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Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation

Iodine-induced cleavage at phosphorothioate DNA (PT-DNA) is characterized by extremely high sensitivity (∼1 phosphorothioate link per 10(6) nucleotides), which has been used for detecting and sequencing PT-DNA in bacteria. Despite its foreseeable potential for wide applications, the cleavage mechani...

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Autores principales: Huang, Qiang, Lee, Ga Young, Li, Jiayi, Wang, Chuan, Zhao, Rosalinda L., Deng, Zixin, Houk, K. N., Zhao, Yi-Lei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: National Academy of Sciences 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9169930/
https://www.ncbi.nlm.nih.gov/pubmed/35439051
http://dx.doi.org/10.1073/pnas.2119032119
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author Huang, Qiang
Lee, Ga Young
Li, Jiayi
Wang, Chuan
Zhao, Rosalinda L.
Deng, Zixin
Houk, K. N.
Zhao, Yi-Lei
author_facet Huang, Qiang
Lee, Ga Young
Li, Jiayi
Wang, Chuan
Zhao, Rosalinda L.
Deng, Zixin
Houk, K. N.
Zhao, Yi-Lei
author_sort Huang, Qiang
collection PubMed
description Iodine-induced cleavage at phosphorothioate DNA (PT-DNA) is characterized by extremely high sensitivity (∼1 phosphorothioate link per 10(6) nucleotides), which has been used for detecting and sequencing PT-DNA in bacteria. Despite its foreseeable potential for wide applications, the cleavage mechanism at the PT-modified site has not been well established, and it remains unknown as to whether or not cleavage of the bridging P-O occurs at every PT-modified site. In this work, we conducted accurate ωB97X-D calculations and high-performance liquid chromatography-mass spectrometry to investigate the process of PT-DNA cleavage at the atomic and molecular levels. We have found that iodine chemoselectively binds to the sulfur atom of the phosphorothioate link via a strong halogen-chalcogen interaction (a type of halogen bond, with binding affinity as high as 14.9 kcal/mol) and thus triggers P-O bond cleavage via phosphotriester-like hydrolysis. Additionally, aside from cleavage of the bridging P-O bond, the downstream hydrolyses lead to unwanted P-S/P-O conversions and a loss of the phosphorothioate handle. The mechanism we outline helps to explain specific selectivity at the PT-modified site but also predicts the dynamic stoichiometry of P-S and P-O bond breaking. For instance, Tris is involved in the cascade derivation of S-iodo-phosphorothioate to S-amino-phosphorothioate, suppressing the S-iodo-phosphorothioate hydrolysis to a phosphate diester. However, hydrolysis of one-third of the Tris-O-grafting phosphotriester results in unwanted P-S/P-O conversions. Our study suggests that bacterial DNA phosphorothioation may more frequently occur than previous bioinformatic estimations have predicted from iodine-induced deep sequencing data.
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spelling pubmed-91699302022-10-19 Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation Huang, Qiang Lee, Ga Young Li, Jiayi Wang, Chuan Zhao, Rosalinda L. Deng, Zixin Houk, K. N. Zhao, Yi-Lei Proc Natl Acad Sci U S A Biological Sciences Iodine-induced cleavage at phosphorothioate DNA (PT-DNA) is characterized by extremely high sensitivity (∼1 phosphorothioate link per 10(6) nucleotides), which has been used for detecting and sequencing PT-DNA in bacteria. Despite its foreseeable potential for wide applications, the cleavage mechanism at the PT-modified site has not been well established, and it remains unknown as to whether or not cleavage of the bridging P-O occurs at every PT-modified site. In this work, we conducted accurate ωB97X-D calculations and high-performance liquid chromatography-mass spectrometry to investigate the process of PT-DNA cleavage at the atomic and molecular levels. We have found that iodine chemoselectively binds to the sulfur atom of the phosphorothioate link via a strong halogen-chalcogen interaction (a type of halogen bond, with binding affinity as high as 14.9 kcal/mol) and thus triggers P-O bond cleavage via phosphotriester-like hydrolysis. Additionally, aside from cleavage of the bridging P-O bond, the downstream hydrolyses lead to unwanted P-S/P-O conversions and a loss of the phosphorothioate handle. The mechanism we outline helps to explain specific selectivity at the PT-modified site but also predicts the dynamic stoichiometry of P-S and P-O bond breaking. For instance, Tris is involved in the cascade derivation of S-iodo-phosphorothioate to S-amino-phosphorothioate, suppressing the S-iodo-phosphorothioate hydrolysis to a phosphate diester. However, hydrolysis of one-third of the Tris-O-grafting phosphotriester results in unwanted P-S/P-O conversions. Our study suggests that bacterial DNA phosphorothioation may more frequently occur than previous bioinformatic estimations have predicted from iodine-induced deep sequencing data. National Academy of Sciences 2022-04-19 2022-04-26 /pmc/articles/PMC9169930/ /pubmed/35439051 http://dx.doi.org/10.1073/pnas.2119032119 Text en Copyright © 2022 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by-nc-nd/4.0/This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND) (https://creativecommons.org/licenses/by-nc-nd/4.0/) .
spellingShingle Biological Sciences
Huang, Qiang
Lee, Ga Young
Li, Jiayi
Wang, Chuan
Zhao, Rosalinda L.
Deng, Zixin
Houk, K. N.
Zhao, Yi-Lei
Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation
title Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation
title_full Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation
title_fullStr Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation
title_full_unstemmed Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation
title_short Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation
title_sort origin of iodine preferential attack at sulfur in phosphorothioate and subsequent p-o or p-s bond dissociation
topic Biological Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9169930/
https://www.ncbi.nlm.nih.gov/pubmed/35439051
http://dx.doi.org/10.1073/pnas.2119032119
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