Dračínský Martin, Šála Michal, Klepetářová Blanka, Šebera Jakub, Fukal Jiří, Holečková Veronika, Tanaka Yoshiyuki, Nencka Radim, Sychrovský Vladimír
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i. , Flemingovo náměstí 2, 16610 Praha, Czech Republic.
Institute of Physics, Academy of Sciences of the Czech Republic , v.v.i, Na Slovance 2, CZ-182 21 Prague 8, Czech Republic.
J Phys Chem B. 2016 Feb 11;120(5):915-25. doi: 10.1021/acs.jpcb.5b11428. Epub 2016 Feb 1.
The (15)N NMR shifts of 9-ethyl-8-oxoguanine (OG) were calculated and measured in liquid DMSO and in crystal. The OG molecule is a model for oxidatively damaged 2'-deoxyguanosine that occurs owing to oxidative stress in cell. The DNA lesion is repaired with human 8-oxoguanine glycosylase 1 (hOGG1) base-excision repair enzyme, however, the exact mechanism of excision of damaged nucleobase with hOGG1 is currently unknown. This benchmark study on (15)N NMR shifts of OG aims their accurate structural interpretation and calibration of the calculation protocol utilizable in future studies on mechanism of hOGG1 enzyme. The effects of NMR reference, DFT functional, basis set, solvent, structure, and dynamics on calculated (15)N NMR shifts were first evaluated for OG in crystal to calibrate the best performing calculation method. The effect of large-amplitude motions on (15)N NMR shifts of OG in liquid was calculated employing molecular dynamics. The B3LYP method with Iglo-III basis used for B3LYP optimized geometry with 6-311++G(d,p) basis and including effects of solvent and molecular dynamic was the calculation protocol used for calculation of (15)N NMR shifts of OG. The NMR shift of N9 nitrogen of OG was particularly studied because the atom is involved in an N-glycosidic bond that is cleaved with hOGG1. The change of N9 NMR shift owing to oxidation of 9-ethylguanine (G) measured in liquid was -27.1 ppm. The calculated N9 NMR shift of OG deviated from experiment in crystal and in liquid by 0.45 and 0.65 ppm, respectively. The calculated change of N9 NMR shift owing to notable N9-pyramidalization of OG in one previously found polymorph was 20.53 ppm. We therefore assume that the pyramidal geometry of N9 nitrogen that could occur for damaged DNA within hOGG1 catalytic site might be detectable with (15)N NMR spectroscopy. The calculation protocol can be used for accurate structural interpretation of (15)N NMR shifts of oxidatively damaged guanine DNA residue.
计算并测量了9-乙基-8-氧代鸟嘌呤（OG）在液态二甲基亚砜（DMSO）和晶体中的¹⁵N核磁共振化学位移。OG分子是细胞中由于氧化应激而产生的氧化损伤2'-脱氧鸟苷的模型。这种DNA损伤由人类8-氧代鸟嘌呤糖基化酶1（hOGG1）碱基切除修复酶进行修复，然而，目前尚不清楚hOGG1切除受损核碱基的确切机制。这项关于OG的¹⁵N核磁共振化学位移的基准研究旨在对其进行准确的结构解释，并校准可用于未来hOGG1酶作用机制研究的计算方案。首先在晶体中评估了核磁共振参考、密度泛函理论（DFT）泛函、基组、溶剂、结构和动力学对计算得到的¹⁵N核磁共振化学位移的影响，以校准性能最佳的计算方法。采用分子动力学计算了大幅度运动对液态OG的¹⁵N核磁共振化学位移的影响。用于计算OG的¹⁵N核磁共振化学位移的计算方案是：采用Iglo-III基组的B3LYP方法，其优化几何结构采用6-311++G(d,p)基组，并包括溶剂和分子动力学效应。特别研究了OG的N9氮的核磁共振化学位移，因为该原子参与了被hOGG1切割的N-糖苷键。在液态中测量的9-乙基鸟嘌呤（G）氧化导致的N9核磁共振化学位移变化为-27.1 ppm。计算得到的OG的N9核磁共振化学位移在晶体和液态中与实验值的偏差分别为0.45 ppm和0.65 ppm。在之前发现的一种多晶型中，由于OG显著的N9-锥形化导致的N9核磁共振化学位移计算变化为20.53 ppm。因此，我们假设在hOGG1催化位点内受损DNA可能出现的N9氮的锥形几何结构可以通过¹⁵N核磁共振光谱检测到。该计算方案可用于对氧化损伤的鸟嘌呤DNA残基的¹⁵N核磁共振化学位移进行准确的结构解释。
