I was wondering about the shapes assumed by mRNA. I have read some sources quoting that it is linear (quora, so not very reliable) and also a source that says a hairpin shape is common (nature, so I would rather go with this one).
I was also wondering what additional factors or features ensure the mRNA has this shape. For instance, the first source says that the mRNA 'is linear so that the ribosomes can bind to it'. But, clearly, all that is required for this is that the ribosome binding site is exposed. In that case, the remainder of the mRNA may either spontaneously unravel as it is being translated, or there may be something slightly more specific taking place catalysed by the ribosome, or there may be an additional enzyme that associates and catalyses the unfolding of the mRNA as it is being translated.
The thing is, I just find it difficult to belive that the mRNA would not fold up on itself, but on the other hand if it did, perhaps it would be too stable and would not be degraded sufficiently easily. We would have accmulation of mRNA in the cell, unless there was a protein that specifically degraded it.
My only other hypothesis, if it truly is the case that the mRNA does not fold up, is that it is down to the DNA in the nucleaus being 'too dense' to permit the mRNA folding in the nucleus, and once it exits via a nuclear pore it is immediately being translated and forming a polyribosome complex. So then it can no longer fold.
I do not think that the DNA content in the nucleus is sufficiently dense for steric effects like this. I have seen electron micrograph images in a book (Molecular Biology of the Cell) of mRNA exiting a nuclear pore. It seems quite coiled up. Unfortunately, I have been unable to find a clear representative image online or the associated paper. But perhaps the mRNA can coil up in the nucleus, but is straightened out as it is pulled throught the nuclear pore. Proteins and factors associated with the nuclear pore may catalyse the breaking of the hydrogen bonds.
Any details on this would be much appreciated.