Crystallographic Structure of Novel Types of AgI-Mediated Base Pairs in Non-canonical DNA Duplex Containing 2′-O,4′-C-Methylene Bridged Nucleic Acids

Metal-mediated base pairs have widespread applications, such as in DNA-metal nanodevices and sensors. Here, we focused on their sugar conformation in duplexes and observed the crystallographic structure of the non-canonical DNA/DNA duplex containing 2 '-O,4 '-C-methylene bridged nucleic acid in the presence of Ag-I ions. The X-ray crystallographic structure was successfully obtained at a resolution of 1.5 angstrom. A novel type of Ag-I-mediated base pair between the N1 positions of anti-conformation of adenines in the duplex was observed. In the central non-canonical region, a hexad nucleobase structure containing Ag-I-mediated base pairs between the N7 positions of guanines was formed. A highly bent non-canonical structure was formed at the origin of Ag-I-mediated base pairs in the central region. The bent duplex structure induced by the addition of Ag-I ions might become a powerful tool for dynamic structural changes in DNA nanotechnology applications.

Automated summary

The study focused on the crystallographic structure of a non-canonical DNA/DNA duplex containing metal-mediated base pairs, revealing a novel type of Ag-I-mediated base pair and its potential application in DNA nanotechnology. This bent duplex structure induced by Ag-I ions could be a powerful tool for dynamic structural changes in DNA nanotechnology applications.