Since mRNA is single-stranded, and (mostly) floats freely within the cytosol, what stops it from folding onto itself (like DNA) and preventing transcription?

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    $\begingroup$ The premise of this question, that mRNA "(mostly) floats freely", is false. I don't have specific references (hence a comment, not an answer) but recent research on RNA interactions shows that mRNA is in fact rarely unbound. Under physiological conditions it's almost universally in a complex with proteins or (other) RNAs. $\endgroup$ Oct 24, 2016 at 14:54
  • $\begingroup$ Yes @KonradRudolph is right. Approximately 60% of a eukaryotic mRNA is expected to be bound by protein biology.stackexchange.com/a/21898/3340. $\endgroup$
    Oct 24, 2016 at 18:02
  • $\begingroup$ @Konrad Rudolph Indeed, as mRNA is always bound to RBPs (RNA binding proteins in vivo), many scientists consider that saying messenger RNP (ribonucleotide particle) is more precise. Isolating protein-free RNA in vitro is actually very hard. $\endgroup$
    – user38945
    Nov 27, 2018 at 16:19

2 Answers 2


It does fold on to itself. There are secondary structures in RNA and some of these secondary structures also have regulatory functions (for example, riboswitches). Some of these structures can also inhibit translation (by different mechanisms such as the masking of the ribosome binding site or analogous eukaryotic sequences, or stalling of ribosome etc). Other non-coding RNAs like tRNAs and rRNAs fold into specific structures that are essential for their function.

Many assays have been developed to study RNA secondary structure in vivo. SHAPE and DMS-seq are some examples.

The translation initiation factor eIF4A has a helicase activity that helps in resolving some secondary structures and facilitate translation (despite this, some structures can impede translation).

Also check out ribosome profiling experiments.


Due respects to everything given here so far (protein associations etc) in reply here as being accurate and part of your answer. There is however the fundamental distinction between RNA and DNA yet to examine: that whole "deoxy-" matter right there in the 'D' of DNA. That's the main key to why DNA more readily attains a double helix than does RNA.

There are at least two known physico-chemical reasons starting from the presence or absence of that 2' hydroxyl for this: (1) DNA can more readily inhabit either an A- or B- form, (whereas RNA is more limited to the A-form). So DNA has more entropic options as a helix former (2) RNA's 2'-hydroxyl can become deprotonated and thus hydrolyzed more easily. So less stability in the long run, not as good an information storage form, less likely to form complementary structures. Not unlikely, just less likely. Here's a good reference about this.


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