Does a mRNA molecule bond to itself? I heard that only tRNAs have hydrogen bonds that let them have second structures, but after searching the web i found multiple answers. If yes, does anybody have a credible reference for that?(books, articles etc.)

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    – David
    Commented Nov 18, 2018 at 10:43

1 Answer 1


It is very common!

Let's have a look at a few examples.

  1. In bacteria, a lot of the genetic expression is regulated at the mRNA level. Certain mRNAs can form complex secondary structure that prevent or allow translation, and can switch from one structure to another based on the presence or absence of a signal molecule. These structures are called riboswitches; a very well-described example is the riboswitch regulating the expression of genes responsible for the biosynthesis of tryptophan. For more details see this short article or this one.
  2. Some mRNAs include internal ribosome entry sites (IRES), usually just upstream of coding sequences in mRNAs that code for several distinct proteins (polycistronic RNAs). IRES are highly structured RNA structures recognized by ribosomes that allow translation to start at a point in the middle of the mRNA. They are very widespread, especially in viral genomes. You can find a detailed explanation in the case of viral genes here:
  3. In eukaryotes, mRNA molecules undergo a maturation process called RNA splicing that results in the excision of unnecessary internal sequences. During splicing, the mRNA forms a loop and a covalent bond is created at the future junction point; this bond is very transient but absolutely necessary for mRNA maturation and correct gene expression. See here for more explanations.
  4. What about engineered RNA molecules? Self-hybridization of mRNAs is very useful in biological engineering. People reprogram riboswitches and IRES, but also use very useful tools based on mRNA self-binding. For example: based on a similar principle as the riboswitches, the transcription starting site can be masked by articificially introducing a (fairly simple) secondary structure called toehold switch that hides the ribosome binding site; however when a competing RNA sequence (which nature is specified by the sequence of the toehold) is present it opens and binds a part of the toehold, thereby making the ribosome binding site available for gene expression. This website shows an explanation and a real-life application of toehold switches for diagnostics.

These are only a few examples of mRNA self-binding processes; all of these have been extensively studied and are well described in many articles and books. There are many others types of self-hybridization in mRNA, and in pretty much all other types of RNAs too!


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