Formation of the second phosphodiester bond creates a 3-nt product. This short transcript is still loosely associated with the RNA polymerase II initiation complex and can dissociate to yield abortive products, which are not further extended. The transcription complex still requires continued ATP-hydrolysis by TFIIH and remains sensitive to single-stranded oligo-nucleotide inhibition.
The open region (“transcription bubble”) expands concomitant with the site of RNA-extension. In this case this region spans positions -9 to +3.
Goodrich, JA, Kugel, JF
Fiedler, U, Timmers, HT, Holstege, FC
DNA-directed 5'-3' RNA polymerase activity of RNA Polymerase II (unphosphorylated):TFIIF complex [nucleoplasm]
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