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**Chapter 11** 

© 2012 Ghosal et al., licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

© 2012 Ghosal et al., licensee InTech. This is a paper distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

**Computational Approaches for** 

Suman Ghosal, Shaoli Das and Jayprokas Chakrabarti

Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/50125

**1. Introduction** 

**Designing Efficient and Specific siRNAs** 

Small RNA mediated RNA interference (RNAi) is a widely adopted mechanism towards immunity in plants and invertebrates. Two types of small RNAs- small interfering RNA (siRNA) and microRNA (miRNA), play key role in RNA interference either through cleaving or through translational repression of the target mRNA by guiding RNA induced silencing complex (RISC) to its target site. siRNA is a small RNA (19-23 nucleotides) which is complementary to part of their target mRNA [1]. siRNAs are very efficient in target gene knockdown that makes synthetic siRNA's perfect choice for use in experiments for silencing genes to examine their function. In addition, siRNA have good potential in drug development for therapeutic purpose [2]. Exogenous synthetic siRNAs are designed to target a part of the coding region in the target mRNA [3]. But, as evident from experiments, all siRNAs are not equally efficient in target gene silencing. The potency of siRNAs is largely dependent upon the selection of the region it targets. A displacement of 5-6 nucleotide position hugely alters the efficiency of siRNA. The reason behind this alteration of efficiency is the alteration in local sequence and structural features of the target region. These variations in sequence and structural features correlate with target accessibility, RISC loading or stimulation of immune response. A lot of study has been done in the field of rational siRNA designing to find appropriate parameters that facilitate designing of effective siRNAs [4]. Several commercial suppliers and non-profit educational institutes contribute to the research for searching appropriate siRNA selection parameters for improving potency of designed siRNAs. Progresses have been made in targeting success rate compared to the early days- from as low as 0-10% targeting success rate, today siRNAs have reached average 50% targeting success rate. Still there are many scopes to improve siRNA designing. For efficient designing, the siRNA selection parameters must be arranged and weighted in such a way that ensures optimal result while selecting the siRNA target site. There are some previously suggested guidelines about parameter weight assignment like rational or

