The short DNA sequences in the cytoplasm of Ehrlich ascites tumor cells are tightly associated with proteins.

Mouse Ehrlich tumor cells harbor extrachromosomal DNA elements in a non-mitochondrial fraction of the cytoplasm (Abken et al., Proc. Natl. Acad. Sci USA 90: 6518-6522, 1993). The cytoplasmic DNA sequences constitute a distinct group of extrachromosomal genetic elements with common properties: (i) the DNA molecules are 50-500 bp in length and of linear configuration, (ii) most of the DNA sequences exhibit the potential to modulate the activity of a transcriptional promoter, and (iii) the DNA elements are preferentially found in tumor cells, not in cells with normal phenotype. Unexpectedly, the extrachromosomal DNA sequences are found to be tightly associated with at least three proteins (52 kD, 62 kD, 64 kD) forming DNA-protein (DNP) complexes. The DNA-protein interaction is stable during extraction with phenol and chloroform and during incubation with proteinase K and pronase P, in the presence of detergents (SDS, NP40), guanidine-HCl, high salt concentrations, and alkali. Hydrolysis of the DNA by DNAse I makes the proteins of the DNP complex accessible to proteolytic degradation. Western blot analyses imply that the proteins associated with the cytoplasmic DNA sequences are antigenically related to nucleomatrix proteins that are covalently bound to certain regions of chromosomal DNA. Covalent bonds between the cytoplasmic DNA and the polypeptides would explain the unexpected high stability of the cytoplasmic DNA-protein complexes in tumor cells.