Structural analysis of proviral DNA in simian foamy virus (LK-3)-infected cells

Proviral DNA of the T-cell lymphotropic simian foamy virus strain LK-3 was characterized. In infected cells, multiple copies of unintegrated linear duplex viral DNA of about 13 kbp length are present. Nuclease S1 treatment of the DNA generated two fragments of 6.5 and 6.0 kbp length that were cloned in phage and plasmid vectors. The proviral DNA contains a single-stranded gap of 109 nucleotides. A DNA fragment spanning the gap was cloned after completing the double strand by DNA synthesis in vitro. At the 3' end, the gap contains a polypurine tract (PPT) similar to the putative initiation site of retroviral plus strand DNA synthesis, suggesting discontinuous DNA synthesis. Further analysis of the genome architecture revealed LTRs of 1.7 kbp length. An additional 1.7 kbp DNA fragment was detected after nuclease S1 digestion of proviral DNA and probably represents trimmed intermediates of "strong-stop" DNA.