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Crystallographic Structure of Novel Types of Ag I ‐Mediated Base Pairs in Non‐canonical DNA Duplex Containing 2′‐ O ,4′‐ C ‐Methylene Bridged Nucleic Acids
Author(s) -
Nakagawa Osamu,
Aoyama Hiroshi,
Fujii Akane,
Kishimoto Yuki,
Obika Satoshi
Publication year - 2021
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.202004819
Subject(s) - duplex (building) , nucleic acid , base pair , crystallography , dna , nucleobase , bent molecular geometry , chemistry , stereochemistry , crystal structure , metal , biochemistry , organic chemistry
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 Å. 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.