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- EMDB-3409: cryo-EM of nanoscale DNA assemblies -

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Basic information

Entry
Database: EMDB / ID: EMD-3409
Titlecryo-EM of nanoscale DNA assemblies
Map dataReconstruction of DNA icosahedron origami
Sample
  • Sample: DNA icosahedron, 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: 20.0 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: 0.0388
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0388
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3409.png

Downloads & links

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Map

FileDownload / File: emd_3409.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of DNA icosahedron origami
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.51 Å/pix.
x 256 pix.
= 642.56 Å		2.51 Å/pix.
x 256 pix.
= 642.56 Å		2.51 Å/pix.
x 256 pix.
= 642.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.51 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0388 / Movie #1: 0.0388
Minimum - Maximum-0.00583043 - 0.07475706
Average (Standard dev.)0.00341404 (±0.00912775)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
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/NS000
NC/NR/NS256256256
D min/max/mean-0.0060.0750.003

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Supplemental data

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Sample components

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Entire : DNA icosahedron, 52-bp edge length

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

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

SupramoleculeName: DNA icosahedron, 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: 2.07 MDa / Theoretical: 2.07 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: 1.01 MDa / Theoretical: 1.01 MDa
SequenceString: TCTTTGCCTT GCCTGTATGA TTTATTGGAT GTTAATGCTA CTACTATTAG TAGAATTGAT GCCACCTTTT CAGCTCGCGC CCCAAATGAA AATATAGCTA AACAGGTTAT TGACCATTTG CGAAATGTAT CTAATGGTCA AACTAAATCT ACTCGTTCGC AGAATTGGGA ...String:
TCTTTGCCTT GCCTGTATGA TTTATTGGAT GTTAATGCTA CTACTATTAG TAGAATTGAT GCCACCTTTT CAGCTCGCGC CCCAAATGAA AATATAGCTA AACAGGTTAT TGACCATTTG CGAAATGTAT CTAATGGTCA AACTAAATCT ACTCGTTCGC AGAATTGGGA ATCAACTGTT ACATGGAATG AAACTTCCAG ACACCGTACT TTAGTTGCAT ATTTAAAACA TGTTGAGCTA CAGCACCAGA TTCAGCAATT AAGCTCTAAG CCATCCGCAA AAATGACCTC TTATCAAAAG GAGCAATTAA AGGTACTCTC TAATCCTGAC CTGTTGGAGT TTGCTTCCGG TCTGGTTCGC TTTGAAGCTC GAATTAAAAC GCGATATTTG AAGTCTTTCG GGCTTCCTCT TAATCTTTTT GATGCAATCC GCTTTGCTTC TGACTATAAT AGTCAGGGTA AAGACCTGAT TTTTGATTTA TGGTCATTCT CGTTTTCTGA ACTGTTTAAA GCATTTGAGG GGGATTCAAT GAATATTTAT GACGATTCCG CAGTATTGGA CGCTATCCAG TCTAAACATT TTACTATTAC CCCCTCTGGC AAAACTTCTT TTGCAAAAGC CTCTCGCTAT TTTGGTTTTT ATCGTCGTCT GGTAAACGAG GGTTATGATA GTGTTGCTCT TACTATGCCT