Small circular DNA of Drosophila melanogaster: chromosomal homology and kinetic complexity

Nucleic acid reassociation techniques were used to determine the kinetic complexity of small circular DNA in cultured cells of Drosophila melanogaster. Two kinetic components are present. One of these constitutes 82% of the mass of the circular DNA and has a complexity of 1.8 x 10(4) nucleotide pairs; the other constitutes 18% of the mass and the a significantly higher but undefined sequence complexity. We have demonstrated that these circular molecules hybridize to middle repetitive chromosomal sequences by hybridization of in vitro-labeled circular DNA tracer with a vast excess of Drosophila chromosomal DNA. Thermal stability measurements indicate that base-pair mismatch between small circular DNA and middle repetitive chromosomal DNA does not exceed 2%. We discuss possible functions of these small circular DNAs in light of the above findings.