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, 6, 20031

siRNAmod: A Database of Experimentally Validated Chemically Modified siRNAs

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siRNAmod: A Database of Experimentally Validated Chemically Modified siRNAs

Showkat Ahmad Dar et al. Sci Rep.

Abstract

Small interfering RNA (siRNA) technology has vast potential for functional genomics and development of therapeutics. However, it faces many obstacles predominantly instability of siRNAs due to nuclease digestion and subsequently biologically short half-life. Chemical modifications in siRNAs provide means to overcome these shortcomings and improve their stability and potency. Despite enormous utility bioinformatics resource of these chemically modified siRNAs (cm-siRNAs) is lacking. Therefore, we have developed siRNAmod, a specialized databank for chemically modified siRNAs. Currently, our repository contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. It is developed and hosted using Linux Apache MySQL PHP (LAMP) software bundle. Standard user-friendly browse, search facility and analysis tools are also integrated. It would assist in understanding the effect of chemical modifications and further development of stable and efficacious siRNAs for research as well as therapeutics. siRNAmod is freely available at: http://crdd.osdd.net/servers/sirnamod.

Figures

Figure 1
Figure 1. Cartoon representation of RNAi mechanism, siRNA molecular structure and its entry in RNAi pathway.
Figure 2
Figure 2
Chemical modification statistics pie charts (a) Overall siRNA modifications, (b) nucleotide component based (sugar, base phosphate), (c) Antisense strand modification distribution and (d) Sense strand modification distribution.
Figure 3
Figure 3. Reverse complement based chemical modification of siRNA position wise on sense and antisense siRNA sequences.
Figure 4
Figure 4
Display of search output with cm-siRNA details (a) Result output of search or browse (b) Details page of individual entry (c) Structure and other chemical information of modification.
Figure 5
Figure 5. Diagrammatic representation of siRNAmod architecture.

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