Benchmark Theoretical and Experimental Study on N-15 NMR Shifts of Oxidatively Damaged Guanine

0458784 - ÚOCHB 2017 RIV US eng J - Journal Article
Dračínský, Martin - Šála, Michal - Klepetářová, Blanka - Šebera, Jakub - Fukal, Jiří - Holečková, Veronika - Tanaka, Y. - Nencka, Radim - Sychrovský, Vladimír
Benchmark Theoretical and Experimental Study on N-15 NMR Shifts of Oxidatively Damaged Guanine.
Journal of Physical Chemistry B. Roč. 120, č. 5 (2016), s. 915-925. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA ČR GA13-27676S; GA ČR GA15-11223S
Institutional support: RVO:61388963
Keywords : NMR spectroscopy * DFT calculations * oxidatively damaged guanine * hOGG1
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 3.177, year: 2016

The N-15 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 N-15 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 N-15 NMR shifts were first evaluated for OG in crystal to calibrate the best performing calculation method. The effect of large-amplitude motions on N-15 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 N-15 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 N-15 NMR spectroscopy. The calculation protocol can be used for accurate structural interpretation of N-15 NMR shifts of oxidatively damaged guanine DNA residue.
Permanent Link: http://hdl.handle.net/11104/0259021