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

Asiedu Ebenezer

. CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.23.917559 doi: bioRxiv preprint Provided the first nucleotide begins the start codon, the target mRNA in this study had 552 nucleotides ( Supplementary Fig. 1) . Target binding site is another parameter that could define siRNA silencing efficacy [16] . Binding sites should occur at 50-100 nucleotides away from the start codon since regulatory proteins bind to those regions [31] . Further comprehensive analysis of the target site was performed with the Sirna algorithm of Sfold server. The module efficiently predicted the target site accessibility of the designed siRNA candidates. The probability of a target site available for siRNA binding was described with probability profiles (Figure 3) . The folding patterns of the target sites were also described with loop specific probability profiles. In Figure 4 Non-specific activities of siRNA in biological systems such as stimulation of immune responses and off-target effects limit efficiency of siRNA-mediated therapy. The occurrence of off-target effect is due to cross matching of siRNA to other mRNA transcripts apart from the target mRNA. A stringent basic local alignment search was performed to identify human genomic and transcript nucleotides that share homology with the designed siRNAs. Sequences that shared more than 75% similarity with the siRNA were considered for further evaluation to . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.23.917559 doi: bioRxiv preprint 9 know whether the homology existed in the seed region. SiRNA-6, siRNA-7, and siRNA-47 all shared 100% similarity with human gremlin-1 transcript ( Supplementary Fig. 3 ) The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.23.917559 doi: bioRxiv preprint