Structure of minicircle kinetoplast DNA from a river perch trypanosome

For the first time the complete primary structure (1599 bp) was determined for a minicircle kinetoplast DNA (kpDNA) of a lower-vertebrate trypanosome. Some features were common with all Trypanosomatidae minicircles, such as the presence of conserved and variable regions within one minicircle, and invariant dodecameric 5'-d(GGGGTTGGTGTA>-3' and hexameric 5'-d(GGGCGT)-3' sequences. On the other hand, the kpDNA under study had some features distinguishing it from the minicircles of higher-vertebrate trypanosomes. It proved to be an incomplete dimer based on two unversal dodecamers as the nuclei of symmetry, the sequences around which form a 130-bp direct repeat with a few substitutions. No bent-helix structures were found. The regions of maximal homology between the minicircle examined and those of other trypanosomatids formed discrete clusters along the molecule. PCR analysis demonstrated that such dimeric type of organization (with two conserved regions) is typical of many minicircle kpDNAs from freshwater fish trypanosomes. At the same time, the kpDNA associates of the latter appear to contain a minor portion of minicircles with a single conserved region.