Figure 6.

Model describing the alternative states that occur for TECs stalled in the absence of the next templated NTP. Schematic representations are as in Fig. S1, Fig. S2, and Fig. S3, with the addition of an empty NTP binding site in the posttranslocated state (open square). TECs may enter three or more states at stall positions (22,46), including arrested (A; shaded oval); backtracked by one template position (B; extension of solid line); pretranslocated (pre; no square) and posttranslocated (post; open square) states, respectively. Rate constants for movement of TECs into, or out of, these states are denoted with subscripts F and R, respectively. Arrested states cannot undergo nucleotide addition without transcription cofactors and hence only one rate constant (k_A) was used to describe movement into this state. Backtracked TECs are considered as paused states with entry and exit rate constants k_BF and k_BR, respectively. TECs oscillate rapidly between the pre- and posttranslocated states, with rate constants k_trans,F and k_trans,R. Binding of the next templated NTP (solid square) with rate constant k_NTP,F traps the TEC in the posttranslocated NTP bound state, which may then undergo nucleotide addition to the next template position. Because the rate-limiting steps here comprise the entry and exit pathways into the backtracked state, the model was simplified by combining the pre- and posttranslocated states with the backtracked state and by lumping the rate constants for these reactions into a single rate constant k_BR.