Identification of highly significant sequence patterns in siRNAs for the optimal design of siRNA

siRNAs for gene silencing studies have a broad range of applications. Studies have addressed the design of siRNAs based on the target sequence patterns, such as the sequence AA around the ends of the siRNA or the avoidance of GGG in siRNA sequences. However, information from just these two patterns is not sufficient for effectively designing siRNA. Nine sequence patterns were identified as highly significantly correlated motifs in studies on oligonucleotides antisense activities. The correlation between the sequence patterns of the siRNA and the gene silencing ratio (GSR) by siRNA has not been described. Understanding this relationship may guide one to a systematic design of the most effective siRNAs. We designed a computer program to calculate the sequence patterns from our siRNA silencing database. Four statistical methods were used to identify the frequency and the distribution of the highly significant sequence patterns from the 1344 combinations for the three, four, and five nucleotide sequences. For the first time, 52 sequence patterns were identified as the highly significant patterns by ANOVA and Pearson correlation analyses with the GSR. These 52 patterns were further clustered into 18 groups. Information from this study may help in the optimized design of siRNA.