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 9NKX | pdb_00009nkx

[TT-5x_Ag4] Tensegrity triangle structure with a T:T base pair hosting a templated 4-atom silver nanocluster

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

  • Deposited: 2025-03-01 Released: 2026-10-14 
  • Deposition Author(s): Vecchioni, S., Perren, L., Sha, R., Ohayon, Y.P.
  • Funding Organization(s): National Science Foundation (NSF, China), Department of Energy (DOE, United States), Office of Naval Research (ONR)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.59 Å
  • R-Value Free: 
    0.248 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9NKX

This is version 1.0 of the entry. See complete history. 

Literature

Topology-enforced synthesis of atomically precise silver nanoclusters in 3D DNA lattices.

Perren, L., Livernois, W., Woloszyn, K., Janowski, J., Singh, V.R., Faiaz, L., Jaffe, M., Colabella, M., McHenry, T.A., Avalos, C.E., Mao, C., Canary, J.W., Ohayon, Y.P., Sha, R., Anantram, M.P., Vecchioni, S.

(2026) Sci Adv 12: eaec2365-eaec2365

  • DOI: https://doi.org/10.1126/sciadv.aec2365
  • Primary Citation Related Structures: 
    9NKV, 9NKW, 9NKX, 9NLA

  • PubMed Abstract: 

    DNA nanotechnology leverages the molecular design resolution of the DNA double helix to fold and tile matter into designer architectures. Recent advances in bioinorganic chemistry have exploited DNA/Ag + affinity to carry out the templated reduction of silver nanoclusters. Here, we develop a unified method that leverages the topology of DNA triangles with embedded silver base pairs to nucleate controlled cluster growth in a mesoporous 3D lattice. Use of confocal fluorescence microscopy allows for the direct observation of reaction kinetics and reconstruction of the optical bandgap. These crystals yield molecular structures of Ag 4 and Ag 6 by x-ray diffraction in varying pyrimidine:pyrimidine pairs. Intercluster distances of less than 2 nanometers show observable electronic coupling, with red shifting observed relative to literature standards. A thorough computational investigation establishes a theoretical basis for our observed behavior and establishes the interplay between cluster size, charge, geometry, and resonance. We anticipate that these results will yield advances in materials synthesis, DNA-based plasmonic crystals, and optically active nanoelectronics.


  • Organizational Affiliation: 
    • Department of Chemistry, New York University, New York, NY, USA.

Macromolecule Content 

  • Total Structure Weight: 13.22 kDa 
  • Atom Count: 862 
  • Modeled Residue Count: 42 
  • Deposited Residue Count: 42 
  • Unique nucleic acid chains: 4

Macromolecules

Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*TP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')21synthetic construct
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*CP*AP*TP*AP*CP*A)-3')7synthetic construct
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')7synthetic construct
Sequence Annotations
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Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')7synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.59 Å
  • R-Value Free:  0.248 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.025α = 90
b = 104.025β = 90
c = 97.35γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
STARANISOdata scaling
AutoSolphasing
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)ChinaGCR-2317843
Department of Energy (DOE, United States)United StatesDE-SC0007991
Office of Naval Research (ONR)United StatesN000141912596

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-14
    Type: Initial release