The ability of detecting sequence variations in a PCR product decreases with increasing length of the products. It is recommended that the size of PCR products be less than 300 bp to increase the chance of picking up sequence variations in the fragments although sequence variations can sometimes be detected in fragments larger than 1,000 bp.
The throughput of SSCP analysis can be increased by running in the same lane two or more small products of different sizes, or several small products generated by restriction digestion of a long PCR product. The gel must of course be large enough for the required separation.