基于DNA原形的平台用于多轴单分子力谱学,揭示了霍莱德连接的隐藏动力学
bioRxiv : the preprint server for biology
|July 15, 2025
概括
研究人员开发了一种多轴的热弹 tweezer (MAESTRO) 来研究在细胞应激下生物分子. 在多轴张力下,MAESTRO揭示了在多轴张力下显著减缓的霍莱德连接动力学,揭示了新的动力学和酶相互作用.
科学领域:
- 生物物理学的生物物理.
- 分子生物学分子生物学
- 生物化学 生物化学
背景情况:
- 生物分子在拥挤的细胞环境中运行,具有复杂的多轴应力.
- 现有的单分子力光谱技术往往沿着单个轴施加力,而不是模仿细胞条件.
- 了解生物分子对多轴张力的反应对细胞生物学至关重要.
研究的目的:
- 开发一种新型的分子工具,用于在多个轴上应用piconewton (pN) 范围的力.
- 在定义的多轴张力下,研究生物分子的动力学,特别是霍莱德连接.
- 探索机械力如何调节生物分子功能和酶活性.
主要方法:
- 一个沿着刚性DNA原形 (MAESTRO) 的多轴热弹的开发.
- 整合MAESTRO与单分子福斯特共振能量转移 (smFRET) 和贝叶斯非参数FRET (BNP-FRET) 进行高通量分析.
- 应用MAESTRO工具来研究霍利代结 (HJ) DNA结构和T7内核酶I活性.
主要成果:
- 马斯特罗成功地将受控的多轴张力应用于生物分子.
- 与无张力条件相比,在多轴张力下,霍莱德连接形状表现出≥5倍较慢的动力学.
- 直接观察中间的开放和不堆叠的HJ形状,以及在四向张力下的动态模式之间的相互转换.
- 机械张力调整了结合解决酶T7内核酶I的功能结果.
结论:
- MAESTRO克服了单轴力光谱学的局限性,使得在复杂的细胞机械力下研究生物分子动力学成为可能.
- 多轴张力显著改变了HJ动力学,并揭示了以前没有观察到的结构动力学.
- 该研究提供了对生物分子结构和功能的机制调节的见解,对同源重组和酶活性有影响.
相关概念视频
The DNA Replication Fork
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DNA Topoisomerases
Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
Types and Mechanism of action
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Forces Acting on Chromosomes
During mitosis, chromosome movements occur through the interplay of multiple piconewton level forces. In prometaphase, these forces help in chromosome assembly or congression at the equatorial plane, eventually leading to their alignment at the metaphase plate. The forces acting on the chromosomes are space and time-dependent; therefore, they vary with the position of the chromosomes as the cell progresses through mitosis.
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Single-Strand DNA Binding Proteins
For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
The DNA Replication Fork
An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork. Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication forks, one in...


