Computational models with thermodynamic and composition features improve siRNA design

Background: Small interfering RNAs (siRNAs) have become an important tool in cell and molecular biology. Reliable design of siRNA molecules is essential for the needs of large functional genomics projects. Results: To improve the design of efficient siRNA molecules, we performed a comparative, thermodynamic and correlation analysis on a heterogeneous set of 653 siRNAs collected from the literature. We used this training set to select siRNA features and optimize computational models. We identified 18 parameters that correlate significantly with silencing efficiency. Some of these parameters characterize only the siRNA sequence, while others involve the whole mRNA. Most importantly, we derived an siRNA position-dependent consensus, and optimized the free-energy difference of the 5' and 3' terminal dinucleotides of the siRNA antisense strand. The positiondependent consensus is based on correlation and t-test analyses of the training set, and accounts for both significantly pref...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Svetlana A. Shabalina, Alexey N. Spiridonov, Aleksey Y. Ogurtsov
• Keywords: BMCBI 2006, SiRNA, SiRNA Molecules, SiRNA Sequence