCGCT CATAGTTAGCAAACCAAAAT TTTAAACAATTCATTGAATCCCCCTAGTAAGA GCAACACTAAGGAATTACGAGGCATCAAATGC ATCATAACCCATAACGCCAA GTTCAGAAAACGTCATAAAT GTAATTTTTTAGTAAAATGTATGTGAGCGAGTTTTTTAACAACCCGCAGCCA TGTAGTTTTTCCAGCTTTCATAGCGTCCAATTTTTTACTGCGGAATCGAGAA TTAGACTGGATCAACATTAA TAAATTAATGTCAAAAATAATTCGCGTCTGGGTTCTAGCTGA AGCTATTTTTTTTTAACCAATAGGAACGCCACCGGAGAGGGT GAGAGATCTATCAGCTCATT ACAAATTTTTCGGCGGATTGGATAGGTCACGTTTTTTTGGTGTAGAGTAACC GTAAATTTTTCGTTAATATTTCGCATTAAATTTTTTTTTTGTTAAACAAAGG ACCGTAAAATTTGTTAATGG CAACTTTTTTAAAGGAATTGAGCCTTTAATTTTTTTGTATCGGTTTGCCGAC AAAAAAGGTTTTTTCACGTTGAAAACAGGAAG ATTGTATACAGAAAAGCCCCAAAAATCTCCAA AGCAAATATTGGTTGATAAT CTCCAAAAGGCGAATAATAA GTATTTTTTTGGGCGCCAGGCACATTAATTGTTTTTCGTTGCGCTCTTCCAG GTGAGCTAACTGTGGTTGCCTG GGGAGATAGATGAGAAGGCG CAAGACAATTCCGCTCAGTAAT AATTCTTTTTGTAATCATGGTTCCTGTGTGATTTTTAATTGTTATCCACACA GAGATTTTTTGGTTTAATTTCATTGTGAATTTTTTTACCTTATGCGCGTTAA TCATATTAATCAACTGCTGT CCGGGGCGAAACAGCTGTACCG CAACTTTTTTGTTGGGAAGGCGGGCCTCTTCTTTTTGCTATTACGCGGGGGA ACTCCTTTTTAACAGGTCAGTACCTTTAATTTTTTTGCTCCTTTTGTTTAAA GCGATGAGAGGATTACGGTG GGTGTTTTTTCTGGAAGTTTCAGTTGATTCCTTTTTCAATTCTGCGTAGTTT CGCCAATATAACATTCCTTCAG TTTCATTTGGTATGCAACTA AAGAATTTTTCCGGATATTCATCATAAGGGATTTTTACCGAACTGAAAGAGG AGCCGTTTTTGAACGAGGCGTCAACGTAACATTTTTAAGCTGCTCACACCAA ATTACCCAAACAGACGGTCA AGCTGTTTTTAAAAGGTGGCGGCAAAGAATTTTTTTAGCAAAATTAGACCCT AATAAATCCTAATAGTAGTAGCATTGTCGAAA TCCGCGACATCGCCTGATAAATTGTAACATCC CTGCTCCATGGATTTGTATC ATACAGGCAAATCAATTCTA
Classification: DNA / Structure: SINGLE STRANDED / Synthetic?: Yes
Source (natural)Organism: synthetic construct (others)
Molecular weightExperimental: 1.03 MDa / Theoretical: 1.03 MDa

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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

Concentration1.54 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
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 80,000 times magnification
Specialist opticsEnergy filter - Name: JEOL
DateApr 7, 2016
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 152 / Average electron dose: 60 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 0.004 µm / Nominal defocus min: 0.0015 µm / Nominal magnification: 40000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe particles were selected manually using EMAN2
CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: O (octahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 40.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 2008

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