5GSK

Crystal structure of duplex DNA3 in complex with Hg(II) and Sr(II)

Summary for 5GSK

• Entry DOI: 10.2210/pdb5gsk/pdb
• Related: 5GSG 5GSH 5GSI 5GSJ
• Descriptor: DNA (5'-D(*GP*GP*TP*CP*GP*TP*CP*C)-3'), MERCURY (II) ION, STRONTIUM ION, ... (4 entities in total)
• Functional Keywords: metallo-base pair, t-hg(ii)-t, dna
• Biological source: unidentified
• Total number of polymer chains: 1
• Total formula weight: 2706.80

Authors

Liu, H.H.,Wang, R.,Yao, Q.Q.,Cheng, Y.Q.,Yang, C.,Luo, Q.,Wu, B.X.,Li, J.X.,Ma, J.B.,Sheng, J.,Gan, J.H. (deposition date: 2016-08-16, release date: 2017-02-08, Last modification date: 2024-03-20)

Primary citation

Liu, H.H.,Cai, C.,Haruehanroengra, P.,Yao, Q.Q.,Chen, Y.Q.,Yang, C.,Luo, Q.,Wu, B.X.,Li, J.X.,Ma, J.B.,Sheng, J.,Gan, J.H.
Flexibility and stabilization of HgII-mediated C:T and T:T base pairs in DNA duplex
Nucleic Acids Res., 45:2910-2918, 2017

PubMed Abstract: Owing to their great potentials in genetic code extension and the development of nucleic acid-based functional nanodevices, DNA duplexes containing HgII-mediated base pairs have been extensively studied during the past 60 years. However, structural basis underlying these base pairs remains poorly understood. Herein, we present five high-resolution crystal structures including one first-time reported C-HgII-T containing duplex, three T-HgII-T containing duplexes and one native duplex containing T-T pair without HgII. Our structures suggest that both C-T and T-T pairs are flexible in interacting with the HgII ion with various binding modes including N3-HgII-N3, N4-HgII-N3, O2-HgII-N3 and N3-HgII-O4. Our studies also reveal that the overall conformations of the C-HgII-T and T-HgII-T pairs are affected by their neighboring residues via the interactions with the solvent molecules or other metal ions, such as SrII. These results provide detailed insights into the interactions between HgII and nucleobases and the structural basis for the rational design of C-HgII-T or T-HgII-T containing DNA nanodevices in the future.

PubMed: 27998930
DOI: 10.1093/nar/gkw1296

Experimental method

X-RAY DIFFRACTION (1.05 Å)