FIGURE 4.

RNAP affinity to downstream fork junction probes depends on the length of the duplex segment. A, shown are representative structures of downstream fork junctions probes used. The SP18 linker that joins non-template strand oligos with short template strand oligos in some probes is shown as a vertical line. In probe names, SP stands for the SP18 linker; N.C.−4/+1 stands for a non-complementary extension of the template strand from −4 to +1. B, RNAP occupancy was measured in samples containing 1 nm RNAP beacon and 2 nm [−11/+14;−8T][+2/+14], [−11/+16;−8T][+2/+16], and [−11/+20;−8T][+2/+20] probes abbreviated as +14, +16, and +20, respectively.