Crystallographic Structure of Novel Types of Ag -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 ions. The X-ray crystallographic structure was successfully obtained at a resolution of 1.5 Å. A novel type of Ag -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 -mediated base pairs between the N7 positions of guanines was formed. A highly bent non-canonical structure was formed at the origin of Ag -mediated base pairs in the central region. The bent duplex structure induced by the addition of Ag ions might become a powerful tool for dynamic structural changes in DNA nanotechnology applications.