8DAP

[GA/TC] Self-Assembled 3D DNA Tensegrity Triangle with 24 bp Arm Length forming a Trigonal Hexagon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.47 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Highly Symmetric, Self-Assembling 3D DNA Crystals with Cubic and Trigonal Lattices.

Lu, B.Vecchioni, S.Ohayon, Y.P.Woloszyn, K.Markus, T.Mao, C.Seeman, N.C.Canary, J.W.Sha, R.

(2023) Small 19: e2205830-e2205830

  • DOI: 10.1002/smll.202205830
  • Primary Citation of Related Structures:  
    8D31, 8DAP

  • PubMed Abstract: 
  • The rational design of nanoscopic DNA tiles has yielded highly ordered crystalline matter in 2D and 3D. The most well-studied 3D tile is the DNA tensegrity triangle, which is known to self-assemble into macroscopic crystals. However, contemporary rational design parameters for 3D DNA crystals nearly universally invoke integer numbers of DNA helical turns and Watson-Crick (WC) base pairs ...

    The rational design of nanoscopic DNA tiles has yielded highly ordered crystalline matter in 2D and 3D. The most well-studied 3D tile is the DNA tensegrity triangle, which is known to self-assemble into macroscopic crystals. However, contemporary rational design parameters for 3D DNA crystals nearly universally invoke integer numbers of DNA helical turns and Watson-Crick (WC) base pairs. In this study, 24-bp edges are substituted into a previously 21-bp (two helical turns of DNA) tensegrity triangle motif to explore whether such unconventional motif can self-assemble into 3D crystals. The use of noncanonical base pairs in the sticky ends results in a cubic arrangement of tensegrity triangles with exceedingly high symmetry, assembling a lattice from winding helical axes and diamond-like tessellation patterns. Reverting this motif to sticky ends with Watson-Crick pairs results in a trigonal hexagonal arrangement, replicating this diamond arrangement in a hexagonal context. These results showcase that the authors can generate unexpected, highly complex, pathways for materials design by testing modifications to 3D tiles without prior knowledge of the ensuing symmetry. This study expands the rational design toolbox for DNA nanotechnology; and it further illustrates the existence of yet-unexplored arrangements of crystalline soft matter.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*GP*CP*CP*TP*AP*CP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*AP*G)-3')C [auth A],
A [auth E],
G [auth I]
24synthetic construct
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*CP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*AP*GP*GP*C)-3')E [auth C],
F [auth D],
B [auth H]
17synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP*CP*G)-3')D [auth B]21synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.47 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.609α = 90
b = 166.609β = 90
c = 119.318γ = 120
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
National Science Foundation (NSF, United States)United StatesCTS1120890
National Science Foundation (NSF, United States)United StatesCCF-1117210
National Science Foundation (NSF, United States)United StatesEFRI-1332411
National Science Foundation (NSF, United States)United StatesCHE-1708776
Office of Naval Research (ONR)United StatesN000141110729
Office of Naval Research (ONR)United StatesN000140911118
Department of Energy (DOE, United States)United StatesDESC0007991

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release