CGTAATTCCT TTTGGCGTTA TGTATCTGCA TTAGTTGAAT GTGGTATTCC TAAATCTCAA CTGATGAATC TTTCTACCTG TAATAATGTT GTTCCGTTAG TTCGTTTTAT TAACGTAGAT TTTTCTTCCC AACGTCCTGA CTGGTATAAT GAGCCAGTTC TTAAAATCGC ATAAGGTAAT TCACAATGAT TAAAGTTGAA ATTAAACCAT CTCAAGCCCA ATTTACTACT CGTTCTGGTG TTCTCGTCAG GGCAAGCCTT ATTCACTGAA TGAGCAGCTT TGTTACGTTG ATTTGGGTAA TGAATATCCG GTTCTTGTCA AGATTACTCT TGATGAAGGT CAGCCAGCCT ATGCGCCTGG TCTGTACACC GTTCATCTGT CCTCTTTCAA AGTTGGTCAG TTCGGTTCCC TTATGATTGA CCGTCTGCGC CTCGTTCCGG CTAAGTAACA TGGAGCAGGT CGCGGATTTC GACACAATTT ATCAGGCGAT GATACAAATC TCCGTTGTAC TTTGTTTCGC GCTTGGTATA ATCGCTGGGG GTCAAAGATG AGTGTTTTAG TGTATTCTTT CGCCTCTTTC GTTTTAGGTT GGTGCCTTCG TAGTGGCATT ACGTATTTTA CCCGTTTAAT GGAAACTTCC TCATGAAAAA GTCTTTAGTC CTCAAAGCCT CTGTAGCCGT TGCTACCCTC GTTCCGATGC TGTCTTTCGC TGCTGAGGGT GACGATCCCG CAAAAGCGGC CTTTAACTCC CTGCAAGCCT CAGCGACCGA ATATATCGGT TATGCGTGGG CGATGGTTGT TGTCATTGTC GGCGCAACTA TCGGTATCAA GCTGTTTAAG AAATTCACCT CGAAAGCAAG CTGATAAACC GATACAATTA AAGGCTCCTT TTGGAGCCTT TTTTTTTGGA GATTTTCAAC GTGAAAAAAT TATTATTCGC AATTCCTTTA GTTGTTCCTT TCTATTCTCA CTCCGCTGAA ACTGTTGAAA GTTGTTTAGC AAAACCCCAT ACAGAAAATT CATTTACTAA CGTCTGGAAA GACGACAAAA CTTTAGATCG TTACGCTAAC TATGAGGGTT GTCTGTGGAA TGCTACAGGC GTTGTAGTTT GTACTGGTGA CGAAACTCAG TGTTACGGTA CATGGGTTCC TATTGGGCTT GCTATCCCTG AAAATGAGGG TGGTGGCTCT GAGGGTGGCG GTTCTGAGGG TGGCGGTTCT GAGGGTGGCG GTACTAAACC TCCTGAGTAC GGTGATACAC CTATTCCGGG CTATACTTAT ATCAACCCTC TCGACGGCAC TTATCCGCCT GGTACTGAGC AAAACCCCGC TAATCCTAAT CCTTCTCTTG AGGAGTCTCA GCCTCTTAAT ACTTTCATGT TTCAGAATAA TAGGTTCCGA AATAGGCAGG GGGCATTAAC TGTTTATACG GGCACTGTTA CTCAAGGCAC TGACCCCGTT AAAACTTATT ACCAGTACAC TCCTGTATCA TCAAAAGCCA TGTATGACGC TTACTGGAAC GGTAAATTCA GAGACTGCGC TTTCCATTCT GGCTTTAATG AAGATCCATT CGTTTGTGAA TATCAAGGCC AATCGTCTGA CCTGCCTCAA CCTCCTGTCA ATGCTGGCGG CGGCTCTGGT GGTGGTTCTG GTGGCGGCTC TGAGGGTGGT GGCTCTGAGG GTGGCGGTTC TGAGGGTGGC GGCTCTGAGG GAGGCGGTTC CGGTGGTGGC TCTGGTTCCG GTGATTTTGA TTATGAAAAG ATGGCAAACG CTAATAAGGG GGCTATGACC GAAAATGCCG ATGAAAACGC GCTACAGTCT GACGCTAAAG GCAAACTTGA TTCTGTCGCT ACTGATTACG GTGCTGCTAT CGATGGTTTC ATTGGTGACG TTTCCGGCCT TGCTAATGGT AATGGTGCTA CTGGTGATTT TGCTGGCTCT AATTCCCAAA TGGCTCAAGT CGGTGACGGT GATAATTCAC CTTTAATGAA TAATTTCCGT CAATATTTAC CTTCCCTCCC TCAATCGGTT GAATGTCGCC CTTTTGTCTT TAGCGCTGGT AAACCATATG AATTTTCTAT TGATTGTGAC AAAATAAACT TATTCCGTGG TGTCTTTGCG TTTCTTTTAT ATGTTGCCAC CTTTATGTAT GTATTTTCTA CGTTTGCTAA CATACTGCGT AATAAGGAGT CTTAATCATG CCAGTTCTTT TGGGTATTCC GTTATTATTG CGTTTCCTCG GTTTCCTTCT GGTAACTTTG TTCGGCTATC TGCTTACTTT TCTTAAAAAG GGCTTCGGTA AGATAGCTAT TGCTATTTCA TTGTTTCTTG CTCTTATTAT TGGGCTTAAC TCAATTCTTG TGGGTTATCT CTCTGATATT AGCGCTCAAT TACCCTCTGA CTTTGTTCAG GGTGTTCAGT TAATTCTCCC GTCTAATGCG CTTCCCTGTT TTTATGTTAT TCTCTCTGTA AAGGCTGCTA TTTTCATTTT TGACGTTAAA CAAAAAATCG TTTCTTATTT GGATTGGGAT AAATAATATG GCTGTTTATT TTGTAACTGG CAAATTAGGC TCTGGAAAGA CGCTCGTTAG C

