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

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

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’ base...

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Main Authors: Yamaguchi, Hiroshi, Šebera, Jakub, Kondo, Jiro, Oda, Shuji, Komuro, Tomoyuki, Kawamura, Takuya, Dairaku, Takenori, Kondo, Yoshinori, Okamoto, Itaru, Ono, Akira, Burda, Jaroslav V., Kojima, Chojiro, Sychrovský, Vladimír, Tanaka, Yoshiyuki
Format: Online
Language:English
Published: Oxford University Press 2014
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973346/
id pubmed-3973346
recordtype oai_dc
spelling pubmed-39733462014-04-04 The structure of metallo-DNA with consecutive thymine–HgII–thymine base pairs explains positive entropy for the metallo base pair formation Yamaguchi, Hiroshi Šebera, Jakub Kondo, Jiro Oda, Shuji Komuro, Tomoyuki Kawamura, Takuya Dairaku, Takenori Kondo, Yoshinori Okamoto, Itaru Ono, Akira Burda, Jaroslav V. Kojima, Chojiro Sychrovský, Vladimír Tanaka, Yoshiyuki Structural Biology 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 (ΔS) for the T–HgII–T base pair formation. The positive ΔS 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. Oxford University Press 2014-04 2013-12-26 /pmc/articles/PMC3973346/ /pubmed/24371287 http://dx.doi.org/10.1093/nar/gkt1344 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Yamaguchi, Hiroshi
Šebera, Jakub
Kondo, Jiro
Oda, Shuji
Komuro, Tomoyuki
Kawamura, Takuya
Dairaku, Takenori
Kondo, Yoshinori
Okamoto, Itaru
Ono, Akira
Burda, Jaroslav V.
Kojima, Chojiro
Sychrovský, Vladimír
Tanaka, Yoshiyuki
spellingShingle Yamaguchi, Hiroshi
Šebera, Jakub
Kondo, Jiro
Oda, Shuji
Komuro, Tomoyuki
Kawamura, Takuya
Dairaku, Takenori
Kondo, Yoshinori
Okamoto, Itaru
Ono, Akira
Burda, Jaroslav V.
Kojima, Chojiro
Sychrovský, Vladimír
Tanaka, Yoshiyuki
The structure of metallo-DNA with consecutive thymine–HgII–thymine base pairs explains positive entropy for the metallo base pair formation
author_facet Yamaguchi, Hiroshi
Šebera, Jakub
Kondo, Jiro
Oda, Shuji
Komuro, Tomoyuki
Kawamura, Takuya
Dairaku, Takenori
Kondo, Yoshinori
Okamoto, Itaru
Ono, Akira
Burda, Jaroslav V.
Kojima, Chojiro
Sychrovský, Vladimír
Tanaka, Yoshiyuki
author_sort Yamaguchi, Hiroshi
title The structure of metallo-DNA with consecutive thymine–HgII–thymine base pairs explains positive entropy for the metallo base pair formation
title_short The structure of metallo-DNA with consecutive thymine–HgII–thymine base pairs explains positive entropy for the metallo base pair formation
title_full The structure of metallo-DNA with consecutive thymine–HgII–thymine base pairs explains positive entropy for the metallo base pair formation
title_fullStr The structure of metallo-DNA with consecutive thymine–HgII–thymine base pairs explains positive entropy for the metallo base pair formation
title_full_unstemmed The structure of metallo-DNA with consecutive thymine–HgII–thymine base pairs explains positive entropy for the metallo base pair formation
title_sort structure of metallo-dna with consecutive thymine–hgii–thymine base pairs explains positive entropy for the metallo base pair formation
description 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 (ΔS) for the T–HgII–T base pair formation. The positive ΔS 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.
publisher Oxford University Press
publishDate 2014
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973346/
_version_ 1612073369435373568

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