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Nanomanipulation of Single RNA Molecules by Optical Tweezers
Published on: August 20, 2014
人类端粒酶RNA伪结的折叠使用离子跳跃和温度灭模拟
Shi Biyun1, Samuel S Cho, D Thirumalai
1Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA.
Journal of the American Chemical Society
|November 16, 2011
概括
RNA折叠是复杂的,涉及多个途径. 分子模拟显示,虽然人类端粒酶RNA (hTR) 在热力学上似乎是一个双态系统,但其折叠动力学涉及复杂的平行路线和初始条件显著影响崩动力学.
科学领域:
- 计算生物学 计算生物学
- 生物物理学的生物物理.
- 分子生物学分子生物学
背景情况:
- RNA折叠是一个多阶段的过程,涉及链条的紧缩和重新排列.
- 对RNA折叠路径的精确序列依赖细节以及崩和折叠之间的联系仍然不太了解.
- 了解RNA折叠对于各种生物过程至关重要,包括基因调节和催化.
研究的目的:
- 为了全面研究一个特定的RNA伪结,人类端粒酶RNA (hTR) 的热力学和折叠动力学.
- 阐明温度和离子度在指导RNA折叠路径中的作用.
- 在RNA折叠过程中识别和描述中间状态.
主要方法:
- 利用hTR.的粗粒度模型的分子模拟.
- 系统地改变温度 (T) 和离子度 (C) 以生成相位图.
- 通过定期改变离子度来探测隐藏状态,进行中断折叠模拟.
主要成果:
- 阶段图表明hTR在热力学上表现为一个明显的两态系统.
- 折叠动力学是复杂的,涉及多条并行路径,在不同的初始条件下 (温度火与离子跳跃) 有不同的链紧缩动力学.
- 紧的形状并不一定是与原生生物相似的,这表明折叠发生在一个由低能量的流体状球体组成的池中.
- 与温度跳跃相比,离子度下降时,展开速度更快.
- 间断折叠模拟显示,hTR通过少数重复访问的连接的形状集群进行导航.
结论:
- RNA折叠是一个复杂的,多路径的过程,在这个过程中,初始条件极大地影响了折叠和崩的动态.
- 即使对于像hTR这样的小系统来说,RNA的折叠景观也以"隐藏"状态为特征,这些状态对于完全理解来说是必不可少的.
- 需要多个实验探头才能充分描述RNA折叠过程中采集的无形状态,如中断折叠模拟和与实验数据的比较所示.
相关概念视频
Telomeres and Telomerase
In eukaryotic DNA replication, a single-stranded DNA fragment remains at the end of a chromosome after the removal of the final primer. This section of DNA cannot be replicated in the same manner as the rest of the strand because there is no 3’ end to which the newly synthesized DNA can attach. This non-replicated fragment results in gradual loss of the chromosomal DNA during each cell duplication. Additionally, it can induce a DNA damage response by enzymes that recognize single-stranded DNA.
Telomeres and Telomerase
In eukaryotic DNA replication, a single-stranded DNA fragment remains at the end of a chromosome after the removal of the final primer. This section of DNA cannot be replicated in the same manner as the rest of the strand because there is no 3’ end to which the newly synthesized DNA can attach. This non-replicated fragment results in gradual loss of the chromosomal DNA during each cell duplication. Additionally, it can induce a DNA damage response by enzymes that recognize single-stranded DNA.
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
Topoisomerases are divided into two main types. Type I...
Types and Mechanism of action
Topoisomerases are divided into two main types. Type I...
Protein Folding
Overview
Translesion DNA Polymerases
Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
Restarting Stalled Replication Forks
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, a...

