Silver-Stabilized Guanine Duplex: Structural and Optical Properties
Silver-Stabilized Guanine Duplex: Structural and Optical Properties
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DOI：
10.1021/acs.jpclett.8b01908
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发表时间：
2018-08-16
影响因子：
5.7
通讯作者：
Lopez-Acevedo, Olga
中科院分区：
文献类型：
--
作者：
Chen, Xi;Makkonen, Esko;Lopez-Acevedo, Olga
最近的实验双链DNA稳定的银阳离子，配对同源链的鸟嘌呤，胞嘧啶，胞嘧啶，腺嘌呤，胸腺嘧啶，胸腺嘧啶，显示出更高的稳定性比沃森-克里克配对的DNA双链体，这些拓宽了DNA纳米技术的应用范围。在这里，我们专注于银稳定的鸟嘌呤双链体在水中。利用混合量子力学/分子力学模拟，我们提出了一个原子结构的Ag+介导的鸟嘌呤双链体与两个核碱基每链，G（2）-Ag-2（+）-G（2）。然后，我们比较实验和含时密度泛函理论模拟的电子圆二色性（ECD）光谱，以验证我们的结果。实验和模拟的ECD在220和280 nm附近共有两个负峰，在测量的波长范围内没有正信号。我们发现结构中碱基的左旋或右旋配置对ECD的符号有决定性的影响。我们的结论是，G（2）-Ag-2（+）-G（2）是左手取向的，这种取向外推到较长的链产生了一个左手取向的平行螺旋稳定的平面间氢键。
Recent experimental duplexes of DNA stabilized by Ag cations, pairing homostrands of guanine-guanine, cytosine-cytosine, adenine-thymine, and thymine-thymine, display much higher stability than the Watson-Crick paired DNA duplexes; these broaden the range of applications for DNA nanotechnology. Here we focus on silver-stabilized guanine duplexes in water. Using hybrid quantum mechanics/molecular mechanics simulations, we propose an atomic structure for the Ag+- mediated guanine duplex with two nucleobases per strand, G(2)-Ag-2(+)-G(2). We then compare experimental and time-dependent density functional theory-simulated electronic circular dichroism (ECD) spectra to validate our results. Both experimental and simulated ECD share two negative peaks around 220 and 280 nm, with no positive signal in the measured wavelength range. We found that the left- or right-handed disposition of bases in the structure has a decisive effect on the signs of the ECD. We conclude that G(2)-Ag-2(+)-G(2) is left-hand-oriented, and extrapolation of this orientation to longer strands gives rise to a left-hand-oriented parallel helix stabilized by interplanar H bonds.