TROD

TROD designs DNA oligonucleotides for synthesizing short interfering RNAs (siRNAs) by in vitro transcription with T7 RNA polymerase to enable gene silencing via RNA interference (RNAi).

Key Features:

• cDNA input: Accepts cDNA sequences as input for target identification.
• Target site scanning and constraints: Scans the cDNA to identify suitable target sites applying constraints required by T7 RNA polymerase transcription and established criteria for effective siRNA-mediated RNAi.
• Oligonucleotide generation: Generates ordered DNA oligonucleotide sequences optimized for production of siRNAs via in vitro transcription with T7 RNA polymerase.
• Prioritization and specificity checks: Outputs a prioritized list of candidate oligonucleotides and provides links for BLAST searches against genomic databases to assess specificity and minimize off-target effects.

Scientific Applications:

• Gene silencing in mammalian cells: Enables design of siRNAs to silence exogenous and endogenous genes for functional genomics and reverse genetics studies.
• In vitro siRNA production: Supports production of large quantities of siRNAs via T7 RNA polymerase in vitro transcription.
• Interferon-response avoidance: Facilitates use of siRNAs instead of long double-stranded RNA to reduce activation of the interferon response in mammalian systems.

Methodology:

Accepts cDNA sequences, scans for target sites using T7 transcription and siRNA efficacy constraints, generates prioritized lists of DNA oligonucleotides optimized for T7 in vitro transcription, and provides BLAST links for specificity checks.