A new pathway in the generation of defective retrovirus DNA.

We used a retrovirus shuttle vector to make molecular clones of circular viral DNA from infected cells. One-third of the molecules examined had deletions that started within or near the U5 domain of the long terminal repeat (LTR) region and extended a variable distance toward the gag gene. We present evidence that some of these deletions arose by cleavage of a single LTR unit, in contrast to the cleavage of tandem LTR units associated with the integration reaction. These results suggest that in the formation of defective circular DNA, the U5 domain can be recognized and cleaved in the absence of an adjacent U3 domain. The cleavage of isolated U5 domains may represent an important mechanism responsible for the generation of certain forms of both defective circular DNA and defective integrated DNA.