9GDM | pdb_00009gdm

Solution structure of a silver ion mediated DNA duplex with universal 7-deazapurine substitutions


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Unveiling the solution structure of a DNA duplex with continuous silver-modified Watson-Crick base pairs.

Javornik, U.Perez-Romero, A.Lopez-Chamorro, C.Smith, R.M.Dobado, J.A.Palacios, O.Bera, M.K.Nyman, M.Plavec, J.Galindo, M.A.

(2024) Nat Commun 15: 7763-7763

  • DOI: https://doi.org/10.1038/s41467-024-51876-8
  • Primary Citation of Related Structures:  
    9GDM

  • PubMed Abstract: 

    The challenge of transforming organized DNA structures into their metallized counterparts persists in the scientific field. In this context, utilizing DNA molecules modified with 7-deazapurine, provides a transformative solution. In this study, we present the solution structure of a DNA duplex that can be transformed into its metallized equivalent while retaining the natural base pairing arrangement through the creation of silver-modified Watson-Crick base pairs. Unlike previously documented X-ray structures, our research demonstrates the feasibility of preserving the intrinsic DNA self-assembly while incorporating Ag I into the double helix, illustrating that the binding of silver does not disrupt the canonical base-pairing organization. Moreover, in our case, the uninterrupted Ag I chain deviates from forming conventional straight linear chains; instead, it adheres to a helical arrangement dictated by the underlying DNA structure. This research challenges conventional assumptions and opens the door to precisely design structures based on the organization of highly stable Ag-DNA assemblies.


  • Organizational Affiliation
    • Slovenian NMR Center, National Institute of Chemistry, SI-1000, Ljubljana, Slovenia.

Macromolecules

Find similar nucleic acids by:  Sequence  

Entity ID: 1
MoleculeChains LengthOrganismImage
ODNI-Ag
A, B
12synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AG
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 B],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
SILVER ION
Ag
FOIXSVOLVBLSDH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Slovenian Research AgencySloveniaP1-0242
Slovenian Research AgencySloveniaJ1-1704
Ministry of Economy and Competitiveness (MINECO)SpainPID2020-120186RB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release