9GDM image
Entry Detail
PDB ID:
9GDM
Keywords:
Title:
Solution structure of a silver ion mediated DNA duplex with universal 7-deazapurine substitutions
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2024-08-06
Release Date:
2024-09-18
Method Details:
Experimental Method:
Conformers Calculated:
100
Conformers Submitted:
10
Selection Criteria:
structures with the lowest energy
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Description:ODNI-Ag
Chain IDs:A, B
Chain Length:12
Number of Molecules:2
Biological Source:synthetic construct
Ligand Molecules
Primary Citation
Unveiling the solution structure of a DNA duplex with continuous silver-modified Watson-Crick base pairs.
Nat Commun 15 7763 7763 (2024)
PMID: 39237564 DOI: 10.1038/s41467-024-51876-8

Abstact

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 AgI into the double helix, illustrating that the binding of silver does not disrupt the canonical base-pairing organization. Moreover, in our case, the uninterrupted AgI 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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