7ART

48 helix bundle DNA origami brick


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution.

Kube, M.Kohler, F.Feigl, E.Nagel-Yuksel, B.Willner, E.M.Funke, J.J.Gerling, T.Stommer, P.Honemann, M.N.Martin, T.G.Scheres, S.H.W.Dietz, H.

(2020) Nat Commun 11: 6229-6229

  • DOI: 10.1038/s41467-020-20020-7
  • Primary Citation of Related Structures:  
    7ARE, 7ARQ, 7ART, 7ARV, 7ARY, 7AS5

  • PubMed Abstract: 
  • The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is folded by many short DNA oligonucleotides, can be employed to make objects comprising hundreds of unique DNA strands and thousands of base pairs, thus in principle providing many degrees of freedom for modelling complex objects of defined 3D shapes and sizes ...

    The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is folded by many short DNA oligonucleotides, can be employed to make objects comprising hundreds of unique DNA strands and thousands of base pairs, thus in principle providing many degrees of freedom for modelling complex objects of defined 3D shapes and sizes. Here, we address the problem of accurate structural validation of DNA objects in solution with cryo-EM based methodologies. By taking into account structural fluctuations, we can determine structures with improved detail compared to previous work. To interpret the experimental cryo-EM maps, we present molecular-dynamics-based methods for building pseudo-atomic models in a semi-automated fashion. Among other features, our data allows discerning details such as helical grooves, single-strand versus double-strand crossovers, backbone phosphate positions, and single-strand breaks. Obtaining this higher level of detail is a step forward that now allows designers to inspect and refine their designs with base-pair level interventions.


    Organizational Affiliation

    Physik Department, Technische Universität München, Garching, Germany. dietz@tum.de.



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Entity ID: 113
MoleculeChainsLengthOrganismImage
STAPLE STRANDID [auth By]40synthetic construct
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Entity ID: 114
MoleculeChainsLengthOrganismImage
STAPLE STRANDJD [auth Bz]49synthetic construct
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Entity ID: 115
MoleculeChainsLengthOrganismImage
STAPLE STRANDKD [auth B0]43synthetic construct
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Entity ID: 116
MoleculeChainsLengthOrganismImage
STAPLE STRANDLD [auth B1]49synthetic construct
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Entity ID: 117
MoleculeChainsLengthOrganismImage
STAPLE STRANDMD [auth B2]38synthetic construct
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Entity ID: 118
MoleculeChainsLengthOrganismImage
STAPLE STRANDND [auth B3]44synthetic construct
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Entity ID: 119
MoleculeChainsLengthOrganismImage
STAPLE STRANDOD [auth B4]35synthetic construct
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Entity ID: 120
MoleculeChainsLengthOrganismImage
STAPLE STRANDPD [auth B5]35synthetic construct
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Entity ID: 121
MoleculeChainsLengthOrganismImage
STAPLE STRANDQD [auth B6]49synthetic construct
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Entity ID: 122
MoleculeChainsLengthOrganismImage
STAPLE STRANDRD [auth B7]49synthetic construct
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Entity ID: 123
MoleculeChainsLengthOrganismImage
STAPLE STRANDSD [auth B8]42synthetic construct
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Entity ID: 124
MoleculeChainsLengthOrganismImage
STAPLE STRANDTD [auth B9]36synthetic construct
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Entity ID: 125
MoleculeChainsLengthOrganismImage
STAPLE STRANDUD [auth CA]35synthetic construct
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Entity ID: 126
MoleculeChainsLengthOrganismImage
STAPLE STRANDVD [auth CB]35synthetic construct
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Entity ID: 127
MoleculeChainsLengthOrganismImage
STAPLE STRANDWD [auth CC]49synthetic construct
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Entity ID: 128
MoleculeChainsLengthOrganismImage
STAPLE STRANDXD [auth CD]42synthetic construct
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Entity ID: 129
MoleculeChainsLengthOrganismImage
STAPLE STRANDYD [auth CE]35synthetic construct
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Entity ID: 130
MoleculeChainsLengthOrganismImage
STAPLE STRANDZD [auth CF]38synthetic construct
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Entity ID: 131
MoleculeChainsLengthOrganismImage
STAPLE STRANDAE [auth CG]51synthetic construct
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Entity ID: 132
MoleculeChainsLengthOrganismImage
STAPLE STRANDBE [auth CH]50synthetic construct
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Entity ID: 133
MoleculeChainsLengthOrganismImage
STAPLE STRANDCE [auth CI]43synthetic construct
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Entity ID: 134
MoleculeChainsLengthOrganismImage
STAPLE STRANDDE [auth CJ]40synthetic construct
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Entity ID: 135
MoleculeChainsLengthOrganismImage
STAPLE STRANDEE [auth CK]37synthetic construct
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Entity ID: 136
MoleculeChainsLengthOrganismImage
STAPLE STRANDFE [auth CL]47synthetic construct
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Entity ID: 137
MoleculeChainsLengthOrganismImage
STAPLE STRANDGE [auth CM]38synthetic construct
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Entity ID: 138
MoleculeChainsLengthOrganismImage
STAPLE STRANDHE [auth CN]40synthetic construct
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Entity ID: 139
MoleculeChainsLengthOrganismImage
STAPLE STRANDIE [auth CO]42synthetic construct
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