Serum albumin (SA) is the most abundant carrier protein in blood. SA carries a diverse range of nutrients, drugs, and metal ions. It has wide clinical and biochemical applications. Human serum albumin (HSA) can be used as a biomarker for kidney and liver diseases. Aptasensor is one of potential HSA detection methods. HSA-specific aptamer was selected for HSA detection. In animals, bovine serum albumin (BSA) and canine serum albumins (CSA) share high sequence similarities to HSA. Thus, it is interesting to explore the possibility of using HSA-selective aptamer for BSA and CSA aptasensor. In this study, molecular dynamics (MD) simulations were initially employed to investigate the binding of aptamer to BSA and CSA in comparison to HSA. Like HSA, both BSA and CSA can bind aptamer, but different binding affinities are observed. BSA shows the tighter binding to aptamer than CSA. Domain III is found to be the aptamer-binding domain although no specific aptamer conformation is captured. However, in all cases, the aptamer utilizes the 3 0-end to attach on an albumin surface. Both nucleobases and phosphate backbones on a DNA aptamer are important for albumin-aptamer complexation. Our results imply the possibility of using HSA-specific aptamer for BSA detection due to tighter binding observed, but may be less effective in CSA. However, the test in actual complicated condition must be further studied.

MicroRNAs (miRNAs) are small noncoding RNA molecules associated with the regulation of gene expression in organisms. MiRNAs are focused on as potential cancer biomarkers due to their involvement in cancer development. New potential techniques for miRNA detection are rapidly developed, while there is a lack of effective extraction approaches, especially for miRNAs. Recently, graphene quantum dots (GQDs) have been involved in many disease biosensor platforms including miRNA detection, but no application in miRNA extraction is studied. To extract miRNAs, miRNA adsorption and desorption on GQDs are the key. Thus, in this work, the adsorption mechanism of miRNA on GQDs in solution is revealed using molecular dynamics simulations. The aim is to explore the possibility of using GQDs for miRNA extraction. The folded miR-29a molecule, one of the key cancer biomarkers, is used as a miRNA model. Two systems with one (1miR) and four (4miR) chains of miR-29a were set. MiR-29a molecules in all systems are simultaneously adsorbed on the GQD surface. Our finding highlights the ability of the GQD in collecting miRNAs in solution. In 1miR, the whole miR-29a chain sits on the GQD face, whereas all miR-29a molecules in 4miR show the “clamping” conformation. No “lying flat” orientation of miR-29a is observed due to the existence of the preserved hairpin region. Interestingly, the 5′ end shows tighter binding than the 3′ terminus. A design of complementary DNA with the recognition segment involving the sequences close to the 3′ end can promote effective miR-29a desorption.

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.

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