siRNA Selection Server

siRNA Selection Server selects optimal 21-nucleotide (nt) short interfering RNAs (siRNAs) for targeted gene silencing by evaluating sequence uniqueness, thermodynamic stability of the double-stranded RNA duplex, GC content, and single nucleotide polymorphisms (SNPs).

Key Features:

• 21-nt Candidate Identification: Automates identification of optimal 21-nucleotide oligonucleotide siRNA candidates for gene targeting.
• Uniqueness Assessment: Evaluates the uniqueness of each candidate siRNA sequence within the genome to minimize off-target effects.
• Thermodynamic Stability Analysis: Analyzes thermodynamic stability of the double-stranded RNA duplex formed by the siRNA.
• GC Content Evaluation: Calculates GC content of candidate 21-nt siRNAs to inform stability and binding considerations.
• SNP Identification: Detects single nucleotide polymorphisms (SNPs) within candidate sequences that may affect efficacy or specificity.
• Published Design Rules: Applies published siRNA design rules to prioritize promising 21-mer candidates.

Scientific Applications:

• Gene knockdown experiments: Selection of siRNAs to reduce or eliminate target gene expression in cell-culture experiments.
• Functional genomics: Generation of siRNAs for interrogating gene function via targeted silencing.
• Therapeutic development: Support for selecting candidate siRNAs for RNAi-based therapeutic development where specificity and efficacy are required.

Methodology:

Automates identification of 21-nt candidate oligonucleotides; applies published siRNA design rules; evaluates sequence uniqueness within the genome; analyzes thermodynamic stability of the siRNA double-stranded RNA duplex; calculates GC content; and identifies SNPs within candidate sequences.