Incorporating miRNA target sites in protein-coding RNA

MicroRNAs are small regulatory RNAs that play an important role in diverse biological processes, by post-transcriptionally regulating the expression of messenger RNAs. Recent advances in genome synthesis technology allow for manipulation of existing genes and the creation of novel genomic sequences to specification, with a tremendous number of applications. Incorporation of miRNA sites in synthetic mRNA sequences allows for enhanced expression control, enables tissue specificity and facilitates dynamic regulatory network interactions. We designed a dynamic programming algorithm to align an miRNA target site with all possible encodings of a protein, allowing for synonymous and/or missense mutations. Our algorithm shares the same asymptotic time and space complexity with string alignment, performing efficiently in practice and identifying potential target miRNA sites when sufficient tolerable amino acid substitutions are available.