Fig. 7: Mechanistic model of Pol I pausing and stalling at Ap sites. | Nature Communications

Fig. 7: Mechanistic model of Pol I pausing and stalling at Ap sites.

From: Cryo-EM uncovers a sequential mechanism for RNA polymerase I pausing and stalling at abasic DNA lesions

Fig. 7

The DNA template and non-template strands are in blue and cyan, RNA is in red, the Ap site is in orange, the incoming nucleotide is in purple, A12 is in yellow, the bridge helix is in dark green and magnesium ions are in light green. Pol I is initially paused as the Ap site occupies the templating position (i + 1), which leads to cleft swiveling. This may allow access of A12-Ct into the funnel for subsequent RNA cleavage or lead to Pol I dissociation from DNA in the open cleft state. Pol I stalled at Ap site allows NTP entry into the E-site (entry), which enables access into the A-site (addition). In the A-site, purines are stabilized by sandwiching between the RNA 3′-end and the bridge helix, with preference for ATP. Phosphodiester bond formation likely leads to an altered hybrid configuration that induces RNA cleavage to minimize lesion bypass. Alternatively A49/A34.5 are lost, which hampers RNA cleavage but induces an intermediate of translocation that compromises nucleotide addition, thus stalling Pol I.

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