OmiR and OmiL: universal primers for DNA fingerprinting?

Among the repeated sequences present in most eukaryotic genomes, SINEs (Short Interspersed Nuclear Elements) are widely used to investigate the evolution of mammalian orders. One of these repetitive sequences, namely MIR (Mammalian Interspersed Repeats), is ubiquitous in all mammals. MIR elements are tRNA-derived SINEs and are identifiable by a conserved core region of about 70 nucleotides. In previous studies PCR amplifications with five MIR-specific primers (MS-PCR) were performed and produced specific DNA patterns of several hundred fragments with lengths ranging between 50 and 1500bp. Since MIRs were found in placental mammals, marsupials and monotremes, their high divergence and their presence at the orthologous sites in different mammalian species suggest that MIRs, at least in part, amplified before the mammalian radiation. In the present study, two MIR-specific primers designed on the core sequence (Omil17 and Omir17) were used to produce a species-specific inter-MIR fingerprinting in different mammalian species. The same primers were also tested in virus, yeast, plant and non-mammalian animals. Surprisingly, we obtained PCR products and species-specific pattern profiles from all samples tested. Further PCR reactions were carried out at different and increasing melting temperatures (from 48 to 60°C) to check the PCR pattern repeatability and stability. The results of our study indicate that repeated sequences similar to MIR are present in non-mammalian organisms and may be exploited to produce inter-repeated sequence species-specific DNA fingerprints.