7XKM image
Deposition Date 2022-04-20
Release Date 2022-07-06
Last Version Date 2024-05-29
Entry Detail
PDB ID:
7XKM
Keywords:
DNA
Title:
Crystal structure of DNA-Ag(I) rod comprising a one-dimensional array of 11 silver ions
Biological Source:
Source Organism:
synthetic construct (Taxon ID: 32630)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.79 Å
R-Value Free:
0.21
R-Value Work:
0.18
R-Value Observed:
0.19
Space Group:
P 61 2 2
7XKM validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*GP*CP*GP*CP*(BRU)P*CP*(BRU)P*CP*GP*CP*G)-3')
Chain IDs:A, B, C, D
Chain Length:12
Number of Molecules:4
Biological Source:synthetic construct
Ligand Molecules
AG
Primary Citation
A Novel Ag I -DNA Rod Comprising a One-Dimensional Array of 11 Silver Ions within a Double Helical Structure.
Angew.Chem.Int.Ed.Engl. 61 e202204798 e202204798 (2022)
PMID: 35641885 DOI: 10.1002/anie.202204798

Abstact

DNA/RNA duplexes containing metal-ion-mediated base pairs (metallo-base pairs) have potential applications in developing nucleic acid-based nanodevices and genetic code expansion. Many metallo-base pairs are formed within duplexes stabilized by Watson-Crick base pairs. Recently, the crystal structure of an AgI -DNA nanowire with an uninterrupted one-dimensional silver array was determined. Here, we present a new DNA helical wire, the "AgI -DNA rod", containing an uninterrupted array of 11 AgI ions. The AgI -DNA rod consisted of only C-AgI -C, G-AgI -G, G-AgI -5-bromouracil (Br U), and Br U-AgI -Br U metallo base pairs, with no Watson-Crick pairs. The AgI -DNA rods were connected by non-canonical G-G pairs in crystals. Notably, data from our absorbance, circular dichroism, nuclear magnetic resonance, and mass spectrometry analyses suggested that the AgI -DNA rods formed in solution, as well as within crystals.

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Primary Citation of related structures
7XKM