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(1)H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives
[Image: see text] 5-Carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and base-excision processes in DNA. In this work, we uti...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9137243/ https://www.ncbi.nlm.nih.gov/pubmed/35637781 http://dx.doi.org/10.1021/acsphyschemau.1c00050 |
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author | Dubini, Romeo C. A. Korytiaková, Eva Schinkel, Thea Heinrichs, Pia Carell, Thomas Rovó, Petra |
author_facet | Dubini, Romeo C. A. Korytiaková, Eva Schinkel, Thea Heinrichs, Pia Carell, Thomas Rovó, Petra |
author_sort | Dubini, Romeo C. A. |
collection | PubMed |
description | [Image: see text] 5-Carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and base-excision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ∼10–20 kJ mol(–1) at 37 °C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the microsecond time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caC’s subtle sensitivity to acidic pH contribute to the long-standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark. |
format | Online Article Text |
id | pubmed-9137243 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-91372432022-05-28 (1)H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives Dubini, Romeo C. A. Korytiaková, Eva Schinkel, Thea Heinrichs, Pia Carell, Thomas Rovó, Petra ACS Phys Chem Au [Image: see text] 5-Carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and base-excision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ∼10–20 kJ mol(–1) at 37 °C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the microsecond time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caC’s subtle sensitivity to acidic pH contribute to the long-standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark. American Chemical Society 2022-02-11 /pmc/articles/PMC9137243/ /pubmed/35637781 http://dx.doi.org/10.1021/acsphyschemau.1c00050 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Dubini, Romeo C. A. Korytiaková, Eva Schinkel, Thea Heinrichs, Pia Carell, Thomas Rovó, Petra (1)H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives |
title | (1)H NMR Chemical Exchange Techniques Reveal
Local and Global Effects of Oxidized Cytosine Derivatives |
title_full | (1)H NMR Chemical Exchange Techniques Reveal
Local and Global Effects of Oxidized Cytosine Derivatives |
title_fullStr | (1)H NMR Chemical Exchange Techniques Reveal
Local and Global Effects of Oxidized Cytosine Derivatives |
title_full_unstemmed | (1)H NMR Chemical Exchange Techniques Reveal
Local and Global Effects of Oxidized Cytosine Derivatives |
title_short | (1)H NMR Chemical Exchange Techniques Reveal
Local and Global Effects of Oxidized Cytosine Derivatives |
title_sort | (1)h nmr chemical exchange techniques reveal
local and global effects of oxidized cytosine derivatives |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9137243/ https://www.ncbi.nlm.nih.gov/pubmed/35637781 http://dx.doi.org/10.1021/acsphyschemau.1c00050 |
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