Structure in nascent RNA leads to termination of slippage transcription byT7 RNA polymerase

T7 RNA polymerase presents a very simple model system for the study of fund amental aspects of transcription. Some time ago it was observed that in the presence of only GTP as a substrate, on a template encoding the initial se quence GGGA..., T7 RNA polymerase will synthesize a 'ladder' of poly-G RNA products. At each step, the ratio of elongation to product release is consi stently similar to0.75 until the RNA reaches a length of similar to 13-14 n t, at which point this ratio drops precipitously. One model to explain this drop in complex stability suggests that the nascent RNA may be structurall y hindered by the protein; the RNA may be exiting via a pathway not taken b y normally synthesized RNA and therefore becomes sterically destabilized. T he fact that the length of RNA at which this occurs is close to the length at which the transition to a stably elongating complex occurs might have le d to other mechanistic proposals. Here we show instead that elongation fall s off due to the cooperative formation of structure in the nascent RNA, mos t likely an intramolecular G-quartet structure. Replacement of GTP by 7-dea za-GTP completely abolishes this transition and G-ladder synthesis continue s with a constant efficiency of elongation beyond the limit of detection. T he polymerase-DNA complex creates no barrier to the growth of the nascent ( slippage) RNA, rather termination is similar to that which occurs in rho-in dependent termination.