DNAs with unusual properties revealed by field inversion gel electrophoresis of agarose-encapsulated DNA from mammalian cells.

Distinct DNA fractions (fr-DNAs), moving separately from bulk DNA, were revealed by field inversion gel electrophoresis of DNA from intact cells lysed and deproteinized in agarose plugs. These fr-DNAs (approximately 2% of the total DNA) were ubiquitously present in nuclei of all mammalian cells studied, including human normal and tumor tissues, and showed a typical electrophoretic pattern (three bands with constant mobilities termed a-, b-, and c-DNA). Characteristic mobility shifts induced by gamma irradiation of a- and b-DNAs suggest their non-linear conformation. In fact, electron microscopy of a- and b-DNAs from Namalwa cells revealed rosette-like structures stabilized by a central protease-resistant knob. Comparative PCR analysis revealed qualitative differences between genomic fingerprints of a- and b-DNAs on the one hand and chromosomal DNA on the other. The results obtained suggest that fr-DNAs originate either from some specific chromatin regions due to non-random cleavages or from an autonomous intranuclear structure, not identified as yet.