Dynamics of spontaneous flipping of a mismatched base in DNA duplex
Dynamics of spontaneous flipping of a mismatched base in DNA duplex
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DNA 双链体中不匹配碱基自发翻转的动力学
DOI：
10.1073/pnas.1400667111
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发表时间：
2014-05
影响因子：
11.1
通讯作者：
Zhao Xin Sheng
中科院分区：
文献类型：
--
作者：
Yin Y;ong;Yang Lijiang;Zheng Guanqun;Gu Chan;Yi Chengqi;He Chuan;Gao Yi Qin;Zhao Xin Sheng
意义单个DNA碱基的自发翻转到非螺旋位置是DNA生物物理学中的一个基本问题。这种损伤或错配碱基的自发翻转的动力学是DNA的一个重要的生物物理特征，用于区分受损的碱基和正常的Watson-Crick配对碱基。因此，识别碱基损伤与修复酶的功能密切相关，几乎所有生物都依赖这一机制来维持其基因组的完整性。然而，在这一过程中获得可靠的热力学和动力学数据仍然具有挑战性。通过发展实验和理论技术，我们测定了DNA自发碱基翻转的自由能和速率，为进一步了解其分子机制提供了进一步的见解。DNA碱基翻转是DNA生物物理学中的一个基本主题。B-DNA碱基自发脱离双螺旋的动力学在各种DNA-蛋白质相互作用中具有重要意义，但人们仍然知之甚少。以前通过亚米诺质子交换实验获得的自发碱基翻转速率最有可能是碱基摆动的速率，而不是翻转的速率。利用扩散减速荧光相关光谱和分子动力学模拟，我们证明了双链DNA中单个不匹配碱基对(T-G、T-T或T-C)的碱基可以自发地翻转出DNA双链。螺旋外寿命约为10ms，螺旋内寿命约为0.3-20 S，这取决于碱基对的稳定性。这些发现提供了对DNA碱基翻转动力学的详细了解，并为充分理解修复蛋白如何在大量匹配的DNA碱基中准确地搜索和定位目标错配碱基奠定了基础。
Significance Spontaneous flipping of a single DNA base to an extrahelical position is a fundamental issue in DNA biophysics. The dynamics of such spontaneous flipping of a lesion or mismatched base is an important biophysical feature of DNA to discriminate damaged base from normal Watson–Crick paired ones. It is therefore closely related to repair enzymes' function to recognize base lesions, a mechanism on which almost all organisms rely to maintain their genome integrity. However, it has remained challenging to obtain reliable thermodynamics and kinetics data on this process. By developing experimental and theoretical techniques, we determined the free energy and rates of DNA spontaneous base flipping, providing further insights into its molecular mechanism. DNA base flipping is a fundamental theme in DNA biophysics. The dynamics for a B-DNA base to spontaneously flip out of the double helix has significant implications in various DNA–protein interactions but are still poorly understood. The spontaneous base-flipping rate obtained previously via the imino proton exchange assay is most likely the rate of base wobbling instead of flipping. Using the diffusion-decelerated fluorescence correlation spectroscopy together with molecular dynamics simulations, we show that a base of a single mismatched base pair (T–G, T–T, or T–C) in a double-stranded DNA can spontaneously flip out of the DNA duplex. The extrahelical lifetimes are on the order of 10 ms, whereas the intrahelical lifetimes range from 0.3 to 20 s depending on the stability of the base pairs. These findings provide detailed understanding on the dynamics of DNA base flipping and lay down foundation to fully understand how exactly the repair proteins search and locate the target mismatched base among a vast excess of matched DNA bases.
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