Angad Sharma, Hari O.S. Yadav, Pradipta Bandyopadhyay
{"title":"了解 Cu+2 与 DNA 的结合:比较 Cu2+ 和 Mg2+ 与 Dickerson DNA 结合的分子动力学研究。","authors":"Angad Sharma, Hari O.S. Yadav, Pradipta Bandyopadhyay","doi":"10.1016/j.bpc.2024.107347","DOIUrl":null,"url":null,"abstract":"<div><div>Cu<sup>2+</sup> ions led DNA damage by reactive oxygen species (ROS) is widely known biological phenomena. The ionic radii of Cu<sup>2+</sup> and Mg<sup>2+</sup> being similar, the binding of Cu<sup>2+</sup> ions to DNA is expected to be similar to that of the Mg<sup>2+</sup> ions. However, little is known how Cu<sup>2+</sup> ions bind in different parts (phosphate, major and minor grooves) of a double-strand (ds) DNA, especially at atomic level. In the present study, we employ molecular dynamic (MD) simulations to investigate the binding of Cu<sup>2+</sup> ions with the Dickerson DNA, a B-type dodecamer double stranded (ds) DNA. The binding characteristics of Cu<sup>2+</sup> and Mg<sup>2+</sup> ions with this dsDNA are compared to get an insight into the differences and similarities in binding behavior of both ions. Unlike Mg<sup>2+</sup> ions, the first hydration shell of Cu<sup>2+</sup> is found to be labile, thus it shows both direct and indirect binding with the dsDNA, i.e., binding through displacement of water from the hydration shell or through the hydration shell. Though the binding propensity of Cu<sup>2+</sup> ions with dsDNA is observed relatively stronger, the binding order to phosphates, major groove, and minor groove is found qualitatively similar (phosphates > major groove > minor groove) for both ions. The study gives a deep understanding of Cu<sup>2+</sup> binding to DNA, which could be helpful in rationalizing the Cu<sup>2+</sup> led ROS-mediated DNA damage.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"316 ","pages":"Article 107347"},"PeriodicalIF":3.3000,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Understanding Cu+2 binding with DNA: A molecular dynamics study comparing Cu2+ and Mg2+ binding to the Dickerson DNA\",\"authors\":\"Angad Sharma, Hari O.S. Yadav, Pradipta Bandyopadhyay\",\"doi\":\"10.1016/j.bpc.2024.107347\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><div>Cu<sup>2+</sup> ions led DNA damage by reactive oxygen species (ROS) is widely known biological phenomena. The ionic radii of Cu<sup>2+</sup> and Mg<sup>2+</sup> being similar, the binding of Cu<sup>2+</sup> ions to DNA is expected to be similar to that of the Mg<sup>2+</sup> ions. However, little is known how Cu<sup>2+</sup> ions bind in different parts (phosphate, major and minor grooves) of a double-strand (ds) DNA, especially at atomic level. In the present study, we employ molecular dynamic (MD) simulations to investigate the binding of Cu<sup>2+</sup> ions with the Dickerson DNA, a B-type dodecamer double stranded (ds) DNA. The binding characteristics of Cu<sup>2+</sup> and Mg<sup>2+</sup> ions with this dsDNA are compared to get an insight into the differences and similarities in binding behavior of both ions. Unlike Mg<sup>2+</sup> ions, the first hydration shell of Cu<sup>2+</sup> is found to be labile, thus it shows both direct and indirect binding with the dsDNA, i.e., binding through displacement of water from the hydration shell or through the hydration shell. Though the binding propensity of Cu<sup>2+</sup> ions with dsDNA is observed relatively stronger, the binding order to phosphates, major groove, and minor groove is found qualitatively similar (phosphates > major groove > minor groove) for both ions. The study gives a deep understanding of Cu<sup>2+</sup> binding to DNA, which could be helpful in rationalizing the Cu<sup>2+</sup> led ROS-mediated DNA damage.</div></div>\",\"PeriodicalId\":8979,\"journal\":{\"name\":\"Biophysical chemistry\",\"volume\":\"316 \",\"pages\":\"Article 107347\"},\"PeriodicalIF\":3.3000,\"publicationDate\":\"2024-10-28\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Biophysical chemistry\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0301462224001765\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Biophysical chemistry","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0301462224001765","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
Understanding Cu+2 binding with DNA: A molecular dynamics study comparing Cu2+ and Mg2+ binding to the Dickerson DNA
Cu2+ ions led DNA damage by reactive oxygen species (ROS) is widely known biological phenomena. The ionic radii of Cu2+ and Mg2+ being similar, the binding of Cu2+ ions to DNA is expected to be similar to that of the Mg2+ ions. However, little is known how Cu2+ ions bind in different parts (phosphate, major and minor grooves) of a double-strand (ds) DNA, especially at atomic level. In the present study, we employ molecular dynamic (MD) simulations to investigate the binding of Cu2+ ions with the Dickerson DNA, a B-type dodecamer double stranded (ds) DNA. The binding characteristics of Cu2+ and Mg2+ ions with this dsDNA are compared to get an insight into the differences and similarities in binding behavior of both ions. Unlike Mg2+ ions, the first hydration shell of Cu2+ is found to be labile, thus it shows both direct and indirect binding with the dsDNA, i.e., binding through displacement of water from the hydration shell or through the hydration shell. Though the binding propensity of Cu2+ ions with dsDNA is observed relatively stronger, the binding order to phosphates, major groove, and minor groove is found qualitatively similar (phosphates > major groove > minor groove) for both ions. The study gives a deep understanding of Cu2+ binding to DNA, which could be helpful in rationalizing the Cu2+ led ROS-mediated DNA damage.
期刊介绍:
Biophysical Chemistry publishes original work and reviews in the areas of chemistry and physics directly impacting biological phenomena. Quantitative analysis of the properties of biological macromolecules, biologically active molecules, macromolecular assemblies and cell components in terms of kinetics, thermodynamics, spatio-temporal organization, NMR and X-ray structural biology, as well as single-molecule detection represent a major focus of the journal. Theoretical and computational treatments of biomacromolecular systems, macromolecular interactions, regulatory control and systems biology are also of interest to the journal.