Oxford Biochemistry interview - mRNA is more complicated than you think

RNA is the bridge between the language of DNA and Protein, the bridge between template and final product. But it is so much more than just a small linear molecule. In your Oxford biochemistry interview, MRNA is likely to come up. So let's explore further! Let's recap the obvious differences that RNA has with DNA:

1) RNA is single-stranded

2) RNA has a 2' OH group in the sugar (ribose instead of deoxyribose).

These changes profoundly change the structure and stability of RNA. RNA does not form a double helix, and the 2' OH group means that RNA is vulnerable to self-hydrolysis of the phosphodiester bond (intramolecular reaction).

This makes mRNA a challenging molecule to work with - the lack of molecular stability means it has to be kept in cold storage for clinical use (see COVID vaccines and personalised cancer vaccines).

mRNA-based vaccines function like mini-factories, and the objective of any factory? Maximise output from a given amount of input. In this case, turn MRNA into protein.

For the MRNA to be efficiently translated, the AUG start codon must be exposed and the chain should remain in a linear format. Then the TRNAs must bind efficiently to the MRNA to establish the translation process. So how can we make translation more efficient? One way is codon optimization. Remember that the codon system is degenerate - multiple codons code for the same amino acid. For a given amino acid, some tRNAs are more common - have higher levels of production - than others. It's the TRNAs that correspond to the MRNA codons from the most expressed genes. So, logically, you can ensure that you always pick the codon with the highest level of corresponding anticodon tRNA - this is codon optimisation.

Different codons for a given amino acid mean that the same protein can be made from MRNA templates with different potential secondary structures. If all the Serines in a polypeptide came from the UC codon family instead of the AG family, that could lead to very different secondary-structure conformations with very different energy profiles.

The goal? To minimise free energy (maximum stability, less secondary structure formation) So optimising for the best MRNA sequence is not easy. Sometimes the MRNA sequence that in theory would maximise codon optimisation is far from the lowest energy - lots of secondary structure formation.

This isn't something you can calculate manually; algorithms are used to determine the optimal trade-off between codon optimization and free energy minimization for a given amino acid sequence.

But honestly, the story doesn't stop there with MRNA. As well as the open reading frame (the codons from the start codon to the stop codon), MRNA has a 5' and 3' prime tail, and these can be modified too, and even the bases themselves, to maximise protein production. This really is beyond the scope of today's article but I'll leave a link for you to explore further.

The key to performing well in your biochemistry interview is showing that you can link the physical and chemical to the biological.

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