Fig. S7.

Molecular modeling of RNA pol II transcriptional pausing and arrest by Py-Im polyamide. (A) Overall view of an arrested pol II complex in the presence of Py-Im polyamide. This model view is derived from 10 subunit RNA pol II elongation complex with Rpb2 omitted. The protein residues are colored gray; RNA, template DNA, and nontemplate DNA are shown in red, blue, and cyan, respectively. The small DNA binding molecule is highlighted in yellow CPK mode. (B) Py-Im polyamide binding causes a widened DNA duplex minor groove. The Py-Im polyamide bound downstream duplex (blue and cyan) was aligned with regular downstream DNA duplex with pol II elongation complex (gray). The arrow indicates the shifted strand caused by Py-Im polyamide binding.