Natmai Saowalak, Kuntip Nattapon, Japrung Deanpen, Pongprayoon Prapasiri
Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
National Nanotechnology Center, National Science and Technology Development Agency, Thailand Science Park, Pathumthani, 12120, Thailand.
J Mol Graph Model. 2022 Nov;116:108267. doi: 10.1016/j.jmgm.2022.108267. Epub 2022 Jul 9.
MicroRNAs (miRNAs) are small non-coding RNAs that play a role in regulating gene expression. MiRNAs are focused on as potential cancer biomarkers due to their involvement in the cancer development. New effective techniques for extracting miRNA from a biological matrix is important. Recently, graphene quantum dots (GQDs) have been used to detect DNA/RNA in many sensor platforms, but the application in miRNA extraction remains limited. To extract miRNAs, the miRNA adsorption and desorption on GQD are the key. Thus, in this work, the adsorption mechanism of excess miRNA on GQD in solution is revealed using Molecular dynamics simulations. The miRNA assemblies on one and two GQDs were studied to explore the possibility of using GQD for miRNA extraction. The folded miR-29a molecule, one of key cancer biomarkers, is used as an miRNA model. Three systems with one (6miR) and two GQDs (with parallel (6miR_2GP) and sandwich (6miR_2GS) organisations) in six-miR-29a solution were set. The data show excess miR-29a can reduce the miR-29a-GQD binding efficiency. The opening of intrabase pairing of GQD-absorbed miR-29a facilitates the interbase coupling resulting in the self-aggregation of miR-29a. The GQD organisation also affects the miR-29a adsorption ability. The additional GQDs result in the tighter miR-29a adsorption which can retard the miR-29a desorption. The proper GQD concentration is thus important to successfully collect all miR-29a and accommodate the easy miR-29a dissociation. Our results can be useful for a design of DNA probe and choosing decent nanosized GRA concentration for experimental setups.
微小RNA（miRNA）是一类在调节基因表达中发挥作用的小型非编码RNA。由于其参与癌症发展过程，miRNA被视为潜在的癌症生物标志物。开发从生物基质中提取miRNA的新型有效技术至关重要。近年来，石墨烯量子点（GQD）已被用于许多传感器平台中检测DNA/RNA，但在miRNA提取方面的应用仍然有限。要提取miRNA，miRNA在GQD上的吸附和解吸是关键。因此，在本研究中，我们使用分子动力学模拟揭示了溶液中过量miRNA在GQD上的吸附机制。通过研究miRNA在单个和两个GQD上的组装情况，探索了利用GQD提取miRNA的可能性。以关键癌症生物标志物之一的折叠型miR-29a分子作为miRNA模型。在六聚体miR-29a溶液中设置了三个系统，分别包含一个GQD（6miR）以及两个GQD（具有平行排列（6miR_2GP）和夹心排列（6miR_2GS））。数据表明，过量的miR-29a会降低miR-29a与GQD的结合效率。GQD吸附的miR-29a内部碱基对的打开促进了碱基间的偶联，导致miR-29a的自我聚集。GQD的排列方式也会影响miR-29a的吸附能力。额外的GQD会导致miR-29a吸附更紧密，从而延缓miR-29a的解吸。因此，合适的GQD浓度对于成功收集所有miR-29a并便于miR-29a解离至关重要。我们的研究结果有助于DNA探针的设计以及为实验设置选择合适的纳米级GRA浓度。
