Chemical Modification of siRNA

Behlke MA (2008) Chemical modification of siRNAs for in vivo use. Oligonucleotides 18 305-319... 

For more detailed information about chemical modifications of siRNAs, we would like to refer to the following review articles (20, 49) (see Note 4). 

Chemical modifications of siRNAs have been extensively studied. Nevertheless, chemical modifications that enhance siRNA... 

Fig. 10.9 Chemical modification of siRNA may substantially decrease levels of off-target activity. Unmodified and modified siRNAs of identical sequences targeting mitogen-activated protein kinase 1 (MAPKl) were introduced into HeLa cells. Gene expression changes were evaluated by Agilent...

Jackson AL, Burchard J, Leake D, Reynolds A, Schelter J, Guo J, et al. Position-specific chemical modification of siRNAs reduces off-target transcript silencing. RNA 2006 12 1197-1205. 

RNAi technology has obvious therapeutic potential as an antisense agent, and initial therapeutic targets of RNAi include viral infection, neurological diseases and cancer therapy. The synthesis of dsRNA displaying the desired nucleotide sequence is straightforward. However, as in the case of additional nucleic-acid-based therapeutic approaches, major technical hurdles remain to be overcome before RNAi becomes a therapeutic reality. Naked unmodified siRNAs for example display a serum half-life of less than 1 min, due to serum nuclease degradation. Approaches to improve the RNAi pharmacokinetic profile include chemical modification of the nucleotide backbone, to render it nuclease resistant, and the use of viral or non-viral vectors, to achieve safe product delivery to cells. As such, the jury remains out in terms of the development and approval of RNAi-based medicines, in the short to medium term at least. 

RNAi has had an important impact on the development of novel disease models in animals, and it is likely that siRNAs, the trigger molecules for RNA silencing, will become an invaluable tool for the treatment of genetic disorders. The rational design of siRNAs, the introduction of chemical modifications into siRNAs to improve their pharmacokinetic and pharmacodynamic properties for in vivo application with high specificity, and the development of efficient delivery system will foster the therapeutic application of RNAi in AD and other neurodegenerative disorders (413,417). 

Lead Optimization of siRNA Lead identification can be visualized as an upside down pyramid (Fig. 4.2) where an initial set of siRNA are filtered through a set of assays in order to hone in on one or more lead designs. Lead optimization, in contrast, best fits the visnal metaphor of a diamond, whereby each potent lead is diversified throngh chemical modification of the nucleotides (Elbashir et al., 2001a Czaudema et al., 2003) and subseqnently refiltered. This process is very much iterative. In each round the... 

Singh, B., Choi, Y.J., Park, I.K., Akaike, T, Cho, C.S., 2014. Chemical modification of chi-tosan with pH-sensitive molecules and specific ligands for efficient DNA transfection and siRNA silencing. J. Nanosci. Nanotechnol. 14 (1), 564—576. 

A number of modified nucleotides have been tested and described in siRNA design. These are mostly modifications of the 2 OH group of the ribose. By the incorporation of chemically modified nucleotides into siRNAs, the on-target efficiency of the siRNAs can be increased (42 4). On the other hand, different types of siRNA off-target effects can be reduced by the use of chemically modified nucleotides immunostimulatory effects (reviewed in (20)) as well as sequence-dependent miRNA-like off-target effects (26, 44,45) and passenger strand incorporation (46, 47). In addition, chemical modifications can be used to improve the cellular delivery of siRNAs in living animals and are important tools to enhance the serum stability of siRNAs (48). 

Bramsen JB, Pakula MM, Hansen TB et al (2010) A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects. Nucleic Acids Res 38 5761-5773... 

While several reviews collected in this volume describe the basic chemical composition of transfection reagent classes, Salcher and Wagner focus on the modification and functionalization of polymeric gene carriers to improve their transfection efficiencies for DNA or siRNA. Such modifications include the introduction of cell-specific ligands or pH-sensitive lytic residues. 

Puthenveetil S, Whitby L, Ren J, et al. Controlling activation of the RNA-dependent protein kinase by siRNAs using site-specific chemical modification. Nucleic Acids Res. 2006 34 4900-4911. 

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