L.T. Da, F. Pardo-Avila, L. Xu, D.A. Silva, L. Zhang, X. Gao, D. Wang, X. Huang
Nat Commun, 7:11244, (2016)
The dynamics of the RNA polymerase II (Pol II) backtracking process is poorly understood.We built a Markov State Model from extensive molecular dynamics simulations to identifymetastable intermediate states and the dynamics of backtracking at atomistic detail. Ourresults reveal that Pol II backtracking occurs in a stepwise mode where two intermediatestates are involved. We ﬁnd that the continuous bending motion of the Bridge helix (BH)serves as a critical checkpoint, using the highly conserved BH residue T831 as a sensing probefor the 30-terminal base paring of RNA:DNA hybrid. If the base pair is mismatched,BH bending can promote the RNA 30-end nucleotide into a frayed state that further leads tothe backtracked state. These computational observations are validated by site-directedmutagenesis and transcript cleavage assays, and provide insights into the key factors thatregulate the preferences of the backward translocation.