Detection of MicroRNAs by Northern Blot

Indirect and sensitive determination of microRNAs by magnetic field-assisted capillary sieving electrophoresis combined with catalytic hairpin assembly

To determine multiple microRNAs (miRNAs) from cells simultaneously is essential for understanding biological functions. Capillary electrophoresis (CE) can simultaneously determine multiple miRNAs by separation. Nevertheless, similar lengths and low concentrations in cells make miRNAs hard to separate and detect. In this study, CE with laser-induced fluorescence detection was combined with catalytic hairpin assembly (CHA) to determine three miRNAs, miR-21, miR-31, and miR-122. The amplification products of CHA, which were DNA duplexes, were designed to have different lengths for different miRNAs. This allowed for easy separation of the duplexes of different miRNAs by CE. The indirect determination of miRNAs was then achieved by separating and detecting these duplexes. A magnetic field was first applied on the capillary sieving electrophoresis to assist in the separation of the duplexes. Under the optimal conditions, the three duplexes could be completely separated within 2.5 min with the detection limits of miRNAs in the range 1.12-4.05 × 10-15 M. MiR-21 and miR-31 were successfully determined from Hela cells, while miR-122 was determined from chicken livers by this method. The recoveries ranged from 97.5% to 118%. The developed method was sensitive and reliable for miRNA determination.

A dual-signal amplification strategy based on rolling circle amplification and APE1-assisted amplification for highly sensitive and specific miRNA analysis for early diagnosis of alzheimer's disease

MicroRNA (miRNA) is involved in the progression of Alzheimer's disease (AD) and emerges as a promising AD biomarker and therapeutic target. Therefore, there is an urgent need to develop convenient and precise miRNA detection methods for AD diagnosis. Herein, a dual-signal amplification strategy based on rolling circle amplification and APE1-assisted amplification for miRNA analysis for early diagnosis of AD was proposed. The strategy consisted of dumbbell-shaped probe (DP) as amplification template and a reporter probe (RP) with an AP site modification. In the presence of the target miRNA, the miRNAs bound to the toehold domain of DP and DP was activated into a circular template. Then, RCA reaction was triggered, producing a large number of long-stranded products containing repeated sequences. After RCA, APE1 enzyme recognized and removed AP site in the complex of RCA/RP products. By coupling RCA with APE1-assisted amplification, this method has high sensitivity with the limit of detection (LOD) of 1.82 fM. Moreover, by using DP as template for RCA reaction, high specificity can be achieved. By detecting miR-206 in serum using this method, the expression of miR-206 can be accurately distinguished between AD patients and healthy individuals, indicating that this method has broad application prospects in clinical diagnosis.

The tsRNAs (tRFdb-3013a/b) serve as novel biomarkers for colon adenocarcinomas

The tsRNAs (tRNA-derived small RNAs) are a novel class of small non-coding RNAs derived from transfer-RNAs. Colon adenocarcinoma (COAD) is the most malignant intestinal tumor. This study focused on the identification and characterization of tsRNA biomarkers in colon adenocarcinomas. Data processing and bioinformatic analyses were performed with the packages of R and Python software. The cell proliferation, migration and invasion abilities were determined by CCK-8 and transwell assays. Luciferase reporter assay was used to test the binding of tsRNA with its target genes. With computational methods, we identified the tRNA fragments profiles within COAD datasets, and discriminated forty-two differentially expressed tsRNAs between paired colon adenocarcinomas and non-tumor controls. Among the fragments derived from the 3' end of tRNA-His-GUG (a histidyl-transfer-RNA), tRFdb-3013a and tRFdb-3013b (tRFdb-3013a/b) were notably decreased in colon and rectum adenocarcinomas, especially, tRFdb-3013a/b might tend to be down-regulated in patients with lymphatic or vascular invasion present. The clinical survival of colorectal adenocarcinoma patients with low tRFdb-3013a/b expression was significantly worse than that of high expression patients. In colon adenocarcinoma cells, tRFdb-3013a could have inhibited cell proliferations, and reduced cell migration and invasion abilities. The enrichment analyses showed that most of tRFdb-3013a correlated-genes were enriched in the extracellular matrix associated GO terms, phagosome pathway, and a GSEA molecular signature pathway. Additionally, the 3'UTR of ST3GAL1 mRNA was predicted to contain the binding site of tRFdb-3013a/b, tRFdb-3013a/b might directly target and regulate ST3GAL1 expression in colon adenocarcinomas. These results suggested that tRFdb-3013a/b might serve as novel biomarkers for diagnosis and prognosis of colon adenocarcinomas, and act a key player in the progression of colon adenocarcinomas.