microRNAs(miRNAs),短单链非编码RNA分子,作为潜在的癌症生物标志物,因为它们参与了癌症的发展。提取miRNA的策略之一是在纳米材料上进行miRNA吸附并通过互补DNA链(DNA探针)解离。最近,发现石墨烯量子点(GQD)显示出良好的吸收miRNA的能力。因此,在这项工作中,使用分子动力学模拟揭示了GQD粘附的miRNA通过其互补DNA捕获的机制。miR-29a,潜在的癌症生物标志物,用作miRNA模型。除了一个和四个互补DNA探针外,还包含一个和四个miR-29a链的三个系统(1R1D,1R4D,和4R4D)进行了研究。GQD是DNA攻击的主要目标。为了保护DNA探针在GQD表面的吸附,需要GQD的全覆盖。在这项工作中,核碱基-主链相互作用是miR-DNA相互作用的主要贡献者。因为miR-29a和它们的探针的大多数核碱基被堆叠以维持它们的二级结构,一些在GQD表面被吸收。显然,通过探针提取miR-29a需要削弱核碱基-GQDπ-π堆叠和内含子配对强度。虽然这里没有发现GQD吸收的miR-29a解吸,获得的基本原理可用于进一步利用GQDs及其衍生物进行miRNA的提取和检测。
MicroRNAs (miRNAs), short single-stranded noncoding RNA molecules, serve as potential cancer biomarkers due to their involvement in cancer development. One of the strategies to extract miRNAs is to perform the miRNA adsorption on nanomaterials and dissociation by a complementary DNA strand (DNA probe). Recently, graphene quantum dots (GQDs) were found to show a good ability to absorb miRNAs. Thus, in this work, the mechanism of the GQD-adhered miRNA capture by its complementary DNA is revealed using molecular dynamics simulations. miR-29a, a potential cancer biomarker, is used as a miRNA model. Three systems containing one and four chains of miR-29a in addition to one and four complementary DNA probes (1R1D, 1R4D, and 4R4D) were studied. GQDs are the prime targets of a DNA attack. The full coverage of GQDs is required to protect the adsorption of DNA probes on the GQD face. The nucleobase-backbone interactions are the main contributors to miR-DNA interactions in this work. The interbase paring becomes small because most nucleobases of miR-29a and their probe are stacked to maintain their secondary structures, and some are absorbed on the GQD surface. Apparently, weakening of the nucleobase-GQD π-π stacking and the intrabase-pairing strength is needed for extracting miR-29a by a probe. Although no GQD-absorbed miR-29a desorption is found here, the basic principles obtained can be useful for further utilization of GQDs and their derivatives for miRNA extraction and detection.