DNA curvature controls termination of plus strand DNA synthesis at the centre of HIV-1 genome

In vivo and in vitro, reverse transcriptase (RT) from human immunodeficiency virus type 1 (HIV-1) terminates plus strand synthesis at the centre of the viral genome. The central termination sequence (CTS) contains curved DNA fragments located upstream of each terminator site. Two different models, relying either on the A-tract or general sequence roll assumptions, were used to predict the extent and the direction of this curvature as well as to design mutants, which abolished it. Straightening of each curved element abolished termination at the site located immediately downstream from the curvature. When synthesis was performed on the other strand and in the opposite direction, the two curved elements C1 and C2 associated with the two termination sites Ter1 and Ter2, led again to termination of DNA synthesis. Therefore, termination occurred as a nascent bent duplex was synthesized within the template primer binding cleft of RT, even when putative strand-specific motifs have been removed by the inversion. Computation of DNA paths upstream of other known arrest sites suggested that this feature was of general relevance for termination. At the CTS, termination occurred more precisely at the 3' end of an AnTm motif (n + m = 7). The possible structures, adopted by this motif, are discussed and confronted with the present crystallographic and biochemical data obtained on HIV-1 RT-DNA interactions and on HIV-1 RT processivity.