Reverse transcription of a naturally occurring nonretroviral RNA produces a precise deletion in the majority of its cDNA products

A precise, reproducible deletion made during in vitro reverse transcription of RNA2 from the icosahedral positive-stranded Helicoverpa armigera stunt virus (Tetraviridae) is described. The deletion, located between two hexame r repeats, is a 50-base sequence that includes one copy of the hexamer repe at. Only the Moloney murine leukemia virus reverse transcriptase and its de rivative Superscript I, carrying a deletion of the carboxy-terminal RNase H region, showed this response, indicating a template-switching mechanism di fferent from one proposed that involves a RNase H-dependent strand transfer , Superscript II, however, which carries point mutations to reduce RNase H activity, does not cause a deletion. A possible mechanism involves the enzy me pausing at the 3' side of a stem-loop structure and the 3' end of the na scent DNA strand separating from the template and reannealing to the upstre am hexamer repeat.