Choodet Cherdpong, Toomjeen Pakawat, Phanchai Witthawat, Matulakul Piyaporn, Thanan Raynoo, Sakonsinsiri Chadamas, Puangmali Theerapong
Department of Physics, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand.
Department of Biochemistry, Faculty of Medicine, Khon Kaen University Khon Kaen 40002 Thailand.
RSC Adv. 2019 Jun 4;9(31):17592-17600. doi: 10.1039/c9ra01497g.
An elevated level of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) in biosamples has been found to correlate to oxidative stress, and it has been assigned as a critical biomarker of various diseases. Herein, insights into the mechanisms of an aptasensor, based on citrate-capped gold nanoparticles (AuNPs), for 8-oxo-dG detection were elucidated using molecular dynamics (MD) simulations and validated experimentally. We found that the binding mechanism for binding between the anti-8-oxo-dG aptamer and 8-oxo-dG has the following characteristic stages: (i) adsorption stage, (ii) binding stage, and (iii) complex stabilization stage. Our simulations also reveal the binding sites between the anti-8-oxo-dG aptamer and 8-oxo-dG formed through hydrogen bonding during complex formation. A shortened anti-8-oxo-dG-aptamer was also engineered using design, which was expected to improve the analytical performance of the colorimetric aptasensor. The mechanisms of the colorimetric aptasensor in the presence and absence of 8-oxo-dG were also investigated, and found to be in good agreement with the experiments. Complete understanding of the mechanism of the colorimetric aptasensor would open the door for development of novel naked-eye aptasensors.
生物样本中8-氧代-7,8-二氢-2'-脱氧鸟苷（8-氧代-dG）水平升高已被发现与氧化应激相关，并且它已被指定为各种疾病的关键生物标志物。在此，基于柠檬酸盐包覆的金纳米颗粒（AuNPs）的适体传感器用于检测8-氧代-dG的机制通过分子动力学（MD）模拟得到阐明，并通过实验进行了验证。我们发现抗8-氧代-dG适体与8-氧代-dG之间的结合机制具有以下特征阶段：（i）吸附阶段，（ii）结合阶段，以及（iii）复合物稳定阶段。我们的模拟还揭示了在复合物形成过程中通过氢键形成的抗8-氧代-dG适体与8-氧代-dG之间的结合位点。还使用设计构建了一种缩短的抗8-氧代-dG适体，预计它将提高比色适体传感器的分析性能。还研究了比色适体传感器在存在和不存在8-氧代-dG时的机制，发现与实验结果非常吻合。对比色适体传感器机制的全面理解将为新型裸眼适体传感器的开发打开大门。
