The kissing hairpin sequence promotes recombination within the HIV-I 5 ' leader region

The role of RNA-RNA template interactions in facilitating recombination dur ing reverse transcription of minus strand DNA has been examined. The tested hypothesis is that template switching by reverse transcriptase is promoted at sites where homologous regions of two RNAs are brought in close proximi ty via stable intertemplate interactions. Frequency and distribution of tem plate switching between homologous donor and acceptor RNAs were examined wi thin the human immunodeficiency virus type 1 (HIV-1) 5 ' -untranslated regi on (UTR) containing the dimer initiation sequence (DIS). Results were compa red with control nondimerizing templates from the pol region. The dimerizin g UTR templates displayed a 4-fold higher transfer efficiency than the cont rol. A striking 53% of transfers in the UTR mapped near the DIS, of which t wo-thirds occurred immediately 5 ' to this sequence. In the UTR template, d eletion of the DIS hairpin disrupted template dimerization and caused a 4-f old drop in transfer efficiency. Insertion of the DIS within the pol templa te increased both dimerization and transfer efficiency. Transfer distributi ons revealed that in both sets of templates, DIS-induced dimerization incre ased the efficiency of transfers across the whole template, with the transf ers peaking around the dimerization site. Overall, these results suggest th at template dimerization facilitated by the unique geometry of the DIS-prom oted kissing interactions effectively promotes recombination within the HIV -1 5 ' -UTR.