Borrelia burgdorferi contains repeated DNA sequences that are species specific and plasmid associated.

Borrelia burgdorferi, the causative agent of Lyme borreliosis, contains linear and supercoiled circular (SC) plasmids. Because SC plasmids are present in multiple copies, these plasmids were examined for species-specific sequences that could serve as high-copy-number target DNAs for a diagnostic probe. Three EcoRI fragments (4.3, 4.2, and 3.5 kilobase pairs [kb]) that hybridized with multiple DNA fragments from B. burgdorferi were identified and cloned from a SC plasmid-enriched fraction. The 4.2- and 3.5-kb fragments were similar in that they hybridized with each other and with similar-sized EcoRI fragments from two unrelated strains of B. burgdorferi. The 4.3-kb fragment did not hybridize with the other two cloned sequences. Both types of sequences hybridized with most of the SC plasmids in seven B. burgdorferi isolates, whereas only a single 49-kb linear plasmid, found in two of the seven strains tested, hybridized with the cloned sequences. None of the cloned sequences hybridized with chromosomal DNA from B. burgdorferi or with total DNA or SC plasmids from Borrelia hermsii, B. turicatae, B. coriaceae, B. parkeri, or B. anserina. These data indicate that the repeated DNA sequences described in this study appear to be plasmid associated and specific to B. burgdorferi. Heteroduplexes formed from the 4.2- and 3.5-kb fragments showed that hybridizing regions in each fragment comprise a 1.8-kb conserved region that is adjacent to a 1.5-kb region that exhibits greater sequence variability. The sequence divergence seen in the variable region is likely the result of genetic drift and may mean that these regions represent closely related genes that encode functionally similar but antigenically distinct proteins.