hairpin-dependent pausing

Possible effects of antisense oligonucleotides on hairpin-dependent pausing. (Top) The mechanism of hairpin-dependent transcriptional pausing. The four components of thehis pause signal are labeled on the paused TC, which is formed in competition with bypass of the site and then slowly escapes back into the elongation pathway. How the pause hairpin inhibits nucleotide addition is unknown, but it presumably disrupts reactive alignment of the RNA 3′OH and incoming NTP (depicted here by separation of the 3′ OH and NTP-binding subsites, i and i + 1; see Fig. 7). (Bottom) In the direct model of hairpin-dependent pausing, a specific interaction between the RNA hairpin and its binding site on RNAP disrupts nucleotide addition in the active site of RNAP (Chan et al. 1997; Wang and Landick 1997). In the indirect model, the hairpin merely defines a particular length of 3′-proximal, single-stranded RNA transcript and thus could both disrupt RNA–RNAP interactions required for elongation or TC stability and prevent backtracking of RNAP along the DNA template (Komissarova and Kashlev 1997b; Nudler et al. 1997). Annealing of antisense oligonucleotides to the nascent RNA would be able to recapitulate indirect effects of hairpins, but not direct effects.


Interaction of a nascent RNA structure with RNA polymerase is required for hairpin-dependent transcriptional pausing but not for transcript release
Irina Artsimovitch and Robert Landick1
Genes & Dev. 1998. 12: 3110-3122