6LBW

Crystal structure of Ag-mediated base pairs in uncanonical DNA duplex

Summary for 6LBW

• Entry DOI: 10.2210/pdb6lbw/pdb
• Descriptor: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*(LCC)P*TP*CP*GP*CP*G)-3'), SILVER ION (3 entities in total)
• Functional Keywords: dna, lna, 2', 4'-bna, metallo-base pair, silver
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 7127.95

Authors

Aoyama, H.,Obika, S.,Nakagawa, O. (deposition date: 2019-11-15, release date: 2020-11-18, Last modification date: 2024-03-27)

Primary citation

Nakagawa, O.,Aoyama, H.,Fujii, A.,Kishimoto, Y.,Obika, S.
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.
Chemistry, 27:3842-3848, 2021

PubMed Abstract: 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.

PubMed: 33274789
DOI: 10.1002/chem.202004819

Experimental method

X-RAY DIFFRACTION (1.501 Å)