If you want to check them for specificity, use the NCBI Primer BLAST tool, check the box for specificity, and put the the name of your organism.

Be warned that it will take some time to do the analysis.

I have developed an algorithm that searches for primers among a set of N sequences or genomes. It may be helpful in this case.

Hello Dina,

to my knowledge the use of available softwares is a bit a gambling game. The most used technique is the stem-loop primer one from Chen, C., Ridzon, D. A., Broomer, A. J., Zhou, Z., Lee, D. H., Nguyen, J. T., et al.(2005). "Real-time quantification of microRNAs by stem-loop RT-PCR" and a bit modified by Kramer, M. F. (2011). "Stem-loop RT-qPCR for miRNAs" or Varkonyi-Gasic, E., and Hellens, R. P. (2011). "Quantitative stem-loop RT-PCRfor detection of microRNAs".

In my current publication, "Identification of extremely GC-rich micro RNAs for RT-qPCR data normalization in human plasma (2023)", in table 2 you can see how to design a specific primer for reverse transcription and the forward and reverse one for qPCR.

Your miRNAs of interest, miR-27a (5p or 3p) and hsa-miR155 (5p or 3p), have estimated 50-60% GC content, so not tricky ones as in my publication.

Take a try and add six miRNA specific bases to our design by hand and test it. Normally it should work very well.

Regards

Hi,if You have to check micro RNA then you check NCBI by- Medline - publication index - Association extractor - Term extractor - miRBase parser - miRBase.

The majority of miRNA publication association in mirpub database have discovered by applying text mining techniques on titles, abstract and full text of all available MEDLINE publication.