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Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone
The influence of hydrogen bonds in model intercalated systems between guanine‐cytosine and adenine‐thymine DNA base pairs (bps) was analyzed with the popular intercalator 1,10‐phenanthroline (phen) and derivatives obtained by substitution with —OH and —NH(2) groups in positions 4 and 7. Semiempirica...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley & Sons, Inc.
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9313584/ https://www.ncbi.nlm.nih.gov/pubmed/35297513 http://dx.doi.org/10.1002/jcc.26836 |
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author | Sánchez‐González, Ángel Grenut, Pierre Gil, Adrià |
author_facet | Sánchez‐González, Ángel Grenut, Pierre Gil, Adrià |
author_sort | Sánchez‐González, Ángel |
collection | PubMed |
description | The influence of hydrogen bonds in model intercalated systems between guanine‐cytosine and adenine‐thymine DNA base pairs (bps) was analyzed with the popular intercalator 1,10‐phenanthroline (phen) and derivatives obtained by substitution with —OH and —NH(2) groups in positions 4 and 7. Semiempirical and Density Functional Theory (DFT) methods were used both including dispersion effects: PM6‐DH2, M06‐2X and B3LYP‐D3 along with the recently developed near linear‐scaling coupled cluster method DLPNO‐CCSD(T) for benchmark calculations. Our results given by QTAIM and non‐covalent interaction analysis confirmed the existence of hydrogen bonds created by —OH and —NH(2). The trends in the energy decomposition analysis for the interaction energy, ΔE (int), showed that the ΔE (elstat) contributions are equal or even a little bit higher than the values for ΔE (disp). Such important ΔE (elstat) attractive contribution comes mainly from the conventional hydrogen bonds formed by —OH and —NH(2) functional groups with DNA not only with bps but specially with the sugar and phosphate backbone. This behavior is very different from that of phen and other classical intercalators that cannot form conventional hydrogen bonds, where the ΔE (disp) is the most important attractive contribution to the ΔE (int). The inclusion of explicit water molecules in molecular dynamics simulations showed, as a general trend, that the hydrogen bonds with the bps disappear during the simulations but those with the sugar and phosphate backbone remain in time, which highlights the important role of the sugar and phosphate backbone in the stabilization of these systems. |
format | Online Article Text |
id | pubmed-9313584 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | John Wiley & Sons, Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-93135842022-07-30 Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone Sánchez‐González, Ángel Grenut, Pierre Gil, Adrià J Comput Chem Research Articles The influence of hydrogen bonds in model intercalated systems between guanine‐cytosine and adenine‐thymine DNA base pairs (bps) was analyzed with the popular intercalator 1,10‐phenanthroline (phen) and derivatives obtained by substitution with —OH and —NH(2) groups in positions 4 and 7. Semiempirical and Density Functional Theory (DFT) methods were used both including dispersion effects: PM6‐DH2, M06‐2X and B3LYP‐D3 along with the recently developed near linear‐scaling coupled cluster method DLPNO‐CCSD(T) for benchmark calculations. Our results given by QTAIM and non‐covalent interaction analysis confirmed the existence of hydrogen bonds created by —OH and —NH(2). The trends in the energy decomposition analysis for the interaction energy, ΔE (int), showed that the ΔE (elstat) contributions are equal or even a little bit higher than the values for ΔE (disp). Such important ΔE (elstat) attractive contribution comes mainly from the conventional hydrogen bonds formed by —OH and —NH(2) functional groups with DNA not only with bps but specially with the sugar and phosphate backbone. This behavior is very different from that of phen and other classical intercalators that cannot form conventional hydrogen bonds, where the ΔE (disp) is the most important attractive contribution to the ΔE (int). The inclusion of explicit water molecules in molecular dynamics simulations showed, as a general trend, that the hydrogen bonds with the bps disappear during the simulations but those with the sugar and phosphate backbone remain in time, which highlights the important role of the sugar and phosphate backbone in the stabilization of these systems. John Wiley & Sons, Inc. 2022-03-17 2022-04-30 /pmc/articles/PMC9313584/ /pubmed/35297513 http://dx.doi.org/10.1002/jcc.26836 Text en © 2022 The Authors. Journal of Computational Chemistry published by Wiley Periodicals LLC. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Articles Sánchez‐González, Ángel Grenut, Pierre Gil, Adrià Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone |
title | Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone |
title_full | Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone |
title_fullStr | Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone |
title_full_unstemmed | Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone |
title_short | Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone |
title_sort | influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with dna: the important role of the sugar and phosphate backbone |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9313584/ https://www.ncbi.nlm.nih.gov/pubmed/35297513 http://dx.doi.org/10.1002/jcc.26836 |
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