Abstract

Early detection and repair of damaged DNA is important for cell functioning and survival. The recently proposed mechanism of intranucleosomal loop formation suggests the relaxation of DNA supercoiling accumulated during transcription through damaged chromatin. The degree of DNA relaxation is affected by the mechanical properties and structure of the double helix. In this work, the consequences from the introduction of a single-stranded break on the mechanical properties of a DNA fragment are studied using molecular dynamics. It is concluded that the introduction of a single-stranded break leads to decreased stiffness and higher elasticity of the damaged DNA molecule as compared to the intact one. This, in turn, may lead to relief in the supercoiling of the defective DNA and to the enzyme arrest.

中文翻译：

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用分子动力学方法研究单链断裂对DNA力学参数的影响

摘要

早期检测和修复受损的DNA对于细胞功能和存活很重要。最近提出的核小体内环形成的机制表明，在转录过程中通过受损的染色质积累的DNA超螺旋的松弛。DNA弛豫的程度受双螺旋的机械性能和结构影响。在这项工作中，使用分子动力学研究了引入单链断裂对DNA片段机械性能的影响。结论是，与完整链断裂相比，单链断裂的引入导致受损的DNA分子的刚度降低和弹性更高。反过来，这可能会导致缺陷DNA的超螺旋的释放和酶的阻滞。