What is it about?
Proteins - that is sequences of amino-acids - are encoded by RNA sequences of nucleotide bases. Every three bases encode for a specific amino-acid. But there are 20 amino-acids and 64 possible base triplets: so the same amino-acid is in general encoded by more than one triplet, and consequently, many RNA sequences encode for the same protein. These sequences, however, are not equivalent in terms of protein yield and other features. We developed a mathematical model to find an optimal one according to known criteria. This model provides a computational method that is much more efficient than literature ones.
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Why is it important?
Increasing protein yield is relevant in Pharma industry. Moreover, some of the feature we incorporate in our model allow to control (e.g. place or perhaps remove) special subsequences - such as the so-called restriction sites - from the designed sequence.
Perspectives
Further developments are likely to implement a fine control of RNA secondary structure, thus affecting such important parameters as RNA stability - which is, for instance, crucial in mRNA vaccination.
Claudio Arbib
Read the Original
This page is a summary of: Codon optimization by 0-1 linear programming, Computers & Operations Research, July 2020, Elsevier,
DOI: 10.1016/j.cor.2020.104932.
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