Note: [] Partially supported by the DFG within the national program SPP
1087 "Selenoprotein - Biochemische Grundlagen und klinische Bedeutung".
Note: [] Supported by DFG Grant No. Jo 291/2-1.
Abstract: Selenocysteine is the 21th amino acid, which occurs in all kingdoms
of life. Selenocysteine is en-coded by the STOP-codon UGA. For its insertion,
it requires a specific mRNA sequence downstream the UGA-codon that forms a
hairpin like structure (called Sec insertion sequence (SECIS). We consider the
computational problem of generating new amino acid sequences containing
selenocysteine. This requires to find an mRNA se-quence that is similar to the
SECIS-consensus, is able to form the secondary structure required for
selenocysteine insertion, and whose translation is maximally similar to the
original amino acid sequence. We show that the problem can be solved in linear
time when considering the hairpin-like SECIS-structure (and, more generally,
when consider-ing a structure that does not contain pseudoknots).
Keywords: selenocysteine, SECIS, protein engineering
