6JR4

Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.798 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.126 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster.

Cerretani, C.Kanazawa, H.Vosch, T.Kondo, J.

(2019) Angew.Chem.Int.Ed.Engl. --: --

  • DOI: 10.1002/anie.201906766

  • PubMed Abstract: 
  • In the last 15 years, scientists have used DNA as a scaffold to stabilize small, atomically monodisperse silver nanoclusters. These DNA-templated nanoclusters have attracted a lot of attention due to their intriguing photophysical properties. Here, w ...

    In the last 15 years, scientists have used DNA as a scaffold to stabilize small, atomically monodisperse silver nanoclusters. These DNA-templated nanoclusters have attracted a lot of attention due to their intriguing photophysical properties. Here, we describe the crystal structure of a DNA-encapsulated, near-infrared emitting Ag16 nanocluster (DNA-Ag16NC) determined by X-ray analysis. The asymmetric unit of the crystal contains two DNA-Ag16NCs and the crystal packing between DNA-Ag16NCs is promoted by several interactions, such as two silver-mediated base pairs between 3'-terminal adenines, phosphate-Ca2+-phosphate interaction and π-stacking between two neighboring thymines. The individual Ag16NC is confined by two DNA decamers that take on a horse-shoe-like conformation. The tight wrapping of the two DNA strands around the cluster indicates that the Ag16NC is almost fully shielded from the solvent environment. The reported structural insight will enable to decipher the structure/photophysical property relationship for this class of emitters and open up a myriad of new research opportunities in fluorescence imaging and sensing using noble metal clusters in general.


    Organizational Affiliation

    Sophia University, Department of Materials and Life Sciences, 7-1 Kioi-cho, Chiyoda-ku, 102-8554, Tokyo, JAPAN.,JAPAN.,DENMARK.,Department of Chemistry and NanoScience Center, University of Copenhagen, DENMARK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*GP*A)-3')A,B,C,D10synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
AG
Query on AG

Download SDF File 
Download CCD File 
A, B, C, D
SILVER ION
Ag
FOIXSVOLVBLSDH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.798 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.126 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 24.241α = 90.00
b = 33.849β = 97.81
c = 58.863γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan17H03033

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release