DNA molecules have two strands intertwined with each other in antiparallel direction with the base-pairing of A with T and C with G. The two strands are complementary to each other, but not identical. The two strands of a PCRamplified product can be separated into single strands by heat. Each single strand can coil around itself to form a 3-dimensional structure (or conformation) through intramolecular (or intrastrand) hydrogen bonds.
This conformation is dependent on the length of the strand and its base composition. The two complementary strands may form different conformers because they are not identical. If the DNA fragment contains a single base change, there are four different single strands on denaturation, which may form four different conformers.
These conformers may have different 3-dimensional sizes and shapes, and hence migrate at different speeds in a polyacrylamide gel. Thus, different samples may give different banding patterns because of the presence of a base change in the amplified DNA region.