7AS5

126 helix bundle DNA nanostructure

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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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: 111
MoleculeChainsLengthOrganismImage
STAPLE STRANDGD [auth Bw]42synthetic construct
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Entity ID: 112
MoleculeChainsLengthOrganismImage
STAPLE STRANDHD [auth Bx]42synthetic construct
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Entity ID: 113
MoleculeChainsLengthOrganismImage
STAPLE STRANDID [auth By]42synthetic construct
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Entity ID: 114
MoleculeChainsLengthOrganismImage
STAPLE STRANDJD [auth Bz]42synthetic construct
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Entity ID: 115
MoleculeChainsLengthOrganismImage
STAPLE STRANDKD [auth B0]42synthetic construct
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Entity ID: 116
MoleculeChainsLengthOrganismImage
STAPLE STRANDLD [auth B1]42synthetic construct
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Entity ID: 117
MoleculeChainsLengthOrganismImage
STAPLE STRANDMD [auth B2]42synthetic construct
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Entity ID: 118
MoleculeChainsLengthOrganismImage
STAPLE STRANDND [auth B3]42synthetic construct
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Entity ID: 119
MoleculeChainsLengthOrganismImage
STAPLE STRANDOD [auth B4]42synthetic construct
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Entity ID: 120
MoleculeChainsLengthOrganismImage
STAPLE STRANDPD [auth B5]42synthetic construct
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Entity ID: 121
MoleculeChainsLengthOrganismImage
STAPLE STRANDQD [auth B6]42synthetic construct
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Entity ID: 122
MoleculeChainsLengthOrganismImage
STAPLE STRANDRD [auth B7]42synthetic 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]42synthetic construct
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Entity ID: 125
MoleculeChainsLengthOrganismImage
STAPLE STRANDUD [auth CA]42synthetic construct
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Entity ID: 126
MoleculeChainsLengthOrganismImage
STAPLE STRANDVD [auth CB]42synthetic construct
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Entity ID: 127
MoleculeChainsLengthOrganismImage
STAPLE STRANDWD [auth CC]42synthetic 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]42