We report on the predicted structural disruption of an adenosine-binding DNA aptamer adsorbed via noncovalent interactions on aqueous graphene. The use of surface-adsorbed biorecognition elements on device substrates is needed for integration in nanofluidic sensing platforms. Upon analyte binding, the conformational change in the adsorbed aptamer may perturb the surface properties, which is essential for the signal generation mechanism in the sensor. However, at present, these graphene-adsorbed aptamer structure(s) are unknown, and are challenging to experimentally elucidate. Here we use molecular dynamics simulations to investigate the structure and analyte-binding properties of this aptamer, in the presence and absence of adenosine, both free in solution and adsorbed at the aqueous graphene interface. We predict this aptamer to support a variety of stable binding modes, with direct base–graphene contact arising from regions located in the terminal bases, the centrally located binding pockets, and the distal loop region. Considerable retention of the in-solution aptamer structure in the adsorbed state indicates that strong intra-aptamer interactions compete with the graphene–aptamer interactions. However, in some adsorbed configurations the analyte adenosines detach from the binding pockets, facilitated by strong adenosine–graphene interactions.

中文翻译：

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石墨烯上的腺苷结合DNA适体的结构破坏：Aptasensor设计的影响。

我们报告了通过在水性石墨烯上的非共价相互作用吸附的腺苷结合DNA适体的预期结构破坏。为了在纳米流体传感平台中集成，需要在设备基板上使用表面吸附的生物识别元件。在分析物结合后，吸附的适体中的构象变化可能会扰乱表面特性，这对于传感器中的信号生成机制至关重要。然而，目前，这些石墨烯吸附的适体结构是未知的，并且在实验上难以阐明。在这里，我们使用分子动力学模拟来研究在存在和不存在腺苷的情况下，该适体的结构和分析物结合特性，该腺苷既在溶液中游离又吸附在水性石墨烯界面上。我们预测该适体将支持多种稳定的结合模式，其中碱基-石墨烯直接接触来自末端碱基，居中位置的结合口袋和远端环区域。溶液中适体结构在吸附状态下的显着保留表明强的适体内相互作用与石墨烯-适体相互作用竞争。但是，在某些吸附配置中，由于强大的腺苷-石墨烯相互作用，分析物的腺苷会从结合袋中分离出来。溶液中适体结构在吸附状态下的显着保留表明强的适体内相互作用与石墨烯-适体相互作用竞争。但是，在某些吸附配置中，由于强大的腺苷-石墨烯相互作用，分析物的腺苷会从结合袋中分离出来。溶液中适体结构在吸附状态下的显着保留表明强的适体内相互作用与石墨烯-适体相互作用竞争。但是，在某些吸附配置中，由于强大的腺苷-石墨烯相互作用，分析物的腺苷会从结合袋中分离出来。