Computer analyses on the structure of junction sites between adenovirus DNA and cellular DNA

In previous work we have cloned and determined the nucleotide sequence of sites of linkage between mammalian cell DNA and foreign (viral) DNA. These investigations have been performed to study details of the mechanism of recombination in mammalian cells. Cloned lines of adenovirus-transformed cells have been used in the analyses because they constituted cell populations in which the foreign DNA had been fixed at certain sites in the cellular genomes. In the present investigation, these nucleotide sequences at sites of linkage have been subjected to computer-aided analyses. A number of sequence motifs have been determined; sequence features common to all junction sites have not been discernible. In some instances, patch homologies have been detected. At several sites of junction, the cellular DNA sequences seem to be transcriptionally active, even in cells that do not carry foreign DNA. Transcriptional activity may be a necessary but perhaps not sufficient precondition for recombination of mammalian DNA sequences with foreign DNA.