{"title":"The base flipping of A-DNA—a molecular dynamic simulation study","authors":"Shudong Wang, Xuan Zheng, Jingjie Wu","doi":"10.1007/s11224-024-02299-0","DOIUrl":null,"url":null,"abstract":"<div><p>Due to different solvent conditions, double helix DNA exists in various conformations, such as B-DNA, A-DNA, C-DNA, and Z-DNA. Studies have found that A-DNA is present in complexes with proteins and has an important biological role in the context of cellular defense mechanisms under harsh conditions. In this study, the well-tempered meta-dynamics (WTM-eABF) were used to explore the free energy barriers for base flipping of the four natural bases, adenine, guanine, cytosine, and thymine, in both A-form and B-form DNA duplex. The results show that the free energy barriers for base flipping were lower in A-DNA than that in B-DNA for all of the four natural bases. We analyzed the factors that may affect base flipping, such as π-π stacking, SASA, H-bonding, and conformational changes, and concluded that conformational changes and π-π stacking are the most important factors affecting base flipping.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"35 5","pages":"1649 - 1656"},"PeriodicalIF":2.1000,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Structural Chemistry","FirstCategoryId":"92","ListUrlMain":"https://link.springer.com/article/10.1007/s11224-024-02299-0","RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
引用次数: 0
Abstract
Due to different solvent conditions, double helix DNA exists in various conformations, such as B-DNA, A-DNA, C-DNA, and Z-DNA. Studies have found that A-DNA is present in complexes with proteins and has an important biological role in the context of cellular defense mechanisms under harsh conditions. In this study, the well-tempered meta-dynamics (WTM-eABF) were used to explore the free energy barriers for base flipping of the four natural bases, adenine, guanine, cytosine, and thymine, in both A-form and B-form DNA duplex. The results show that the free energy barriers for base flipping were lower in A-DNA than that in B-DNA for all of the four natural bases. We analyzed the factors that may affect base flipping, such as π-π stacking, SASA, H-bonding, and conformational changes, and concluded that conformational changes and π-π stacking are the most important factors affecting base flipping.
由于溶剂条件不同，双螺旋 DNA 存在多种构象，如 B-DNA、A-DNA、C-DNA 和 Z-DNA。研究发现，A-DNA 存在于与蛋白质的复合物中，在严酷条件下的细胞防御机制中具有重要的生物学作用。在本研究中，我们使用好脾气元动力学（WTM-eABF）探讨了腺嘌呤、鸟嘌呤、胞嘧啶和胸腺嘧啶这四种天然碱基在 A 型和 B 型 DNA 双链中发生碱基翻转的自由能垒。结果表明，对于所有四种天然碱基，A-DNA 中碱基翻转的自由能垒均低于 B-DNA 中的自由能垒。我们分析了可能影响碱基翻转的因素，如π-π堆积、SASA、H 键和构象变化，得出结论：构象变化和π-π堆积是影响碱基翻转的最重要因素。
期刊介绍：
Structural Chemistry is an international forum for the publication of peer-reviewed original research papers that cover the condensed and gaseous states of matter and involve numerous techniques for the determination of structure and energetics, their results, and the conclusions derived from these studies. The journal overcomes the unnatural separation in the current literature among the areas of structure determination, energetics, and applications, as well as builds a bridge to other chemical disciplines. Ist comprehensive coverage encompasses broad discussion of results, observation of relationships among various properties, and the description and application of structure and energy information in all domains of chemistry.
We welcome the broadest range of accounts of research in structural chemistry involving the discussion of methodologies and structures,experimental, theoretical, and computational, and their combinations. We encourage discussions of structural information collected for their chemicaland biological significance.
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