Abstract
All cellular RNA polymerases are capable of both forward and retrograde movement (“backtracking”) on the DNA template. Forward movement is favored by the binding of nucleoside triphosphates (NTPs), while backtracking occurs especially when the enzyme encounters an impediment, such as DNA damage. We have determined the X‐ray structures of RNA polymerase II transcribing complexes in various backtracked states. The backtracked RNA is specifically bound by the polymerase, indicative of the functional significance of the backtracked state. The site of binding the backtracked RNA clashes with the site of interaction previously reported for the transcription elongation factor TFIIS. The results are pertinent to the action of TFIIS in recovery from the backtracked state and to the mechanism of proofreading the nascent transcript.
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