CoDe

CoDe deoptimizes RNA or DNA coding sequences by altering codon usage bias to reduce protein expression while preserving the original amino acid sequence.

Key Features:

• Codon usage deoptimization: Increases the frequency of underrepresented codons or codon pairs in coding sequences to reduce protein expression while maintaining the encoded amino acid sequence.
• Codon pair analysis: Identifies codon pairs that are underrepresented in a specified organism's genome and targets those pairs for frequency increase.
• Targeted sequence modification: Allows specification of particular regions or selected amino acids within a sequence for localized deoptimization.
• Restriction enzyme site identification: Detects restriction enzyme target sites in both wild-type and codon-deoptimized sequences to inform downstream molecular cloning decisions.

Scientific Applications:

• Gene function analysis: Controlled downregulation or silencing of specific genes to probe gene function and interactions.
• Synthetic biology construct design: Engineering genetic constructs with reduced protein expression for circuit tuning and pathway control.
• Therapeutic construct development: Designing genetic sequences with modulated expression levels for therapeutic applications.
• Cloning strategy support: Using restriction site information from wild-type and deoptimized sequences to plan cloning and molecular assembly.

Methodology:

Computational analysis identifies underrepresented codon pairs in a given organism's genome and systematically increases the frequency of those pairs in the target sequence without altering the encoded protein.