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When it comes to gene transcription, random pauses aren’t quite so random, study finds

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"Kristina made these totally cool DNA templates that have the same 240-base pair sequence repeated over and over again eight times in a row," Block said. When molecules of RNAP were attached to the templates, they behaved as predicted, pausing briefly at all of the backtrack and hairpin pause sites, but not actually backtracking or forming hairpins.

"That's great," Block said. "It's telling us that the enzyme is doing just what it should. After all, it's seen the same sequence eight times in a row, so it had better do the same thing eight times in a row. It also paused at several other sites as well, which is interesting. Sometimes it paused longer, sometimes shorter, but the average was remarkably the same--about a second or so. We also discovered that it just didn't stop at any old sequence but at very specific places where there's a signal in the DNA that basically says, 'Pause here.'"

That signal, he added, occurred for specific sequences in the DNA "We found that there is always a G near a specific pause position, and always a T or a C at another nearby position," he said. "So the pause seems to be sequence dependent. It's not always the same duration every time, but it's more likely to pause at one of these sites than at any other sites in between, so it's not just some random phenomenon that happens every once in a while. If I'm running down the road and I trip, that would be a random phenomenon. But if I run down the road and every time I trip there's a pothole, then that's not random."

Some researchers have argued that all pauses might be associated with either hairpin formation or backtracking, but the Cell study contradicts that assumption. "Most ubiquitous pauses have nothing whatsoever to do with backtracking or hairpins," Block said. "We think ubiquitous pauses are the most common and probably most important kind of pause, and the models that some biochemists have been using are just wrong."


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Source:Stanford University


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