8GZK

Crystal structure of Cd2+-bound DNA aptamer T10A mutant

Summary for 8GZK

• Entry DOI: 10.2210/pdb8gzk/pdb
• Descriptor: 25-mer DNA, CADMIUM ION, BARIUM ION, ... (4 entities in total)
• Functional Keywords: dna aptamer, cd2+-binding, complex, dna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 16311.38

Authors

Gan, J.H.,Liu, H.H.,Gao, Y.Q. (deposition date: 2022-09-27, release date: 2023-08-09, Last modification date: 2024-05-29)

Primary citation

Liu, H.,Gao, Y.,Mathivanan, J.,Armour-Garb, Z.,Shao, Z.,Zhang, Y.,Zhao, X.,Shao, Q.,Zhang, W.,Yang, J.,Cao, C.,Li, H.,Sheng, J.,Gan, J.
Crystal structures and identification of novel Cd2+-specific DNA aptamer.
Nucleic Acids Res., 51:4625-4636, 2023

PubMed Abstract: Cadmium (Cd) is one of the most toxic heavy metals. Exposure to Cd can impair the functions of the kidney, respiratory system, reproductive system and skeletal system. Cd2+-binding aptamers have been extensively utilized in the development of Cd2+-detecting devices; however, the underlying mechanisms remain elusive. This study reports four Cd2+-bound DNA aptamer structures, representing the only Cd2+-specific aptamer structures available to date. In all the structures, the Cd2+-binding loop (CBL-loop) adopts a compact, double-twisted conformation and the Cd2+ ion is mainly coordinated with the G9, C12 and G16 nucleotides. Moreover, T11 and A15 within the CBL-loop form one regular Watson-Crick pair and stabilize the conformation of G9. The conformation of G16 is stabilized by the G8-C18 pair of the stem. By folding and/or stabilizing the CBL-loop, the other four nucleotides of the CBL-loop also play important roles in Cd2+ binding. Similarly to the native sequence, crystal structures, circular dichroism spectrum and isothermal titration calorimetry analysis confirm that several variants of the aptamer can recognize Cd2+. This study not only reveals the underlying basis for the binding of Cd2+ ions with the aptamer, but also extends the sequence for the construction of novel metal-DNA complex.

PubMed: 37013991
DOI: 10.1093/nar/gkad239

Experimental method

X-RAY DIFFRACTION (2.94 Å)