8DYK image
Entry Detail
PDB ID:
8DYK
Keywords:
Title:
Room temperature neutron structure of a fluorescent Ag8 cluster templated by a multistranded DNA scaffold
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2022-08-04
Release Date:
2023-08-02
Method Details:
Experimental Method:
Resolution:
2.10 Å
R-Value Free:
0.28
R-Value Work:
0.22
R-Value Observed:
0.23
Space Group:
P 41 21 2
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*AP*AP*CP*CP*CP*C)-3')
Chain IDs:A, B
Chain Length:6
Number of Molecules:2
Biological Source:synthetic construct
Ligand Molecules
Primary Citation
Mapping H + in the Nanoscale (A 2 C 4 ) 2 -Ag 8 Fluorophore.
J Phys Chem Lett 13 11317 11322 (2022)
PMID: 36453924 DOI: 10.1021/acs.jpclett.2c03161

Abstact

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 (A2C4)2-Ag8, 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 (A2C4)2-Ag8 suggest that silvers perturb the electron distribution in the aromatic nucleobases. The different protonation states in (A2C4)2-Ag8 suggest that atomic level structures can pinpoint how to control and tune the electronic spectra of these nanoscale chromophores.

Legend

Protein

Chemical

Disease

Primary Citation of related structures