Open AccessAssessment of siRNA as a therapeutic molecule in Transient Receptor Potential Channel 5 gene silencing: a computational approach
Author(s) -
Bhooma Vijayaraghavan,
Giri Padmanabhan,
Kumaresan Ramanathan
Publication year - 2018
Publication title -
biomedical research and therapy
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.135
H-Index - 1
ISSN - 2198-4093
DOI - 10.15419/bmrat.v5i1.405
Subject(s) - gene silencing , rna interference , small interfering rna , trpc5 , chemistry , microbiology and biotechnology , computational biology , rna , gene , biology , receptor , biochemistry , trpc1 , transient receptor potential channel
Background: Ion channels play a crucial role in Glomerular filter damage that contributes to albuminuria. Transient receptor potential channel 5 (TRPC5) gene mediating such damage, demand for its target specific inhibition by RNA interference mechanism. Designing and selecting potential siRNA for TRPC5 gene silencing by computational analysis.
Materials & Methods: The mRNA sequence was retrieved from NCBI (National Center for Biotechnology Information). siRNA sequences were designed specifically from target genes using InvivoGen siRNA wizard software. Thermodynamic RNA-RNA interactions were used to evaluate the gene silencing efficiency by minimum free energy of hybridization; the hybridization structures were also obtained using BIBISERV2-RNAHybrid.
Results: The minimum free energy of hybridization of the three designed siRNAs (siRNA1, siRNA2 and siRNA3) were as follows: -28.2 kcal/mol, -24.1 kcal/mol, and-25.6 kcal/mol. Their corresponding GC content were 47.62%, 52.38% and 47.62%, respectively. Thus, siRNA1 had the least minimum free energy of hybridization (i.e. -28.2 kcal/mol) with low GC content (47.62%), and high linearity with minimal h-b index and loop structure.
Conclusion: RNAi therapy can provide a new platform for efficient and targeted therapeutics. Further in vivo investigations are necessary to further validate their efficacy.