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Macromolecule #2: Synthetic DNA oligonucleotides

MacromoleculeName: Synthetic DNA oligonucleotides / type: dna / ID: 2 / Name.synonym: Staple strand
Details: CAAGAACCGGATTTTTTATTCATTACGGATCTTCATTTTTTTAAAGCCAGAA CTTGATATTCGTAACAAAGCTGCTCATTCAGAGACGATTGGC ACAAACGAATCCAAATCAAC GATTTTAATAATCATTGTGAATTACAAGAGT AATCTTGACTGGCTGACCTTCATCCTTATGC ...Details: CAAGAACCGGATTTTTTATTCATTACGGATCTTCATTTTTTTAAAGCCAGAA CTTGATATTCGTAACAAAGCTGCTCATTCAGAGACGATTGGC ACAAACGAATCCAAATCAAC GATTTTAATAATCATTGTGAATTACAAGAGT AATCTTGACTGGCTGACCTTCATCCTTATGC TGAATAAGGCTTTTTTTGCCCTGACGACGATAAAAACTTTTTCAAAATAGCG AATTACGAGGCTTTTTATAGTAAGAGGAGATGGTTTATTTTTATTTCAACTT ACGAGTAGTAATAACCCTCGTTTACCAGACGAGAACACCAGA AATTGGGCTTCAACACTATC GAATCGTCGACTGGATAGCGTCCACATAACG CCAAAAGGCAACTAATGCAGATAATACTGCG ATATCGCGTTTTTTTTTAATTCGAGCGGGGTAATAGTTTTTTAAAATGTTTA CAAAAGAAGTACCAGACCGGAAGCAAACTCCAGAGGCTTTTG TTTGCCAGAGTTCAAAGCGA GCTCAACATTAATTGCTGAATCTGCCCGAAA GACTTCAAAAGATTAAGAGGAAGGTGCTGTA CGAGCTGAAAATTTTTGGTGGCATCATTTTTGCGGATTTTTTGGCTTAGAGC CTCCTTTTGATAGTAGTAGCATTAGAATAACACCTTTAATTG TAAGAGGTCAATTCTACTAA AGAATTGACTAATATCAGAGAGATTTTTCAT TTGGGGCGACCTGTTTAGCTATAAACCCACA AACAGGTCAGGTTTTTATTAGAGAGTATAAAAACAGGTTTTTGAAGCGCATTGACAGGAGGTTTTTTTGAGGCAGGTC TTAACTGAACACCAGAGCCGCCGCCAGCATTAGACGGGAGAA ACCCTGAACACAGAACCACC ACCGGAACCGCTTTTTCTCCCTCAGACACCACCCTCATTTTTGAGCCGCCAC CTCAGAGCGCCGCCACCCTCAGAACTGAATT TACCGTTCTGGAAAGCGCAGTCTCCGCCACC CGGGATCGTCATTTTTCCCTCAGCAGTTTTAACGGGGTTTTTTCAGTGCCTTCCCTGCCTATTTTTTTTCGGAACCTA TTAATGCCGAGTAACAGTGCCCGTGGAACCA GAGCCACCATAATCAAAATCACCATAAACAG AGGAGTGTACCATCGGAACGAGGGTAGCAACTTTGATGATAC TGGTAATAAGCGAAAGACAG CAGTAAGCGTCTTTTTATACATGGCTGGCTACAGAGGTTTTTCTTTGAGGACTGTACAGACCATTTTTGGCGCATAGG GTCGAAATCCGTTTTTCGACCTGCTCTCAATCATAAGTTTTTGGAACCGAACAACGGGTAAAATTTTTTACGTAATGC TCATGAGGAATGAAAGAGGACAGATGAACGGTAAAGACTTTT GTTTCCATTATGACCAACTT GCAGACGGCATGTTACTTAGCCGGAAAAATC TACGTTAACAGGACGTTGGGAAGAACGAGGC AAGGAATTAGTGAGAATAGAAAGGCGCCTGA TAAATTGTGGAGATTTGTATCATAACAACTA GAACTGGCTCATTTTTTTATACCAGTTAAAACGAACTTTTTTAACGGAACAAGAGATTTAGGATTTTTATACCACATT TGCTAAACAAATGAATTTTCTGTAAAAGATT CATCAGTTCATTATTACAGGTAGTGGGGTTT CCTGTAGCATTTTTTTCCACAGACAAGTCGTCTTTCCTTTTTAGACGTTAGT AAAGTTTTCCCTCATAGTTAGCGTCAGTTCA GAAAACGACTCAAATGCTTTAAAAACGATCT AGGGCGACTGGTTTACCAGCGCTAGTACAAA CTACAACGTGAGTTTCGTCACCAAAGACAAA ATAAATATTCATTTTTTTGAATCCCCGAATGACCATATTTTTAATCAAAAATAGCAAAGCGGATTTTTTTGCATCAAA