Fig. S1.

RNA pol II was persistently arrested by Py-Im polyamides. (A) RNA pol II transcription elongation is blocked by Py-Im polyamides in both binding orientations (TS and NTS). C, control lanes in the absence of Py-Im polyamides; 1, 2, 3, and 4 represent the transcription inhibition results by four compounds listed in Fig. 1A. The incubation time for this transcription assay was 20 h. RNA pol II failed to bypass the blockage with prolonged incubation. (B) Traces of lanes in the presence of different compounds. (C) Pol II elongation complex (EC) was persistently arrested by the polyamides and no obvious free RNA transcript is released. The pol II EC stability experiment was performed in 4% (wt/vol) native PAGE with ³²P labeled in the RNA transcript. Lane 1: pol II EC assembled as described in the method in the absence of Py-Im polyamide 1; lane 2: pol II EC in the presence of Py-Im polyamide 1; lanes 3–5: Pol II transcription elongation in the presence of 1 after the designated time points (10 min, 1 h, and 20 h, respectively); lane 6: the 20-h time point sample heated at 95 °C for 10 min before loading. Free RNA transcript is released upon heat treatment (indicated by the blue arrow). (D) The arrested pol II EC was slowly recovered upon treatment of the DNA duplex competitor. The control lane is the arrested EC in the presence of compound 1 after 1 h transcription elongation. The duplex competitor with 5′-WGGWCW-3′ binding site (ds-1) was subsequently added into the arrested EC mixture. As comparison, the DNA duplex without the designed binding site (ds-2) was incubated with the arrested EC as well. The sample without any competitor (–) was also analyzed. The EC was 50 nM, the compound 1 was 1 µM, and the competitor DNA duplex was 10 µM. Time points were 1, 4, 18, and 42 h.