Dual-Target RNA Designer: A Hybrid saRNA/siRNA Discovery Engine
Dual-Target RNA Designer: A Hybrid saRNA/siRNA Discovery Engine
The Dual-Target RNA Designer is an advanced computational biology tool engineered to discover hybrid RNA candidates capable of modulating two distinct genetic targets simultaneously. It identifies sequences that can act as a Small Activating RNA (saRNA) for one gene while functioning as a Small Interfering RNA (siRNA) for another, or target two separate mRNAs for silencing.
While traditional RNA designs focus on a single target, this platform calculates the mathematical intersection of two different nucleotide sequences. This approach is essential for developing multi-targeted therapeutics in complex diseases such as oncology.
Dynamic Sliding Window Analysis: The JavaScript-based engine performs a simultaneous n-mer analysis across both target sequences to identify potential common candidates within seconds.
Thermodynamic Scoring (Nearest-Neighbor Model): Binding affinity (Δ G) is calculated using the Nearest-Neighbor thermodynamic model. Stable sequences with Δ G < -25 kcal/mol are prioritized by the algorithm.
Stringent Molecular Filters:
GC Content Control: Filters candidates within a 35%-65% range to ensure optimal compatibility with the AGO2 protein.
Homopolymer Elimination: Automatically excludes GGGG sequences to avoid G-quadruplex formation and toxicity risks. It also removes AAAAA/CCCCC motifs to prevent slippage.
3' End Asymmetry: Enforces A/T richness at the 3' end to facilitate the preferential loading of the guide strand into the RISC complex.
Automated Sense/Antisense Generation: The tool automatically generates the 5' to 3' passenger and guide strand designs ready for laboratory synthesis.
Molecular Duplex Visualizer: Provides a structural preview by visualizing the alignment and base-pairing between the RNA strands.
Industrial-Grade Data Export: Candidates can be exported in FASTA format for synthesis providers, CSV for data analysis, and professional PDF reports for academic or R&D presentations.