{"title":"Energy spectrum of the ideal DNA knot on a torus","authors":"Xuguang Shi","doi":"10.1007/s00249-023-01670-z","DOIUrl":null,"url":null,"abstract":"<div><p>In this study, we consider DNA as a torus knot that is formed by an elastic string. In order to determine what kinds of knot could be formed, we present its energy spectrum by combining Euler rotation, DNA’s mechanical properties, and the modified Faddeev–Skyrme model. Our results theoretically demonstrated that the flexural rigidity of DNA plays an important role. If it is smaller than a critical value, DNA is likely to form a coiled structure. Conversely, above the critical value, DNA forms a twisting structure. The energy spectrum provides a way to identify the types of knots that are most likely to be created by DNA, according to the principle of energy minimisation, and with implications for its functional and packaging states in the cell nucleus.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 8","pages":"651 - 660"},"PeriodicalIF":2.2000,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"1","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"European Biophysics Journal","FirstCategoryId":"2","ListUrlMain":"https://link.springer.com/article/10.1007/s00249-023-01670-z","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"BIOPHYSICS","Score":null,"Total":0}
引用次数: 1
Abstract
In this study, we consider DNA as a torus knot that is formed by an elastic string. In order to determine what kinds of knot could be formed, we present its energy spectrum by combining Euler rotation, DNA’s mechanical properties, and the modified Faddeev–Skyrme model. Our results theoretically demonstrated that the flexural rigidity of DNA plays an important role. If it is smaller than a critical value, DNA is likely to form a coiled structure. Conversely, above the critical value, DNA forms a twisting structure. The energy spectrum provides a way to identify the types of knots that are most likely to be created by DNA, according to the principle of energy minimisation, and with implications for its functional and packaging states in the cell nucleus.
期刊介绍：
The journal publishes papers in the field of biophysics, which is defined as the study of biological phenomena by using physical methods and concepts. Original papers, reviews and Biophysics letters are published. The primary goal of this journal is to advance the understanding of biological structure and function by application of the principles of physical science, and by presenting the work in a biophysical context.
Papers employing a distinctively biophysical approach at all levels of biological organisation will be considered, as will both experimental and theoretical studies. The criteria for acceptance are scientific content, originality and relevance to biological systems of current interest and importance.
Principal areas of interest include:
- Structure and dynamics of biological macromolecules
- Membrane biophysics and ion channels
- Cell biophysics and organisation
- Macromolecular assemblies
- Biophysical methods and instrumentation
- Advanced microscopics
- System dynamics.
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