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- EMDB-0028: Sequence-programmable covalent bonding of designed DNA assemblies... -

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Basic information

Entry
Database: EMDB / ID: EMD-0028
TitleSequence-programmable covalent bonding of designed DNA assemblies, brick-like_object_with_TT-motifs_(1)-(3)_crosslinked_PBS
Map dataNone
Sample
  • Complex: DNA origami
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 17.0 Å
AuthorsDietz H / Kube M
CitationJournal: Sci Adv / Year: 2018
Title: Sequence-programmable covalent bonding of designed DNA assemblies.
Authors: Thomas Gerling / Massimo Kube / Benjamin Kick / Hendrik Dietz /
Abstract: Bottom-up fabrication of custom nanostructures using the methods of DNA nanotechnology has great potential for applications in many areas of science and technology. One obstacle to applications ...Bottom-up fabrication of custom nanostructures using the methods of DNA nanotechnology has great potential for applications in many areas of science and technology. One obstacle to applications concerns the constrained environmental conditions at which DNA objects retain their structure. We present a general, site-selective, and scalable method for creating additional covalent bonds that increase the structural stability of DNA nanostructures. Placement of thymidines in close proximity within DNA nanostructures allows the rational creation of sites for covalent cyclobutane pyrimidine dimer (CPD) bonds induced via ultraviolet irradiation. The additional covalent bonds may be used in a sequence-programmable fashion to link free strand termini, to bridge strand breaks at crossover sites, and to create additional interhelical connections. Thus designed multilayer DNA origami objects can remain stable at temperatures up to 90°C and in pure double-distilled water with no additional cations present. In addition, these objects show enhanced resistance against nuclease activity. Cryo-electron microscopy (cryo-EM) structural analysis of non-cross-linked and cross-linked objects indicated that the global shape and the internal network of crossovers are preserved after irradiation. A cryo-EM map of a CPD-stabilized multilayer DNA origami object determined at physiological ionic strength reveals a substantial swelling behavior, presumably caused by repulsive electrostatic forces that, without covalent stabilization, would cause disassembly at low ionic strength. Our method opens new avenues for applications of DNA nanostructures in a wider range of conditions.
History
DepositionMay 23, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseAug 29, 2018-
UpdateAug 29, 2018-
Current statusAug 29, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.061
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.061
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0028.png

Downloads & links

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Map

FileDownload / File: emd_0028.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 2.3 Å
Density
Contour LevelBy AUTHOR: 0.061 / Movie #1: 0.061
Minimum - Maximum-0.13955715 - 0.2636265
Average (Standard dev.)0.0010613761 (±0.015270425)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 920.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.32.32.3
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z920.000920.000920.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1400.2640.001

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Supplemental data

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Sample components

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Entire : DNA origami

EntireName: DNA origami
Components
  • Complex: DNA origami

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Supramolecule #1: DNA origami

SupramoleculeName: DNA origami / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: synthetic construct (others)

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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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160000
FSC plot (resolution estimation)

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