Random Amplified Polymorphic DNA (RAPD)

In RAPD analysis, the target sequences to be amplified are unknown. Typically, a 10-nucleotide primer of arbitrary sequence is designed, e.g. by a computer program, and used for an initial PCR amplification. PCR fragments will result only from regions of the DNA where forward (sense) and reverse (antisense) primers are complementary to the target DNA within a reasonable distance (up to 2000 nucleotides apart). This will  reduce the complexity and increase resolution compared with restriction endonuclease analysis. Based on differences in the genomic sequences, different PCR fragment patterns will result following agarose gel electrophoresis, and this can be used for typing and classification of bacteria.