Genomic Fingerprinting by Application of rep-PCR

Several families of short repetitive DNA sequences, widely distributed in the genome, have been identified in bacteria (1 ). They have an intercistronic location, are not translated, and their function is unclear, although they may be involved in transcription termination, mRNA stability or chromosomal organization. Repetitive extragenic palindrome (REP) elements (2 ), also known as palindromic units (PU) (3 ), and enterobacterial repetitive intergeinc consensus (ERIC) sequences (4 ) are the best characterized of these elements and were mitially identified in Salmonella typhimurium and Eschenchla colt , respectively. The REP consensus sequence was formulated through DNA sequence comparisons of intercistronic regions of different operons (3 ,5 ) and comprises a 38 nucleotide palindromic sequence that can form a stable stem-loop structure with a 5-bp variable loop m the central region (2 ). There may be 50—1000 copies of the REP sequence in the genome, frequently present in complex clusters (2 ), with each cluster comprising as many as 10 copies (6 ). REP sequences have been located between genes within an operon or at the end of an operon, in different orientations and in tandem arrays, and in operons distributed throughout the genome (2 ,3 ). The REP sequence has been identified in intergenic regions within operons from different bacterial species (7 ,8 ). REP like sequences have been shown to exist throughout the eubacterial kingdom, although the consensus sequences may differ among different bacteria 9 11 ).