7D32

The TBA-Pb2+ complex in P41212 space group

Summary for 7D32

• Entry DOI: 10.2210/pdb7d32/pdb
• Descriptor: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'), LEAD (II) ION (3 entities in total)
• Functional Keywords: quadruplex, pb2+-binding, dna aptamer, dna
• Biological source: synthetic construct
• Total number of polymer chains: 6
• Total formula weight: 29701.51

Authors

Liu, H.H.,Gao, Y.Q.,Sheng, J.,Gan, J.H. (deposition date: 2020-09-18, release date: 2021-09-22, Last modification date: 2023-11-29)

Primary citation

Liu, H.,Gao, Y.,Mathivanan, J.,Shen, F.,Chen, X.,Li, Y.,Shao, Z.,Zhang, Y.,Shao, Q.,Sheng, J.,Gan, J.
Structure-guided development of Pb 2+ -binding DNA aptamers.
Sci Rep, 12:460-460, 2022

PubMed Abstract: Owing to its great threat to human health and environment, Pb pollution has been recognized as a major public problem by the World Health Organization (WHO). Many DNA aptamers have been utilized in the development of Pb-detection sensors, but the underlying mechanisms remain elusive. Here, we report three Pb-complexed structures of the thrombin binding aptamer (TBA). These high-resolution crystal structures showed that TBA forms intramolecular G-quadruplex and Pb is bound by the two G-tetrads in the center. Compared to K-stabilized G-quadruplexes, the coordinating distance between Pb and the G-tetrads are much shorter. The T3T4 and T12T13 linkers play important roles in dimerization and crystallization of TBA, but they are changeable for Pb-binding. In combination with mutagenesis and CD spectra, the G8C mutant structure unraveled that the T7G8T9 linker of TBA is also variable. In addition to expansion of the Pb-binding aptamer sequences, our study also set up one great example for quick and rational development of other aptamers with similar or optimized binding activity.

PubMed: 35013452
DOI: 10.1038/s41598-021-04243-2

Experimental method

X-RAY DIFFRACTION (1.707 Å)