Institute for Frontier Materials, Deakin University , Geelong, Victoria 3216, Australia.
ACS Sens. 2017 Nov 22;2(11):1602-1611. doi: 10.1021/acssensors.7b00435. Epub 2017 Nov 7.
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.
我们报告了一种通过非共价相互作用吸附在水石墨烯上的腺嘌呤结合 DNA 适体的预测结构破坏。在纳米流体传感平台中，需要在器件衬底上使用表面吸附的生物识别元件。在分析物结合后，吸附适体的构象变化可能会干扰表面性质，这对于传感器中的信号产生机制至关重要。然而，目前，这些吸附在石墨烯上的适体结构尚不清楚，并且难以通过实验阐明。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嘌呤的情况下，这种适体在溶液中和吸附在水石墨烯界面上的结构和分析物结合特性。我们预测这种适体可以支持多种稳定的结合模式，直接与石墨烯接触的区域来自位于末端碱基、位于中央的结合口袋和位于远端环区域的碱基。在吸附状态下保留了相当多的溶液中适体结构，表明强的适体内相互作用与石墨烯-适体相互作用竞争。然而，在一些吸附构型中，腺嘌呤分析物通过与石墨烯的强相互作用从结合口袋中脱离。
