{"title":"作为 DNA/RNA 链测序材料的六芒星磷烯纳米片--第一原理研究","authors":"V. Nagarajan , N. Reseeka , R. Chandiramouli","doi":"10.1016/j.jmgm.2024.108845","DOIUrl":null,"url":null,"abstract":"<div><p>In this study, we utilised hex-star phosphorene as the main detecting material to identify the nucleobases. Nucleobases, being crucial carriers of hereditary information are identified through specific hydrogen bonding and steric interactions such as adenine pairing with thymine (or) uracil and guanine pairing with cytosine. The stable hex-star phosphorene possesses negative formation energy of −5.194 eV. The hex-star phosphorene exhibits a semiconductor nature with an energy band gap of 1.658 eV, which is deployed as the adsorbing substrate for nucleobases. Based on the Mulliken charge analysis, adsorption energy, relative band gap variation, and the detection efficiency of hex-star phosphorene towards nucleobases are examined. The outcome confirms the physisorption of nucleobases on hex-star phosphorene and strongly supports that hex-star phosphorene can be used as sequencing material for <span>DNA</span> and RNA.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"132 ","pages":"Article 108845"},"PeriodicalIF":2.7000,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Hex-star phosphorene nanosheets as sequencing material for DNA/RNA strands – A first-principles investigation\",\"authors\":\"V. Nagarajan , N. Reseeka , R. Chandiramouli\",\"doi\":\"10.1016/j.jmgm.2024.108845\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>In this study, we utilised hex-star phosphorene as the main detecting material to identify the nucleobases. Nucleobases, being crucial carriers of hereditary information are identified through specific hydrogen bonding and steric interactions such as adenine pairing with thymine (or) uracil and guanine pairing with cytosine. The stable hex-star phosphorene possesses negative formation energy of −5.194 eV. The hex-star phosphorene exhibits a semiconductor nature with an energy band gap of 1.658 eV, which is deployed as the adsorbing substrate for nucleobases. Based on the Mulliken charge analysis, adsorption energy, relative band gap variation, and the detection efficiency of hex-star phosphorene towards nucleobases are examined. The outcome confirms the physisorption of nucleobases on hex-star phosphorene and strongly supports that hex-star phosphorene can be used as sequencing material for <span>DNA</span> and RNA.</p></div>\",\"PeriodicalId\":16361,\"journal\":{\"name\":\"Journal of molecular graphics & modelling\",\"volume\":\"132 \",\"pages\":\"Article 108845\"},\"PeriodicalIF\":2.7000,\"publicationDate\":\"2024-08-09\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of molecular graphics & modelling\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1093326324001451\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMICAL RESEARCH METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of molecular graphics & modelling","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1093326324001451","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
摘要
在这项研究中，我们利用六星磷烯作为主要检测材料来识别核碱基。核碱基是遗传信息的重要载体，可通过特定的氢键和立体相互作用（如腺嘌呤与胸腺（或）尿嘧啶配对、鸟嘌呤与胞嘧啶配对）来识别。稳定的六星磷烯具有-5.194 eV 的负形成能。六星磷烯具有半导体性质，能带隙为 1.658 eV，可用作核碱基的吸附基底。基于 Mulliken 电荷分析，研究了六星磷烯对核碱基的吸附能量、相对带隙变化和检测效率。结果证实了核碱基在六角星状磷烯上的物理吸附作用，并有力地证明了六角星状磷烯可用作 DNA 和 RNA 的测序材料。
Hex-star phosphorene nanosheets as sequencing material for DNA/RNA strands – A first-principles investigation
In this study, we utilised hex-star phosphorene as the main detecting material to identify the nucleobases. Nucleobases, being crucial carriers of hereditary information are identified through specific hydrogen bonding and steric interactions such as adenine pairing with thymine (or) uracil and guanine pairing with cytosine. The stable hex-star phosphorene possesses negative formation energy of −5.194 eV. The hex-star phosphorene exhibits a semiconductor nature with an energy band gap of 1.658 eV, which is deployed as the adsorbing substrate for nucleobases. Based on the Mulliken charge analysis, adsorption energy, relative band gap variation, and the detection efficiency of hex-star phosphorene towards nucleobases are examined. The outcome confirms the physisorption of nucleobases on hex-star phosphorene and strongly supports that hex-star phosphorene can be used as sequencing material for DNA and RNA.
期刊介绍：
The Journal of Molecular Graphics and Modelling is devoted to the publication of papers on the uses of computers in theoretical investigations of molecular structure, function, interaction, and design. The scope of the journal includes all aspects of molecular modeling and computational chemistry, including, for instance, the study of molecular shape and properties, molecular simulations, protein and polymer engineering, drug design, materials design, structure-activity and structure-property relationships, database mining, and compound library design.
As a primary research journal, JMGM seeks to bring new knowledge to the attention of our readers. As such, submissions to the journal need to not only report results, but must draw conclusions and explore implications of the work presented. Authors are strongly encouraged to bear this in mind when preparing manuscripts. Routine applications of standard modelling approaches, providing only very limited new scientific insight, will not meet our criteria for publication. Reproducibility of reported calculations is an important issue. Wherever possible, we urge authors to enhance their papers with Supplementary Data, for example, in QSAR studies machine-readable versions of molecular datasets or in the development of new force-field parameters versions of the topology and force field parameter files. Routine applications of existing methods that do not lead to genuinely new insight will not be considered.
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