8SJT

[3T14+10] Self-assembling left-handed tensegrity triangle with 14 interjunction base pairs and a 10 bp linker with R3 symmetry

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

  • Deposited: 2023-04-18 Released: 2024-04-24 
  • Deposition Author(s): Janowski, J., Vecchioni, S., 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), National Aeronautic Space Administration (NASA, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 9.38 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Engineering tertiary chirality in helical biopolymers.

Janowski, J.Pham, V.A.B.Vecchioni, S.Woloszyn, K.Lu, B.Zou, Y.Erkalo, B.Perren, L.Rueb, J.Madnick, J.Mao, C.Saito, M.Ohayon, Y.P.Jonoska, N.Sha, R.

(2024) Proc Natl Acad Sci U S A 121: e2321992121-e2321992121

  • DOI: https://doi.org/10.1073/pnas.2321992121
  • Primary Citation of Related Structures:  
    8SJM, 8SJN, 8SJO, 8SJP, 8SJQ, 8SJR, 8SJS, 8SJT, 8SJU, 8SJV, 8SJW, 8SL5, 8SZ5

  • PubMed Abstract: 

    Tertiary chirality describes the handedness of supramolecular assemblies and relies not only on the primary and secondary structures of the building blocks but also on topological driving forces that have been sparsely characterized. Helical biopolymers, especially DNA, have been extensively investigated as they possess intrinsic chirality that determines the optical, mechanical, and physical properties of the ensuing material. Here, we employ the DNA tensegrity triangle as a model system to locate the tipping points in chirality inversion at the tertiary level by X-ray diffraction. We engineer tensegrity triangle crystals with incremental rotational steps between immobile junctions from 3 to 28 base pairs (bp). We construct a mathematical model that accurately predicts and explains the molecular configurations in both this work and previous studies. Our design framework is extendable to other supramolecular assemblies of helical biopolymers and can be used in the design of chiral nanomaterials, optically active molecules, and mesoporous frameworks, all of which are of interest to physical, biological, and chemical nanoscience.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*AP*CP*GP*TP*GP*GP*AP*CP*AP*GP*GP*AP*G)-3')14synthetic construct
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*CP*CP*TP*CP*CP*TP*GP*AP*GP*GP*TP*CP*GP*AP*GP*C)-3')17synthetic construct
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*CP*GP*CP*TP*CP*AP*GP*CP*CP*TP*GP*AP*CP*TP*CP*A)-3')17synthetic construct
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*GP*AP*GP*TP*CP*TP*CP*CP*AP*CP*GP*T)-3')14synthetic construct
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*AP*CP*TP*CP*TP*GP*CP*TP*A)-3')E [auth X]10synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*TP*TP*AP*GP*CP*AP*GP*AP*G)-3')F [auth Y]10synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 9.38 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.243α = 90
b = 212.243β = 90
c = 164.272γ = 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
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
National Aeronautic Space Administration (NASA, United States)United States2020 NASA Center Innovation Fund

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