Estimation of the optimal electrophoretic temperature of DNA single-strand conformation polymorphism by DNA base composition.

To explore the relation between DNA base composition and the optimal single-strand conformation polymorphism (SSCP) electrophoretic temperature (T(s)), we analyzed DNA base composition and T(s) of 24 DNA fragments from different genes and found that T(s) was positively correlative with the ratio of base C/base A. T(s) could be estimated by the formula T(s) = [80 x C/(A+1)]/[2.71 + [C/(A+1)]]. T(s) could be increased dramatically by the complementary sequences in both 5'-and 3'-ends of a DNA single-strand.