SINGLE-STRAND CONFORMATION POLYMORPHISM (SSCP) ANALYSIS: A RAPID AND SENSITIVE METHOD FOR DETECTION OF GENETIC DIVERSITY AMONG VIRUS POPULATION

ABSTRACTHere we present a review of the single-strand conformation polymorphism (SSCP) method, which allows DNA fragments that have been amplified with specific primers and polymerase chain reaction (PCR) to be scanned rapidly for any sequence variation. The general principles of the method are described, as well as the major factors that must be considered in developing an optimal SSCP strategy, namely the length of the PCR fragment and the temperature of the gel run. Options for sample denaturing gel characteristics and detection of DNA fragments are discussed. The application of these techniques to screen for mutations in the various viral genes is also described.