Sequence arrangements in clonal isolates of polyoma defective DNA

Five clonal isolates of purified polyoma defective DNA [Fried, M. (1974) J. Virol. 13, 939-946] have been examined by electron microscopy. Four isolates (D-92, D-74, D-50, and D-47) are largely homogeneous in sequence, whereas, the fifth isolate (D-80) is somewhat heterogeneous.Polyoma nondefective DNA is cleaved in a unique region of the genome by the EcoR(I) endonuclease. Hybridization of the resulting linear molecules with randomly nicked defective DNA reveals distinguishable types of heteroduplex structures for each of the different defective DNAs. Although the defective DNAs are shorter than polyoma nondefective DNA, the heteroduplex experiments demonstrate that they are not simply deletion mutants containing only a portion of the viral genome. Three isolates (D-92, D-50, and D-47) contain regions of homology to polyoma DNA covalently linked to non-homologous regions. One isolate (D-74) contained no regions of detectable homology to polyoma DNA. Another isolate (D-80) contained a large proportion of molecules with duplicated-inverted regions. Some of these isolates of defective DNA may contain specific host sequences at the site(s) of integration of the polyoma genome during the lytic cycle in mouse cells. A process we term "abortive replication" may explain the formation of different types of defective DNAs.