{"title":"Dynamics of Double-Knotted DNA Molecules under Nanochannel Confinement","authors":"Runfang Mao, and , Kevin D. Dorfman*, ","doi":"10.1021/acs.macromol.4c00525","DOIUrl":null,"url":null,"abstract":"<p >Langevin dynamics simulations of double-knotted DNA molecules in a nanochannel reveal that the interactions between the two knots differ with the degree of channel confinement. In relatively wide channels, the two knots can intertwine with each other, forming a persistently intertwined knot. Moreover, the two knots can pass through each other in large channels. In contrast, for small channel sizes, the knots tend to remain separated, and their crossing is inhibited. The change in knot–knot interactions as the channel size decreases is rationalized through an analysis of the magnitude of the transverse fluctuations, which must be large enough to allow one knot to swell to accommodate the intertwined state.</p>","PeriodicalId":51,"journal":{"name":"Macromolecules","volume":null,"pages":null},"PeriodicalIF":5.1000,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Macromolecules","FirstCategoryId":"92","ListUrlMain":"https://pubs.acs.org/doi/10.1021/acs.macromol.4c00525","RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"POLYMER SCIENCE","Score":null,"Total":0}
引用次数: 0
Abstract
Langevin dynamics simulations of double-knotted DNA molecules in a nanochannel reveal that the interactions between the two knots differ with the degree of channel confinement. In relatively wide channels, the two knots can intertwine with each other, forming a persistently intertwined knot. Moreover, the two knots can pass through each other in large channels. In contrast, for small channel sizes, the knots tend to remain separated, and their crossing is inhibited. The change in knot–knot interactions as the channel size decreases is rationalized through an analysis of the magnitude of the transverse fluctuations, which must be large enough to allow one knot to swell to accommodate the intertwined state.
对纳米通道中的双结 DNA 分子进行的朗格文动力学模拟显示,两个结之间的相互作用随通道的封闭程度而不同。在相对较宽的通道中,两个结可以相互缠绕,形成一个持续缠绕的结。此外,在大通道中,两个结可以相互穿过。与此相反,在较小的水道中,水结往往保持分离状态,它们之间的交叉受到抑制。通过分析横向波动的大小,我们可以合理地解释随着通道尺寸的减小,结与结之间相互作用的变化。
期刊介绍:
Macromolecules publishes original, fundamental, and impactful research on all aspects of polymer science. Topics of interest include synthesis (e.g., controlled polymerizations, polymerization catalysis, post polymerization modification, new monomer structures and polymer architectures, and polymerization mechanisms/kinetics analysis); phase behavior, thermodynamics, dynamic, and ordering/disordering phenomena (e.g., self-assembly, gelation, crystallization, solution/melt/solid-state characteristics); structure and properties (e.g., mechanical and rheological properties, surface/interfacial characteristics, electronic and transport properties); new state of the art characterization (e.g., spectroscopy, scattering, microscopy, rheology), simulation (e.g., Monte Carlo, molecular dynamics, multi-scale/coarse-grained modeling), and theoretical methods. Renewable/sustainable polymers, polymer networks, responsive polymers, electro-, magneto- and opto-active macromolecules, inorganic polymers, charge-transporting polymers (ion-containing, semiconducting, and conducting), nanostructured polymers, and polymer composites are also of interest. Typical papers published in Macromolecules showcase important and innovative concepts, experimental methods/observations, and theoretical/computational approaches that demonstrate a fundamental advance in the understanding of polymers.