The in silico design of stem-loop Real-time PCR for detection of hsa-miR-140-3p expression on human Osteoarthritis

Abstract

The deregulation of microRNA-140 (miRNA-140) has been reported to be involved in human pathogenesis of Osteoarthritis (OA). However, in Vietnam, to our knowledge, there are limit study of evaluation of miRNA-140 expression. The commercial kits for the quantitation of miRNA-140 are more expensive. Thus, for the aim to establish the less cost assay for quantitation of miRNAs in developing countries, we designed the set of specific primers to quantify the expression of microRNA for further application on the local population. The sequence of hsa-miR-140-3p was input from miRNA database using the accession number of MI0000456. Following bioinformatics tools, including RNAfold Web Server, BioEdit, IDT Oligo analyzer, were used to design the set of specific primers. As the result, we successfully designed the set of specific primers, including stem-loop primer, named as StL-miR-140-3p, which specific to target sequence of hsa-miR-140-3p, and specific forward primer and reversed primer, named as StL-F-miR-140-3p, and StL-F-miR-140-3p, respectively, which designed for target to the sequence of hsa-miR-140-3p. For further study, it is required to conduct the assay, which based on those designed primers, on the clinical samples to evaluate the specificity, sensitivity, limit of detection, as well as carried on the local population.