Precise and efficient siRNA design: a key point in competent gene silencing

Abstract

RNA interference-related strategies have become appealing methods in various fields of research. Exact sequence design of these small molecules is an essential step in the silencing procedure. Numerous researchers have tried to define some algorithms in order to increase the chance of short interfering RNA's (siRNA's) success. In recent decades, online designing software has aimed at promoting the quality of siRNA designing based on the most cited algorithms. According to our previous experiments, a combination of different criteria would be helpful. That is, siRNAs suggested by a combination of tools seem to be more efficient. Furthermore, different factors such as distance of target region to transcription start site, nucleotide composition, absence of off-target effects and secondary structures in the target site and siRNA and the presence of asymmetry and energy valley within the siRNA will increase the efficiency of siRNAs. Despite application of different online tools and fulfilling the criteria, there is no guarantee for designing an effective siRNA. However, meticulous designing of siRNAs according to the suggested algorithms and scoring systems and using different siRNAs for targeting the same gene would lead to improved silencing outcome. In this review, we focus on common algorithms and online software, and introduce a new scoring system used in our experiments.

Silencing the roadblocks to effective triple-negative breast cancer treatments by siRNA nanoparticles

“…These effects were first observed in nematode worms in 1998, where expression of par-1 mRNA was temporarily depleted following introduction of double-stranded small interfering RNA (siRNA) (Fakhr, et al 2016; Young, et al 2016). Further studies identified additional molecular players in the RNAi machinery, including Dicer and the RNA-induced silencing complex (RISC) (Kobayashi and Tomari 2016).…”

“…1). If the antisense strand is perfectly complement to the mRNA, the mRNA is cleaved by argonaute 2 (Ago2), the catalytic subunit of the RISC complex (Azlan, et al 2016; Fakhr et al 2016). Limited complementarity to the target mRNA leads to translational repression, a function that is associated with micro RNAs (miRNAs) (Young et al 2016).…”

“…Recent advances in next generation high throughput sequencing, has revealed extraordinary genetic complexity and heterogeneity in cancer models (Hoelder, et al 2012). Because siRNAs are readily synthesized and can be optimized to maximize gene silencing (Fakhr et al 2016), siRNA nanoparticles can be easily adapted to silence virtually any gene in mammalian cells. Various siRNA design software that enable the optimization of siRNA length, specificity, and nucleotide content based on a number of criteria are available online (Fakhr et al 2016).…”

One-cell model for inhibiting Cav3.3 mRNA expression by RNA interference

“…RNA interference (RNAi) technology, which is a new technology that has been widely used to explore gene function, infectious diseases and malignant tumour gene therapy, can specifically remove or inhibit target gene expression [14][15][16]. The first step in its mechanism is that the double-stranded RNA induces highly conserved and homologous mRNA degradation.…”

Double gene siRNA knockdown of mutant p53 and TNF induces apoptosis in triple-negative breast cancer cells

“…The RNAi pathway mediated through artificially synthesized small interfering RNAs (siRNAs) determines potentially different RNAi gene silencing mechanisms and presents higher specificity and efficiency compared to other antisense oligonucleotide strategies 5. siRNA is a putative knockdown tool for investigating various molecular pathways in numerous diseases and biological processes at the posttranscriptional level 6. Since cancer involves multiple alterations within various cell signaling pathways, it becomes quite essential that targeting multiple oncogenes could bring new information and help understand the complex mechanisms of oncogenic pathways;7 it could also be used for developing therapeutic tools.…”