Abstract
Cauliflower mosaic virus (CaMV) is a DNA plant virus which replicates by reverse transcription. During our examination of CaMV replication intermediates by 2-D gel electrophoresis, we have discovered a population of bizarre linear double-stranded hairpin DNAs. The largest hairpin is the size of the CaMV genome; hairpin loop ends of smaller molecules map to several sites around the genome but the open ends are all located close to the origin of reverse transcription at the primer binding site. We believe that the hairpin DNAs are generated in vivo by reverse transcription of CaMV RNA followed by self-primed second strand synthesis. The accumulation of hairpin DNAs in vivo might represent a side reaction of the CaMV reverse transcriptase although an essential role for them in the virus replication cycle cannot be discounted. The structure of the hairpin DNAs provides further evidence for the location of the start site and of the polarity of reverse transcription in CaMV.