9EOQ

Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructure V4 and TBA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Designing Rigid DNA Origami Templates for Molecular Visualization Using Cryo-EM.

Khoshouei, A.Kempf, G.Mykhailiuk, V.Griessing, J.M.Honemann, M.N.Kater, L.Cavadini, S.Dietz, H.

(2024) Nano Lett 24: 5031-5038

  • DOI: https://doi.org/10.1021/acs.nanolett.4c00915
  • Primary Citation of Related Structures:  
    9EOQ

  • PubMed Abstract: 

    DNA origami, a method for constructing nanostructures from DNA, offers potential for diverse scientific and technological applications due to its ability to integrate various molecular functionalities in a programmable manner. In this study, we examined the impact of internal crossover distribution and the compositional uniformity of staple strands on the structure of multilayer DNA origami using cryogenic electron microscopy (cryo-EM) single-particle analysis. A refined DNA object was utilized as an alignment framework in a host-guest model, where we successfully resolved an 8 kDa thrombin binding aptamer (TBA) linked to the host object. Our results broaden the spectrum of DNA in structural applications.


  • Organizational Affiliation

    Laboratory for Biomolecular Nanotechnology, Department of Biosciences, School of Natural Sciences, Technical University of Munich, Am Coulombwall 4a, 85748 Garching, Germany.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (42-MER)42synthetic construct
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*TP*AP*TP*AP*GP*CP*GP*TP*GP*GP*AP*AP*GP*T)-3')15synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union101018465
German Research Foundation (DFG)Germany--
Germanys Excellence StrategyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references