Single-strand conformational polymorphism (SSCP) analysis is one of the most popular methods for mutation scanning
Single-stranded DNA has a tendency to fold up and form complex structures stablilized by weak intramolecular bonds, notably base-pairing hydrogen bonds. The electrophoretic mobilities of such structures on nondenaturing gels will depend not only on their chain lengths but also on their conformations, which are dictated by the DNA sequence. For SSCP, amplified DNA samples (which may be RT-PCR
products) are denatured and loaded on a nondenaturing polyacrylamide gel. Primers can be radiolabeled, or unlabeled products can be detected by silver staining. Control samples must be run, so that differences from the wild-type pattern can be noticed. SSCP is simple and adequately sensitive for fragments up to 200 bp long, but it does not reveal the nature or position of any mutation detected (
Sheffield
et al., 1993). SSCP and heteroduplex analysis can be combined on a single gel. The precise pattern of bands seen is very dependent on details of the conditions. An elaboration of SSCP,
dideoxy fingerprinting, analyzes each band in a sequencing ladder by SSCP, and is claimed to give 100% sensitivity (
Sarkar
et al., 1992).