Direct NMR detection of alkali metal ions bound to G-quadruplex DNA
Direct NMR detection of alkali metal ions bound to G-quadruplex DNA
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DOI：
10.1021/ja709975z
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发表时间：
2008-03-19
影响因子：
15
通讯作者：
Wu, Gang
中科院分区：
文献类型：
--
作者：
Ida, Ramsey;Wu, Gang
我们描述了一种通用的多核（H-1、Na-23、Rb-87）NMR 方法，用于直接检测与 G-四链体 DNA 结合的碱金属离子。这项研究的动机是我们最近发现，与 G-四链体 DNA 紧密结合的碱金属离子（Na+、K+、Rb+）实际上在溶液中“NMR 可见”（Wong, A.；Ida, R.；Wu, G. Biochem. Biophys. Res. Commun. 2005, 337, 363）。这里开发了溶液和固态 NMR 方法，用于研究离子与由三种 DNA 寡聚物形成的经典 G 四链体结构的结合：d(TG(4)T)、d(G(4)T(3)G(4)) 和 d(G(4)T(4)G(4))。本研究得出以下主要发现。 (1) 与G-四链体DNA紧密结合的碱金属离子可以在溶液中通过NMR直接观察到。 (2) 与 G-四链体通道位点结合的竞争性离子可以通过同时 NMR 检测两个竞争性离子来直接监测。 (3)发现Na+离子位于由d(G4T4G4)的两条链形成的G四链体的对角线T-4环区域。这是第一次发现碱金属离子与溶液中对角 T4 环结合的直接 NMR 证据。我们认为环Na+离子位于末端G四联体上方，与末端G四联体的四个鸟嘌呤06原子和环胸腺嘧啶碱基的一个02原子和一个水分子配位。这种 Na+ 离子配位得到了 23Na 化学位移的量子化学计算的支持。变温 23Na NMR 结果表明 d(G(4)T(4)G(4)) 中的通道和环 Na+ 离子表现出非常不同的离子迁移率。环 Na+ 离子在 15°C 时的停留寿命为 220 μs，而 G-四链体通道内的 Na+ 离子的停留寿命长 2 个数量级。 (4) 我们发现直接 23Na NMR 证据表明，当溶液中同时存在 Na+ 和 K+ 离子时，混合的 K+ 和 Na+ 离子占据 d(G4T4G4) G-四联体通道。 (5)本研究观察到的高光谱分辨率在生物大分子的溶液23Na NMR研究中是前所未有的。我们的结果强烈表明，多核 NMR 是研究离子与 G-四链体 DNA 结合的可行技术。
We describe a general multinuclear (H-1, Na-23, Rb-87) NMR approach for direct detection of alkali metal ions bound to G-quadruplex DNA. This study is motivated by our recent discovery that alkali metal ions (Na+, K+, Rb+) tightly bound to G-quadruplex DNA are actually "NMR visible" in solution (Wong, A.; Ida, R.; Wu, G. Biochem. Biophys. Res. Commun. 2005, 337, 363). Here solution and solid-state NMR methods are developed for studying ion binding to the classic G-quadruplex structures formed by three DNA oligomers: d(TG(4)T), d(G(4)T(3)G(4)), and d(G(4)T(4)G(4)). The present study yields the following major findings. (1) Alkali metal ions tightly bound to G-quadruplex DNA can be directly observed by NMR in solution. (2) Competitive ion binding to the G-quadruplex channel site can be directly monitored by simultaneous NMR detection of the two competing ions. (3) Na+ ions are found to locate in the diagonal T-4 loop region of the G-quadruplex formed by two strands of d(G4T4G4). This is the first time that direct NMR evidence has been found for alkali metal ion binding to the diagonal T4 loop in solution. We propose that the loop Na+ ion is located above the terminal G-quartet, coordinating to four guanine 06 atoms from the terminal G-quartet and one 02 atom from a loop thymine base and one water molecule. This Na+ ion coordination is supported by quantum chemical calculations on 23Na chemical shifts. Variable-temperature 23Na NMR results have revealed that the channel and loop Na+ ions in d(G(4)T(4)G(4)) exhibit very different ion mobilities. The loop Na+ ions have a residence lifetime of 220 mu s at 15 degrees C, whereas the residence lifetime of Na+ ions residing inside the G-quadruplex channel is 2 orders of magnitude longer. (4) We have found direct 23Na NMR evidence that mixed K+ and Na+ ions occupy the d(G4T4G4) G-quadruplex channel when both Na+ and K+ ions are present in solution. (5) The high spectral resolution observed in this study is unprecedented in solution 23Na NMR studies of biological macromolecules. Our results strongly suggest that multinuclear NMR is a viable technique for studying ion binding to G-quadruplex DNA.