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By Martin Depken Eric A. Galburt


techniques. Examples of the first type of pauses include can be described as a one-dimensional random walk alonga state that is stabilized by a RNA hairpin forming in the nascent transcript (3,4), and the ubiquitous pause (5) (both with lifetimes <25 s). The ubiquitous pause is thought to correspond to an internal structural rearrangement of the enzyme, but has not been characterized at the biochemical level (6). The second type of pause is referred to as a back-track, manifesting itself through a displacement of the RNAP molecule in the upstream direction opposite to normal tran-scriptional elongation (7–10). Pauses from both classes may be preceded by yet another pause state, the elemental the DNA strand (15–18). It has previously been suggested that backtracking may be able to account for both short- and long-time pauses, since a random-walk mechanism can give rise to a nonexponential distribution of pause durations (15,19). While this is an attractive explanation for the experimentally measured broad distribution of return times (5,15,19), it is not clear that this simple mechanism alone will generate the two distinct pop-ulations of pauses that are observed. Here we show that a random-walk pause scheme will naturally do this, and is able to account for characteristics of the short-time ubiqui-tous and long-time backtracked pauses. Specifically, we calculate the force dependence of such pauses and their respective average trajectories, and compare these to pub-lished experimental data. This comparison enables us t

Year: 2008
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