Present-Day Computer-Aided Primer Designing Tools for Noncoding RNA

MicroRNAs (miRNAs) are a class of noncoding RNAs 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 microRNAs. Designing the primers for qualitative assessment of microRNA expression is a challenge in terms of methodology owing 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 microRNAs. That is why specialized platforms have been created that are adapted to unique structural and functional properties of microRNAs. These platforms ensure exact design of primers that can be reproduced. The current review considers present-day computer-aided software tools specially developed to design primers for short noncoding RNAs with emphasis on their functional characteristics and ability to design primers for the most commonly used method of qualitative assessment of microRNA expression—stem-loop RT-PCR.