通过动态修复酶内核酶III进行氧导向DNA扫描
Ayaz Hassan1,2, Filipe C D A Lima3, Frank N Crespilho1
1São Carlos Institute of Chemistry, University of São Paulo (USP), São Carlos, SP 13566-590, Brazil.
Biochemistry
|February 4, 2025
概括
细胞内核酶III的使用
科学领域:
- 生物化学 生物化学
- 分子生物学分子生物学
- 生物物理学的生物物理.
背景情况:
- 内核酶III (EndoIII) 对于通过基切除修复 (BER) 途径进行DNA修复至关重要.
- 它的 [4Fe4S] 集群对于通过电荷转移进行DNA修复至关重要.
- 集群的氧化还原状态会影响EndoIII的DNA结合和活性.
研究的目的:
- 在dsDNA结合过程中调查 [4Fe4S] 集群中的结构和电子变化.
- 了解氧化还原状态如何影响EndoIII的DNA修复功能.
- 将电化学特性与DNA结合特性相关联.
主要方法:
- 福里埃变换红外光谱法 (FTIR) 用于分析振动模式.
- 密度函数理论 (DFT) 对电子结构的计算.
- 机器学习 (ML) 模型用于预测绑定相互作用.
主要成果:
- 观察到Fe-S键振动模式的变化表明集群稳定.
- 氧化后的 [4Fe4S] 集群在负电荷的DNA附近稳定.
- ML模型准确地预测了酶-DNA结合距离.
- 一个150mV的稳定潜力与DNA结合性相关.
结论:
- [4Fe4S]集群的氧化还原状态对于EndoIII的结构稳定性和DNA修复至关重要.
- 与dsDNA结合稳定了4Fe4S集群的氧化状态.
- 这项研究为DNA修复中的EndoIII功能提供了机制性的见解.
相关概念视频
Homologous Recombination
50.1K
The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
50.1K
Restriction Enzymes
29.5K
Restriction enzymes are bacterial enzymes used to cut DNA in a sequence-specific manner. To cleave DNA, they bind to specific palindromic sequences called restriction sites. Such palindromic DNA sequences or inverted repeats are commonly found in regions of functional significance, such as the origin of replication, gene operator sites, and regions containing transcription termination signals.
The host bacteria protect their own genomic DNA from these enzymes by methylating these sites. Some...
The host bacteria protect their own genomic DNA from these enzymes by methylating these sites. Some...
29.5K
Maxam-Gilbert Sequencing
11.1K
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
Challenges of the Maxam-Gilbert Method
The...
11.1K
Nucleotide Excision Repair
36.8K
Overview
36.8K
Base Excision Repair
21.9K
One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of...
The first step of...
21.9K


