Single strand conformation polymorphism (SSCP) has been widely used for mutation detecting. But the theory about it is not strong enough to guide application. Recently, many computer programs have been designed for predicting the folding of single strand DNA or RNA. Second structures of three DNA segments with RNAstructure 3.2 have been predicted and have been compared with their results of SSCP. The comparison shows there is closely relation between them. The kinds of prediction can guide operator to select primers for SSCP analysis and accurately estimate mutated ratio.