{"title":"Computer Simulation of Short DNA Fragments Induced by High-LET Charged Particles","authors":"Y. A. Eidelman, I. V. Salnikov, S. G. Andreev","doi":"10.1134/S0006350924700222","DOIUrl":null,"url":null,"abstract":"<p>The formation of short DNA fragments, up to 3 kbp, induced in chromatin by nitrogen (LET 97 keV/μm) and iron (LET 190 keV/μm) ions was studied by computer simulation. Chromatin models with different structure parameters and Monte Carlo track structure simulation were used to assess the impact of chromatin fiber structure and LET on the DNA fragment size distribution. For the structures modeled (different types of solenoids, a chain of nucleosomes), the fragment size distribution had a maximum in the region of ~100 bp corresponding to the formation of DNA breaks in two neighboring turns of the helix on the nucleosome. For the solenoid type of chromatin, the calculation predicted the peak in the region around 1000 bp, corresponding to the formation of DNA breaks in two neighboring turns of the solenoid. Additionally, the assumption of the variety of chromatin structures under irradiation was studied. It allowed to explain the experimentally observed size distributions of the short DNA fragments induced by high-LET charged particles.</p>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 2","pages":"201 - 208"},"PeriodicalIF":4.0330,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Biophysics","FirstCategoryId":"4","ListUrlMain":"https://link.springer.com/article/10.1134/S0006350924700222","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}
引用次数: 0
Abstract
The formation of short DNA fragments, up to 3 kbp, induced in chromatin by nitrogen (LET 97 keV/μm) and iron (LET 190 keV/μm) ions was studied by computer simulation. Chromatin models with different structure parameters and Monte Carlo track structure simulation were used to assess the impact of chromatin fiber structure and LET on the DNA fragment size distribution. For the structures modeled (different types of solenoids, a chain of nucleosomes), the fragment size distribution had a maximum in the region of ~100 bp corresponding to the formation of DNA breaks in two neighboring turns of the helix on the nucleosome. For the solenoid type of chromatin, the calculation predicted the peak in the region around 1000 bp, corresponding to the formation of DNA breaks in two neighboring turns of the solenoid. Additionally, the assumption of the variety of chromatin structures under irradiation was studied. It allowed to explain the experimentally observed size distributions of the short DNA fragments induced by high-LET charged particles.
通过计算机模拟研究了氮离子（LET 97 keV/μm）和铁离子（LET 190 keV/μm）在染色质中诱导形成的短 DNA 片段（最长 3 kbp）。采用不同结构参数的染色质模型和蒙特卡罗轨道结构模拟来评估染色质纤维结构和 LET 对 DNA 片段大小分布的影响。对于所模拟的结构（不同类型的螺线管、核小体链），片段大小分布在约100 bp的区域有一个最大值，这与核小体上两个相邻螺旋转折处DNA断裂的形成相对应。对于螺线型染色质，计算预测在 1000 bp 左右的区域出现峰值，这与螺线上两个相邻转折处形成的 DNA 断裂相对应。此外，还研究了染色质结构在辐照下的多样性假设。这可以解释实验观察到的高LET带电粒子诱导的短DNA片段的大小分布。
BiophysicsBiochemistry, Genetics and Molecular Biology-Biophysics
CiteScore
1.20
自引率
0.00%
发文量
67
期刊介绍：
Biophysics is a multidisciplinary international peer reviewed journal that covers a wide scope of problems related to the main physical mechanisms of processes taking place at different organization levels in biosystems. It includes structure and dynamics of macromolecules, cells and tissues; the influence of environment; energy transformation and transfer; thermodynamics; biological motility; population dynamics and cell differentiation modeling; biomechanics and tissue rheology; nonlinear phenomena, mathematical and cybernetics modeling of complex systems; and computational biology. The journal publishes short communications devoted and review articles.
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