Pausing patterns and hotspots of intersubtype recombination during reverse transcription on the 115-A and 120-A RNA donor template. Hotspots of recombination were mapped in the C1-C4 region as part of a previous study (A). RNA-dependent DNA synthesis is catalyzed by reverse transcriptase and a 20 nt 5' [32P]-labeled DNA primer on the 115-A and 120-A RNA donor templates (225 nt). Reactions were in the presence or absence of D-89 acceptor (225 nt) and NC (Figure 1D). Reactions were stopped at 30 s, 1, 2, 4, 8, 16, 32, and 64 min and run on a 8% denaturing polyacrylamide gel. Products of these reactions are shown in the autoradiographs of panel B (A-115 donor) and panel C (A-120 donor). The positions of the primer (P), and full extended products derived from the donor template (D, 225 nt) and the strand transfer products (T, 245 nt). A major pause site during DNA synthesis was observed in the C3 region of 115-A donor template and is indicated by the "dumbbell" symbol. A putative V4 stem-loop is also outlined (see Figure 5 for details). Graphs of transfer efficiency vs. time for reactions with A-115 as both donor and acceptor (panel D) or A-115 (circles) or A-120 (triangles) as donor and D-89 as acceptor (panel E) are shown. Filled shapes are without NC and open with. The % transfer efficiency is defined as the amount of transfer product (T) divided by the sum or transfer plus full-length donor directed (D) products times 100 ((T/(T + D)) × 100).