On the move

Abstract

Single-molecule experiments have shed new light on the mechanisms responsible for the movement of RNA polymerase along DNA during transcription.

Keywords: Brownian ratchet; Optical tweezers; RNA polymerase II; S. cerevisiae; backtracking; transcription elongation; translocation.

Figure 1.. Transcription and backtracking.

Active transcription (top left to right) involves an enzyme called RNA polymerase (yellow) moving forward along a DNA template (red) and adding nucleotides to one end of an RNA transcript (green). Alternatively, the RNA polymerase may enter the backtracking pathway (top left to bottom) which pauses the synthesis of RNA. The RNA polymerase is part of a larger structure called the transcription elongation complex (TEC) that comprises RNA polymerase, DNA and the nascent RNA transcript. The main reaction pathway for the addition of nucleotides has three steps, and it starts (top left) with the TEC in a ‘pre-translocated state’ and with n nucleotides in the RNA transcript. The first step involves the RNA polymerase moving to ‘post-translocated state’ (second from left). The second step involves a molecule of nucleotide triphosphate (NTP) binding to the active site of the RNA polymerase. The third step is a chemical reaction that results in the nucleotide (green dot) being added to the RNA transcript (to give n+1 nucleotides) and the TEC returning to a pre-translocated state; the energy needed to drive this reaction come from the nucleotide condensation reaction, with pyrophosphate (PPi) being released as a by-product of this process. The widths of the grey arrows are proportional to the rates of the various transitions reported by in Dangkulwanich et al.; it can be seen that the translocation steps are not in equilibrium, whereas the NTP binding steps are in equilibrium.