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. 2016 Apr 19;7:11244. doi: 10.1038/ncomms11244

Figure 6. Cartoon model of the backtracking mechanism in Pol II EC.

Figure 6

Bending of the BH towards the i+1 site serves as a checkpoint to examine the stabilities of the base pair in the active site using residue T831 as a sensing probe. If the base pairing at i+1 is unstable (for example, mismatched), BH bending can trigger the motion of the RNA 3′-end nucleotide to the frayed state (S2 state). Next, the Pol II EC moves to S3 state where BH residue Y836 stacks with DNA TN and Rpb2 residue Y769 stacks with RNA 3′-end nucleotide through their aromatic rings. Finally, the movement of the RNA:DNA hybrid takes place. Refer to the Fig. 4a for details of the representations. The MFPTs for each transition calculated from the MSM are also provided.