9GDM | pdb_00009gdm

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

• PDB DOI: https://doi.org/10.2210/pdb9GDM/pdb
• NAKB: 9GDM
• BMRB: 34942

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


• Deposited: 2024-08-06 Released: 2024-09-18 
• Deposition Author(s): Javornik, U., Plavec, J., Galindo, M.A.
• Funding Organization(s): Slovenian Research Agency, Ministry of Economy and Competitiveness (MINECO)

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Experimental Data Snapshot

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

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

• PubMed: 39237564 
• DOI: https://doi.org/10.1038/s41467-024-51876-8
• Primary Citation 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.

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Organizational Affiliation: 
• Slovenian NMR Center, National Institute of Chemistry, SI-1000, Ljubljana, Slovenia.
Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000, Ljubljana, Slovenia.
Departamento de Química Inorgánica, Universidad de Granada, 18001, Granada, Spain.
Department of Chemistry, Oregon State University, Corvallis, OR, 97331-4003, USA.
Departamento de Química Orgánica, Universidad de Granada, 18001, Granada, Spain.
Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain.
NSF's ChemMatCARS, Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.
Department of Chemistry, Oregon State University, Corvallis, OR, 97331-4003, USA. [e-mail].
Slovenian NMR Center, National Institute of Chemistry, SI-1000, Ljubljana, Slovenia. [e-mail].
Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000, Ljubljana, Slovenia. [e-mail].
Departamento de Química Inorgánica, Universidad de Granada, 18001, Granada, Spain. [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: NMR Distance Restraints, mass spectrometry, SAXS

Macromolecule Content 

• Total Structure Weight: 8.61 kDa 
• Atom Count: 498 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
ODNI-Ag	A, B	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AG	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

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-18 
Deposition Author(s): Javornik, U., Plavec, J., Galindo, M.A.

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Funding Organization	Location	Grant Number
Slovenian Research Agency	Slovenia	P1-0242
Slovenian Research Agency	Slovenia	J1-1704
Ministry of Economy and Competitiveness (MINECO)	Spain	PID2020-120186RB-I00

Revision History  

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