在in-silicon模型中不同基本假设对DNA损伤和修复预测的影响
John W Warmenhoven1,2, Nicholas T Henthorn1,2, Aimee L McNamara3
1Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom.
Radiation research
|November 28, 2023
概括
对DNA双链断裂 (DSB) 的计算模型进行比较,揭示了初始损伤假设如何影响癌症放射治疗的预测. 标准化数据格式对于精确的DNA修复和细胞死亡的in silico建模至关重要.
科学领域:
- 辐射瘤学 辐射瘤学
- 计算生物学 计算生物学
- 分子生物学分子生物学
背景情况:
- DNA双链断裂 (DSB) 是放射治疗癌症治疗中的关键目标.
- 现有的DSB感应和修复的in silico模型经常使用自定义数据格式,限制了模型之间的比较.
- 了解辐射,DSB诱导和细胞死亡之间的关系需要强大的计算方法.
研究的目的:
- 用标准数据格式评估独立开发的DNA损伤和修复模型的组合.
- 确定模型对DSB诱导和修复中的明确和隐含假设的敏感性.
- 强调模型间比较对于理解基础假设的重要性.
主要方法:
- 使用标准数据格式报告DNA损伤.
- 评估了不同的组合,独立开发了用于DSB诱导和修复的in silico模型.
- 分析了不同假设对初始DSB产量和随后的DNA修复建模的影响.
主要成果:
- 在DNA损伤诱导模型中的差异显著影响预测的初始DSB产量.
- 初始损伤模型中的差异需要在修复模型中随机DSB终端扩散的不同速率.
- 结合不同的损伤和修复模型导致对生物终点负责的机制的分歧.
结论:
- 考虑到纳米级的初始DNA损伤对于准确的建模至关重要.
- 模型间的比较对于揭示和理解计算模型中的基本假设至关重要.
- 标准化数据格式有助于对放射生物学的in silico模型进行可靠的评估和比较.
相关概念视频
Overview of DNA Repair
31.1K
In order to be passed through generations, genomic DNA must be undamaged and error-free. However, every day, DNA in a cell undergoes several thousand to a million damaging events by natural causes and external factors. Ionizing radiation such as UV rays, free radicals produced during cellular respiration, and hydrolytic damage from metabolic reactions can alter the structure of DNA. Damages caused include single-base alteration, base dimerization, chain breaks, and cross-linkage.
Chemically...
Chemically...
31.1K
Nucleotide Excision Repair
3.5K
DNA Distortion and Damage
Cells are regularly exposed to mutagens—factors in the environment that can damage DNA and generate mutations. UV radiation is one of the most common mutagens and is estimated to introduce a significant number of changes in DNA. These include bends or kinks in the structure, which can block DNA replication or transcription. If these errors are not fixed, the damage can cause mutations, which in turn can result in cancer or disease depending on which sequences are...
Cells are regularly exposed to mutagens—factors in the environment that can damage DNA and generate mutations. UV radiation is one of the most common mutagens and is estimated to introduce a significant number of changes in DNA. These include bends or kinks in the structure, which can block DNA replication or transcription. If these errors are not fixed, the damage can cause mutations, which in turn can result in cancer or disease depending on which sequences are...
3.5K
Mismatch Repair
4.9K
Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
4.9K
DNA Damage can Stall the Cell Cycle
9.2K
In response to DNA damage, cells can pause the cell cycle to assess and repair the breaks. However, the cell must check the DNA at certain critical stages during the cell cycle. If the cell cycle pauses before DNA replication, the cells will contain twice the amount of DNA. On the other hand, if cells arrest after DNA replication but before mitosis, they will contain four times the normal amount of DNA. With a host of specialized proteins at their disposal,cells must use the right protein at...
9.2K
Long-patch Base Excision Repair
7.0K
Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:
7.0K
Fixing Double-strand Breaks
12.6K
The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
12.6K


