The structure of metallo-DNA with consecutive thymine-Hg II-thymine base pairs explains positive entropy for the metallo base pair formation

Hiroshi Yamaguchi, Jakub Šebera, Jiro Kondo, Shuji Oda, Tomoyuki Komuro, Takuya Kawamura, Takenori Dairaku, Yoshinori Kondo, Itaru Okamoto, Akira Ono, Jaroslav V. Burda, Chojiro Kojima, Vladimír Sychrovský, Yoshiyuki Tanaka

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Abstract

We have determined the three-dimensional (3D) structure of DNA duplex that includes tandem HgII-mediated T-T base pairs (thymine-HgII- thymine, T-HgII-T) with NMR spectroscopy in solution. This is the first 3D structure of metallo- DNA (covalently metallated DNA) composed exclusively of 'NATURAL' bases. The T-HgII-T base pairs whose chemical structure was determined with the 15N NMR spectroscopy were well accommodated in a B-form double helix, mimicking normal Watson-Crick base pairs. The Hg atoms aligned along DNA helical axis were shielded from the bulk water. The complete dehydration of Hg atoms inside DNA explained the positive reaction entropy ("S) for the T-HgII-T base pair formation. The positive "S value arises owing to the HgII dehydration, which was approved with the 3D structure. The 3D structure explained extraordinary affinity of thymine towards HgII and revealed arrangement of T-HgII-T base pairs in metallo-DNA.

Original languageEnglish
Pages (from-to)4094-4099
Number of pages6
JournalNucleic acids research
Volume42
Issue number6
DOIs
Publication statusPublished - 2014 Apr

ASJC Scopus subject areas

  • Genetics

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    Yamaguchi, H., Šebera, J., Kondo, J., Oda, S., Komuro, T., Kawamura, T., Dairaku, T., Kondo, Y., Okamoto, I., Ono, A., Burda, J. V., Kojima, C., Sychrovský, V., & Tanaka, Y. (2014). The structure of metallo-DNA with consecutive thymine-Hg II-thymine base pairs explains positive entropy for the metallo base pair formation. Nucleic acids research, 42(6), 4094-4099. https://doi.org/10.1093/nar/gkt1344