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SECISDesign designs SECIS (Selenocysteine Insertion Sequence) elements and arbitrary RNA structures within coding sequences of mRNA to enable accurate selenocysteine incorporation while preserving encoded protein similarity.

Key Features:

• SECIS and RNA structure design: Designs SECIS elements and other arbitrary RNA secondary structures embedded in coding sequences.
• Coding-sequence-aware optimization: Operates within the mRNA coding sequence while enforcing sequence constraints to conserve the encoded protein.
• RNA structural integrity preservation: Maintains required structural features of SECIS elements necessary for function.
• Sequence constraint enforcement: Enforces specific sequence constraints required for functional incorporation into proteins.
• Protein similarity conservation: Preserves amino acid composition to retain a high degree of similarity to the original protein.
• Selenocysteine incorporation: Produces mRNA designs that permit accurate selenocysteine incorporation during translation.

Scientific Applications:

• Recombinant selenoprotein expression: Enables design of mRNAs for recombinant expression of selenoproteins.
• Expression in non-native hosts: Facilitates expression of selenoproteins in non-native systems such as Escherichia coli.
• mRNA engineering: Supports engineering of mRNAs with custom RNA elements embedded in coding sequences.
• Protein expression requiring mRNA modification: Supports expression of proteins that require precise mRNA modifications for functional incorporation of selenocysteine.

Methodology:

Balances preservation of RNA structural features with enforcement of sequence constraints to maintain amino acid composition when designing SECIS elements and other RNA structures within coding sequences.