观察DNA聚合酶 η产生基键
Teruya Nakamura1, Ye Zhao, Yuriko Yamagata
1Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
Nature
|July 13, 2012
概括
这项研究可视化了DNA合成,通过使用时间解析的X射线晶体学跟踪二结合的形成. 包括金属离子协调和核转换在内的关键步骤被确定为DNA聚合的速度限制因素.
科学领域:
- 生物化学 生物化学
- 结构生物学 结构生物学
- 分子生物学分子生物学
背景情况:
- DNA合成对生命至关重要,但化学反应机制仍然不太了解.
- 之前的研究缺乏在DNA聚合过程中基键形成的直接可视化.
研究的目的:
- 实时可视化DNA合成的化学反应.
- 阐明DNA聚合过程中的结构中间体和速度限制步骤.
主要方法:
- 时间分辨率的X射线晶体学被用来捕捉反应的结构快照.
- 原生人类DNA聚合酶 η,DNA和dATP被共同结晶,反应开始与Mg2+).
- 晶体在不同的时间点被快速结以进行结构分析.
主要成果:
- 基质和两个Mg2+) 离子在40秒内对齐,但在80秒后观察到键形成.
- 结构显示了从基质到产品的过渡,表明了核酸转移反应.
- 过渡的电子密度表明,去质子化和糖转换是速度限制的.
结论:
- 这项研究提供了DNA基结形成的第一个结构可视化.
- 脱和糖转换被确定为关键的速度限制步骤.
- 第三个Mg2+) 离子可能在稳定反应中间体方面发挥作用,可能完善两金属离子机制模型.
相关概念视频
01:01Phosphodiester Linkages
Overview
Phosphodiester bond forms when a phosphoric acid molecule (H3PO4) links with two hydroxyl groups (–OH) of two other molecules, forming two ester bonds. Two water molecules are released in this process. The phosphodiester bond is commonly found in nucleic acids (DNA and RNA) and plays a critical role in their structure and function.
Phosphodiester Bonds Link Nucleotides Together
DNA and RNA are polynucleotides or long chains of nucleotides that are linked together. A nucleotide is...
Phosphodiester bond forms when a phosphoric acid molecule (H3PO4) links with two hydroxyl groups (–OH) of two other molecules, forming two ester bonds. Two water molecules are released in this process. The phosphodiester bond is commonly found in nucleic acids (DNA and RNA) and plays a critical role in their structure and function.
Phosphodiester Bonds Link Nucleotides Together
DNA and RNA are polynucleotides or long chains of nucleotides that are linked together. A nucleotide is...
01:31Proofreading
Synthesis of new DNA molecules is carried out by the enzyme DNA polymerase, which adds nucleotides on the daughter strand complementary to the template DNA strand. DNA polymerase has a higher affinity to add the correct base and ensures fidelity during DNA replication. Furthermore, it exhibits proofreading activity during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.
Errors During Replication are Corrected by the DNA Polymerase Enzyme
Errors During Replication are Corrected by the DNA Polymerase Enzyme
01:43Proofreading
Overview
03:01The Replisome
DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...
03:01The Replisome
DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...
02:31Replication in Eukaryotes
Overview