James Versalovic

Repetitive Sequence-based PCR (rep-PCR) DNA Fingerprinting of Bacterial Genomes

Bacterial chromosomes contain multiple interspersed repetitive sequences that occupy intergenic regions at sites dispersed throughout the genome. Such blocks of noncoding, repetitive sequences can serve as multiple genetic targets for oligonucleotide probes, enabling the generation of unique DNA profiles or fingerprints for individual bacterial strains. DNA fingerprinting requires the resolution of differently sized DNA fragments derived from chromosomal or plasmid DNA by restriction endonuclease-mediated digestion and/or DNA amplification to yield a band pattern that serves as a unique identifier. These unique “bar codes” or DNA fingerprints define each bacterial chromosome without the need for measuring gene expression or enzyme function. Genotypic or molecular approaches differ with respect to the level of resolution of individual bacterial species or strains into distinct categories (Figure 34-1).

Interspersed Repetitive Sequences in Bacterial Genomes

Prokaryotic and eukaryotic genomes contain dispersed repetitive sequences separating longer single-copy DNA sequences (Lupski and Weinstock, 1992). Various classes of repeated DNA sequences are present in diverse prokaryotic genomes. Coding sequences, such as ribosomal RNA genes (see Chapter 21) and insertion sequences (see Chapters 4 and 20), may be repeated multiple times per genome but are usually present in relatively low copy numbers. Conserved motifs or subsequences within related genes, such as those encoding transfer RNA (tRNA), may also be repeated multiple times within individual genomes.