ATTTTGTCGCAAAGACACCACGGAACTATTA TAGTCAGACAGGTCTTTACCCTGATAAGTTT AAGACTCCTTATTTTTTTACGCAGTAGTGGCAACATATTTTTTAAAAGAAAC ACATAAAGTGTTAGCAAACGTAGAGTTTCAT TCCATGTAGTACGGTGTCTGGAAAAATACAT CCGAAGCCCTTTTTTTTTTAAGAAAAGAAACCGAGGATTTTTAACGCAATAAAAAATCACCAGTTTTTTAGCACCATT ATTTGGGAATCCCAAAAGAACTGGCATGATTCGACTTGAGCC TAGAGCCAGCTAACGGAATA TGTTTTAAATATTTTTTGCAACTAAAACAGTTGATTCTTTTTCCAATTCTGCACATTTCGCAATTTTTATGGTCAATA ACCAGAAGGTAAGCAGATAGCCGAGTTTGAC CATTAGATGAACGAGTAGATTTAACAAAGTT AAGTCAGAGGGTTTTTTAATTGAGCGGTTAAGCCCAATTTTTTAATAAGAGCATTAGCGTTTGTTTTTCCATCTTTTC AAATAGCAATATTTTCGGTCATAGCCCCCTTAAGAAACAATG AGCTATCTTATTTCATCGGC CGCTTTTGTGAGGCTTGCAGGGAGAACCTAA AACGAAAGCACTACGAAGGCACCTTAAAGGC TGAGACTCCTCTTTTTAAGAGAAGGAATAACCGATATTTTTTATTCGGTCGC ACAGCTTGATATTTTTCCGATAGTTGGCGGATAAGTGTTTTTCCGTCGAGAG GGGGTTTTGCGACAACAACCATCGCCCACGCTTAGGATTAGC TCAGTACCAGCGCCGACAAT AGGCGAAAGAATTTTTTACACTAAAAAAGCGCGAAACTTTTTAAAGTACAAC TTTCTTAATTATCAGCTTGCTTTCCCCAGCG ATTATACCCACTCATCTTTGACCGAGGTGAA GAAACCATCGATTTTTTAGCAGCACCTAGCGTCAGACTTTTTTGTAGCGCGT TTTGCCTTGTAATCAGTAGCGACAAAAGTAT TAAGAGGCTTATTCTGAAACATGGAATCAAG TAGGTGTAGGTTGATATAAGTATAGGAAACG TCACCAATACCATTAGCAAGGCCGCCCGGAA AACTTTCAACATTTTTGTTTCAGCGGGCGAATAATAATTTTTTTTTTTCACGGGAACCCATGTTTTTTACCGTAACAC TCACCGTACTCTTTTTAGGAGGTTTAACCGCCACCCTTTTTTCAGAGCCACCGGAGCCTTTAATTTTTTTGTATCGGT CAAAAAAAAATCAGGGATAGCAAGCCCAATATTGAAAATCTC GGCTCCAAAAACCCTCATTT ACAATCAATAGTTTTTAAAATTCATAATTCAACCGATTTTTTTGAGGGAGGGAAGGTGAATTATTTTTTCACCGTCAC CCCTCAGAGTACCGCCACCCTCAGGGAAATT ATTCATTAAAGGTAAATATTGACAACCGCCA
Classification: DNA / Structure: SINGLE STRANDED / Synthetic?: Yes
Source (natural)Organism: synthetic construct (others)
Molecular weightExperimental: 1.06 MDa / Theoretical: 1.06 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

Concentration1.05 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
Details5k * 4k
DateOct 5, 2015
Image recordingCategory: CCD / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Number real images: 180 / Average electron dose: 63 e/Å2
Details: Every image is the average of 60 frames recorded by the direct electron detecto
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: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 25000
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: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 3650

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