In-silico Approaches for RNAi Post-Transcriptional Gene Regulation: Optimizing siRNA Design and Selection

Abstract

RNA interference (RNAi) is a naturally occurring endogenous biological posttranscriptional cellular mechanism that regulates against foreign genetic elements such as viruses and inserted gene transcripts as well as in-house gene expression regulation. Small interfering RNA (siRNA) molecules utilize this mechanism to promote homology dependent messenger RNA (mRNA) degradation. The utilization of siRNA as a molecular target to silence gene expression has been used extensively as a research tool in functional genomics. The unprecedented advantage of siRNA molecules, which is mainly related to the ability of effective and specific inhibition of disease causing genes, elicited great expectations in therapeutic applications and drug discovery. siRNAs’ potential as a drugs was investigated in viral and cancer models, and showed successful results with diseases such as HIV, HCV and several types of cancer; as most of these diseases have no cure. One advantage of siRNA-based drugs is their feasibility in clinical trials following approval of phase 1. Moreover, they do not rely on an intact immune system which give the advantage over other long double stranded RNA (dsRNA). However, several factors challenge the design of selective siRNA molecules with highly guaranteed silencing efficiency. Therefore, careful selection of siRNAs complying with all necessary properties is crucial for efficient functional performance. This Chapter discusses RNA interference using small interfering RNS (siRNA) starting with the biological nature of mRNA and siRNA. Then it tackles factors contributing to siRNAmRNA silencing from both biological and bioinformatics aspects that should affect siRNA effectiveness. Then, it represents step wise workflow for rational siRNA design considering state of the art tools and algorithms. By the end of this chapter, various tools are presented for siRNA evaluation phases that are used to predict siRNA efficiency and efficacy, with a practical example applying the proposed methodology.