Agarose-based system for separation of short tandem repeat loci

Short tandem repeats (STRs) are traditionally analyzed on large polyacrylamide electrophoresis gels. We demonstrate in this study that a small (10-cm-long, 1-mm-thick) agarose gel is sufficient for analysis of multiplexed samples for several commonly used STR loci. A system was developed using a high-resolution agarose, MetaPhor. Within an hour of electrophoresis, sufficient resolution was obtained to allow discrimination of triple-multiplexed STR loci. We show that this agarose is capable of resolving di- as well as tetranucleotide ladders. Using PCR conditions similar to those routinely used with sensitive detection systems, we found that direct staining of gels with SYBR Green I stain was comparable with silver staining, autoradiography or fluorescently tagged primers for sample detection and was considerably easier. This procedure significantly simplifies STR analysis and is much faster than many standard protocols.