Designing Effective small interfering RNA for Post-Transcriptional Silencing of Human GREM1: A Comprehensive Bioinformatics Approach

Asiedu Ebenezer

RNAi-based therapy mediated by siRNA can offer a more specific inhibition of tumor growth than traditional chemotherapy [36] and has more potential than other methods of gene therapy [37] . Effective design of siRNA candidates is crucial, as non-specific siRNAs can produce unwanted effects. Several research groups reported sequence-based features of effective siRNAs and developed guidelines for siRNA design. In this study, guidelines proposed by three different research groups were used to select the best siRNA from a number of candidates designed using reliable computational algorithms. In Table 2 , the highest scoring siRNA candidates are shown. These siRNA candidates achieved more than 75% based on the scoring criteria, hence, satisfy the sequence requirements for effective siRNA. Small interfering RNA molecules that satisfy the Ui-Tei guidelines were able to cause a significant reduction in firefly luciferase activity and also in chick embryo [22] . Meanwhile, siRNA candidates that obeyed the nucleotide composition demands of the Amarzguioui guidelines were described as functional [24] . Nucleotide sequence preference improve siRNA silencing efficiency as bases at particular positions define target recognition and cleavage [23] . For example, 'A' but not 'G' or 'C' is preferred at the 19 th position of the sense strand (Reynolds rule) in order to facilitate selection of siRNA entry into RISC [38] . Formation of stable intramoleular hairpin secondary structure may reduce availability of siRNA strands to mediate gene silencing. The secondary structures for all selected siRNA candidates were predicted with Sfold. The Srna algorithm of Sfold generate the secondary structure of the RNA with the minimum free energy (Table 2 ).