监控不稳定中的循环化DNA寡核酸,由复制品交换分子动力学模拟预测
Carsten Hamerla1, Padmabati Mondal2, Rainer Hegger1
1Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany. burghardt@chemie.uni-frankfurt.de.
Physical chemistry chemical physics : PCCP
|September 23, 2023
概括
对光控制的DNA寡核酸的循环化策略显著破坏了它们的稳定性,降低了大约30K的化温度. 这项计算研究验证了预测核酸光控制中这种效应的方法.
科学领域:
- 分子生物学分子生物学
- 生物物理学的生物物理.
- 计算化学计算化学
背景情况:
- 时空控制对于光调节寡核酸活性至关重要.
- 光性保护组 (PPG) 通常用于寡核酸脱,但可能需要多次应用.
- 循环化策略,如光接,为寡核酸光调节提供了替代方法.
研究的目的:
- 为了计算性地描述循环化,中的DNA寡核酸的不稳定.
- 验证一个用于预测循环化对寡核酸稳定性影响的计算协议.
- 评估用于设计定制光控制核酸的计算工具的潜力.
主要方法:
- 使用复制品交换分子动力学 (REMD) 模拟.
- 对于32核酸 (nt) DNA寡核酸的化温度 (Tm) 被计算出来.
- 分析了自由能源景观,以确认不稳定模式.
主要成果:
- 计算的化温度与实验数据有很好的一致性.
- 循环化的寡核酸体表现出显著的不稳定,与原生DNA相比,Tm减少约为30K.
- 对自由能源景观的分析证实了观察到的不稳定.
结论:
- 计算协议,如REMD,可以准确预测循环化的寡核酸的不稳定.
- 循环化显著降低了寡核酸的稳定性,影响了它们的光控制活性.
- 这些计算工具对光控制核酸系统的理性设计具有前景.
相关概念视频
Conservative Site-specific Recombination and Phase Variation
6.0K
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
The recognition sites for Cre recombinase called LoxP...
6.0K
Restarting Stalled Replication Forks
5.8K
DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart,...
5.8K


