A nuclear magnetic resonance investigation of the energetics of basepair opening pathways in DNA
A nuclear magnetic resonance investigation of the energetics of basepair opening pathways in DNA
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DOI：
10.1529/biophysj.105.065763
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发表时间：
2005-11-01
影响因子：
3.4
通讯作者：
Russu, IM
中科院分区：
文献类型：
--
作者：
Coman, D;Russu, IM
碱基对的开放在DNA复制、转录、修复和修饰等过程中起着关键作用。阳离子酶在这篇文章中，我们使用质子交换。在两个DNA 17-mer双链体中碱基对打开的途径的能量学。亚氨基质子与溶剂质子的交换速率通过NMR光谱法测量每个DNA双链体，作为交换催化剂浓度和温度的函数。测量提供了在不同温度下单个碱基对的开放反应的速率和平衡常数。这些温度依赖性用于计算每个碱基对的开放势垒和开放状态的自由能和自由能。结果表明，在开环反应中存在三种不同的焓变模式。这些图案在动力学打开屏障相对于打开状态的位置上彼此不同。邻近碱基，即从开放碱基对中移除的一个或多个位置，影响开放途径的重复模式。发现开放势垒的自由能与开放态的自由能成线性关系。这种相关性进行了分析的速率平衡自由能的关系，以前在其他系统中观察到的，并建议在开放反应的过渡态是更接近本地封闭状态的碱基对比其开放状态。
The opening of basepairs plays a key role in DNA replication and transcription, and in the action of DNA repair and modi. cation enzymes. In this article, we have used proton exchange to de. ne the energetics of the pathways for basepair opening in two DNA 17-mer duplexes. The rates of exchange of imino protons with solvent protons were measured by NMR spectroscopy for each DNA duplex, as a function of the concentration of exchange catalyst and of temperature. The measurements provided the rates and the equilibrium constants of the opening reactions for individual basepairs at different temperatures. These temperature dependences were used to calculate the enthalpies and the free energies of the barrier to opening and of the open state for each basepair. The results reveal the existence of three distinct patterns of enthalpy changes in the opening reactions. The patterns differ from each other in the location of the kinetic opening barrier relative to the open state. Neighboring bases, which are one or more positions removed from the opening basepair, influence the enthalpic pattern of the opening pathway. The free energies of the opening barriers are found to be linearly related to the free energies of the open state. This correlation is analyzed in terms of rate-equilibrium free energy relationships previously observed in other systems, and suggests that the transition state in the opening reaction is closer to the native closed state of the basepair than to its open state.