When during synthesis does the tail gets cut off?

Jee told us that the tail on lab puzzles gets cut off during synthesis. But now it is relevant for me to know when during synthesis it gets cut off, in the beginning, middle or end of the process?

And what causes it to be cut of at that exact spot?

Actually, the tail never gets cut off – the entire RNA sequence is synthesized. We aren’t able to collect chemical mapping data for the tail however, because our experimental procedure involves binding a piece of DNA to this end segment and then extending it backward with reverse transcription.

The data we get back are for the chemical modification rate of any nucleotide upstream of this ‘primer binding site’. However, to reiterate, the whole RNA is synthesized, and the data reflect the shape of the entire sequence, along with its tail.

Also, I’m looking forward to seeing the latest on the melting analysis…

Hi Rhiju!

Thanks for the answer. This actually makes great sense. I have claimed that the neckarea is energeticly pressured. Brourd have found proof that the neck is pressured from the multiloop end of the neck.

Therefore I was interested in if neck was under energetic pressure from the tail/hook end of the neck too. And when the tail stays on during synthesis, I think it is. I think the tail acts sort of like a big loop.

It makes sense if there is pressure from both ends of the neck, as the same repetitative pattern in the neck shows up in the whole of the neck area, not just in the multiloop end of the neck. (Pattern gets especially visible if the neck is longer (at least 5 nt’s long or longer)

More will come in a post on the topic soon.