Single Strand Conformational Polymorphism (SSCP) reveals differences in electrophoretic mobility between normal and mutant single strands of DNA (4). In SSCP, normal and mutant duplex DNA are denatured to form single stranded molecules of equal length. These molecules can re-anneal onto themselves and based on the varying degree of intrastrand base pairing, form different three-dimensional structures. These structures, differ in electrophoretic mobility and can be separated on a chilled non-denaturing polyacrylamide gel.The electrophoretic mobility of these “conformers” change depending on temperature and buffer ionic strength. For accurate characterization of mutations within these re-folded single strands, it is essential that the buffer temperature be tightly controlled within each electrophoresis procedure, usually between 4°-15°C. If the gel temperature is not precisely controlled, the resolution will suffer because of the loss of intrastrand base pairing and change in the overall shape of the 3-dimensional conformer.
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