7U43

[L334] Self-assembling tensegrity triangle with three turns, three turns and four turns of DNA per axis by extension and linker addition with P1 symmetry

  • Classification: DNA
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2022-02-28 Released: 2022-09-28 
  • Deposition Author(s): Woloszyn, K., Vecchioni, S., Seeman, N.C., Sha, R., Ohayon, Y.P.
  • Funding Organization(s): Office of Naval Research (ONR), Department of Energy (DOE, United States), National Science Foundation (NSF, United States), Human Frontier Science Program (HFSP)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.55 Å
  • R-Value Free: 0.124 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.116 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Augmented DNA Nanoarchitectures: A Structural Library of 3D Self-Assembling Tensegrity Triangle Variants.

Woloszyn, K.Vecchioni, S.Ohayon, Y.P.Lu, B.Ma, Y.Huang, Q.Zhu, E.Chernovolenko, D.Markus, T.Jonoska, N.Mao, C.Seeman, N.C.Sha, R.

(2022) Adv Mater 34: e2206876-e2206876

  • DOI: https://doi.org/10.1002/adma.202206876
  • Primary Citation of Related Structures:  
    7U3O, 7U3P, 7U3Q, 7U3R, 7U3S, 7U3T, 7U3U, 7U3V, 7U3W, 7U3X, 7U3Y, 7U3Z, 7U40, 7U41, 7U42, 7U43, 7U44, 7U45

  • PubMed Abstract: 

    The DNA tensegrity triangle is known to reliably self-assemble into a 3D rhombohedral crystalline lattice via sticky-end cohesion. Here, the library of accessible motifs is expanded through covalent extensions of intertriangle regions and sticky-end-coordinated linkages of adjacent triangles with double helical segments using both geometrically symmetric and asymmetric configurations. The molecular structures of 18 self-assembled architectures at resolutions of 3.32-9.32 Å are reported; the observed cell dimensions, cavity sizes, and cross-sectional areas agree with theoretical expectations. These data demonstrate that fine control over triclinic and rhombohedral crystal parameters and the customizability of more complex 3D DNA lattices are attainable via rational design. It is anticipated that augmented DNA architectures may be fine-tuned for the self-assembly of designer nanocages, guest-host complexes, and proscriptive 3D nanomaterials, as originally envisioned. Finally, designer asymmetric crystalline building blocks can be seen as a first step toward controlling and encoding information in three dimensions.


  • Organizational Affiliation

    Department of Chemistry, New York University, New York, NY, 10003, USA.


Macromolecules
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (31-MER)31synthetic construct
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*TP*AP*GP*CP*AP*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP*GP*GP*CP*TP*CP*T)-3')B [auth E]24synthetic construct
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*GP*TP*GP*CP*TP*TP*GP*CP*GP*TP*CP*GP*CP*TP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')C [auth D]24synthetic construct
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')D [auth B]21synthetic construct
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*CP*TP*GP*AP*TP*GP*TP*GP*GP*TP*AP*GP*G)-3')E [auth F]14synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (31-MER)F [auth C]31synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*AP*CP*AP*CP*CP*GP*AP*TP*CP*AP*CP*CP*TP*GP*CP*CP*AP*CP*CP*G)-3')G [auth M]21synthetic construct
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*CP*TP*CP*TP*GP*CP*TP*AP*CP*TP*AP*CP*GP*TP*CP*AP*GP*CP*A)-3')H [auth X]21synthetic construct
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Entity ID: 9
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*CP*TP*GP*CP*TP*GP*AP*CP*GP*TP*AP*GP*TP*AP*GP*CP*AP*GP*AP*G)-3')I [auth Y]21synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.55 Å
  • R-Value Free: 0.124 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.116 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.586α = 98.642
b = 101.71β = 109.491
c = 134.339γ = 101.44
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Office of Naval Research (ONR)United StatesN000141912596
Department of Energy (DOE, United States)United StatesDE-SC0007991
National Science Foundation (NSF, United States)United States2106790
Human Frontier Science Program (HFSP)FranceRPG0010/2017
National Science Foundation (NSF, United States)United StatesDMR-1420073

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 1.1: 2022-12-21
    Changes: Database references
  • Version 1.2: 2023-08-16
    Changes: Data collection, Other
  • Version 1.3: 2023-10-25
    Changes: Refinement description