Selection of highly efficient small interference RNA (SiRNA) targeting mammalian genes

Abstract

RNAi is the method of\rsilencing the expression of targeted genes.\rRNAi applications include gene function analysis and target validation.\rDesigning highly efficient small interference\rRNA (siRNA) sequence with maximum target specificity for mammalian RNAi\ris one of important topics in recent years. In this work, a statistical\ranalysis of the information for a large number (3734) of siRNA presented in the\rdatabase available on the internet is done.\rThis is to improve the design of efficient siRNA molecules. The (3734)\rsiRNAs are classified according to their efficiency\rto three groups (high efficient, moderate efficient and low efficient).\rThirteen properties (positional and thermodynamics) are identified in the high\refficient group in the primary statistical study. In the final statistical\rstudy, the average weight of each identified\rproperty is calculated. A very good linear correlation was found between\rthe average percentage efficiency and the\rweighted score of siRNA properties. It is found that the most important\rfeature of highly efficient siRNA is the difference in binding energy between\rthe 5’ end and the 3’ end of the anti-sense strand. The (RISC) activation step\ris a critical step in RNAi process where the efficiency of this process depends\ron the instability of the 5’ end of the anti-sense strand.