DSSR-PyMOL cartoon-block schematics: PDB entry 7xkm

PDB-id

7xkm; DSSR-derived features in text and JSON formats

Class

DNA

Method

X-ray (2.79 Å)

Summary

Crystal structure of DNA-ag(i) rod comprising a one-dimensional array of 11 silver ions

Reference

Atsugi T, Ono A, Tasaka M, Eguchi N, Fujiwara S, Kondo J (2022): "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., e202204798. doi: 10.1002/anie.202204798.

Abstract

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 Ag_I -DNA nanowire with an uninterrupted one-dimensional silver array was determined. Here, we present a new DNA helical wire, the "Ag_I -DNA rod", containing an uninterrupted array of 11 Ag_I ions. The Ag_I -DNA rod consisted of only C-Ag_I -C, G-Ag_I -G, G-Ag_I -5-bromouracil (_Br U), and _Br U-Ag_I -_Br U metallo base pairs, with no Watson-Crick pairs. The Ag_I -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 Ag_I -DNA rods formed in solution, as well as within crystals.