Present-Day Computer-Aided Primer Designing Tools for Non-Coding RNA

MicroRNA (miRNA) is a class of non-coding RNA that play the pivotal role in post-transcriptional regulation of expression of genes involved in the control of fundamental cellular processes. Their high diagnostic yield and predictive value in various human diseases predetermined the need for highly specific design of primers for qualitative analysis of the expression of a variety of microRNA. Designing the primers for qualitative assessment of microRNA expression is a challenge in terms of methodology due to short matrix and high homology between the family members. Quite often conventional tools, initially aimed at longer targets, are not efficient enough when working with shorter sequences of mature microRNA. That is why, specialized platforms have been created that are adapted to unique structural and functional properties of microRNA. These platforms ensure exact design of primers that can be reproduced. Current review considers present-day computer-aided software tools specially developed to design primers for short non-coding RNA with emphasis on their functional characteristics and ability to design primers for most commonly used method of qualitative assessment of microRNA expression – Stem-loop RT-PCR.