8DYK | pdb_00008dyk

Room temperature neutron structure of a fluorescent Ag8 cluster templated by a multistranded DNA scaffold


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.287 (Depositor) 
  • R-Value Work: 
    0.226 (Depositor) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Mapping H + in the Nanoscale (A 2 C 4 ) 2 -Ag 8 Fluorophore.

David, F.Setzler, C.Sorescu, A.Lieberman, R.L.Meilleur, F.Petty, J.T.

(2022) J Phys Chem Lett 13: 11317-11322

  • DOI: https://doi.org/10.1021/acs.jpclett.2c03161
  • Primary Citation Related Structures: 
    8DYK

  • PubMed Abstract: 

    When strands of DNA encapsulate silver clusters, supramolecular optical chromophores develop. However, how a particular structure endows a specific spectrum remains poorly understood. Here, we used neutron diffraction to map protonation in (A 2 C 4 ) 2 -Ag 8 , a green-emitting fluorophore with a "Big Dipper" arrangement of silvers. The DNA host has two substructures with distinct protonation patterns. Three cytosines from each strand collectively chelate handle-like array of three silvers, and calorimetry studies suggest Ag + cross-links. The twisted cytosines are further joined by hydrogen bonds from fully protonated amines. The adenines and their neighboring cytosine from each strand anchor a dipper-like group of five silvers via their deprotonated endo- and exocyclic nitrogens. Typically, exocyclic amines are strongly basic, so their acidification and deprotonation in (A 2 C 4 ) 2 -Ag 8 suggest that silvers perturb the electron distribution in the aromatic nucleobases. The different protonation states in (A 2 C 4 ) 2 -Ag 8 suggest that atomic level structures can pinpoint how to control and tune the electronic spectra of these nanoscale chromophores.


  • Organizational Affiliation
    • Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States.

Macromolecule Content 

  • Total Structure Weight: 4.66 kDa 
  • Atom Count: 265 
  • Modeled Residue Count: 12 
  • Deposited Residue Count: 12 
  • Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*AP*CP*CP*CP*C)-3')
A, B
6synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AG
(Subject of Investigation/LOI)

Query on AG



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth B]
SILVER ION
Ag
FOIXSVOLVBLSDH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.287 (Depositor) 
  • R-Value Work:  0.226 (Depositor) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.568α = 90
b = 33.568β = 90
c = 63.741γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Mantiddata reduction
LAUENORMdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1611451
National Science Foundation (NSF, United States)United StatesCHE-2002910
National Science Foundation (NSF, United States)United StatesOIA-1655740

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-02
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection
  • Version 1.2: 2026-03-04
    Changes: Refinement description, Structure summary