A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects.

Small interfering RNAs (siRNAs) are now established as the preferred tool to inhibit gene function in mammalian cells yet trigger unintended gene silencing due to their inherent miRNA-like behavior. Such off-target effects are primarily mediated by the sequence-specific interaction between the siRNA seed regions (position 2-8 of either siRNA strand counting from the 5'-end) and complementary sequences in the 3'UTR of (off-) targets. It was previously shown that chemical modification of siRNAs can reduce off-targeting but only very few modifications have been tested leaving more to be identified. Here we developed a luciferase reporter-based assay suitable to monitor siRNA off-targeting in a high throughput manner using stable cell lines. We investigated the impact of chemically modifying single nucleotide positions within the siRNA seed on siRNA function and off-targeting using 10 different types of chemical modifications, three different target sequences and three siRNA concentrations. We found several differently modified siRNAs to exercise reduced off-targeting yet incorporation of the strongly destabilizing unlocked nucleic acid (UNA) modification into position 7 of the siRNA most potently reduced off-targeting for all tested sequences. Notably, such position-specific destabilization of siRNA-target interactions did not significantly reduce siRNA potency and is therefore well suited for future siRNA designs especially for applications in vivo where siRNA concentrations, expectedly, will be low.

A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity.

The use of chemically synthesized short interfering RNAs (siRNAs) is currently the method of choice to manipulate gene expression in mammalian cell culture, yet improvements of siRNA design is expectably required for successful application in vivo. Several studies have aimed at improving siRNA performance through the introduction of chemical modifications but a direct comparison of these results is difficult. We have directly compared the effect of 21 types of chemical modifications on siRNA activity and toxicity in a total of 2160 siRNA duplexes. We demonstrate that siRNA activity is primarily enhanced by favouring the incorporation of the intended antisense strand during RNA-induced silencing complex (RISC) loading by modulation of siRNA thermodynamic asymmetry and engineering of siRNA 3'-overhangs. Collectively, our results provide unique insights into the tolerance for chemical modifications and provide a simple guide to successful chemical modification of siRNAs with improved activity, stability and low toxicity.

Preparation of zwitterionic ribonucleoside phosphoramidites for solid-phase siRNA synthesis.

RNA oligomers, carrying 2'-O-modified nucleosides, proved to be extremely useful in different antisense strategies, including RNAi. The 2'-O-alkyl modification, carrying an amino functionality, deserves special attention due to its ability to neutralize the negatively charged phosphate backbone, leading to improved physicochemical and pharmaceutical properties of antisense agents. Here, we report a very short, convenient, and straightforward synthesis of phosphoramidites for all four 2'-aminoethyl-modified natural ribonucleosides, where the aminoethyl group is introduced in a single alkylation step.

Synthesis of 2'-O-modified adenosine building blocks and application for RNA interference.

RNA-interference has been recognized as a powerful tool to control gene function and has been used for gene silencing by knocking down mRNA. Chemically modified RNAs, especially 2'-O-modification, successfully improved their physicochemical and pharmaceutical properties such as stability, nuclease resistance and delivery. Here, we report the synthesis of adenosine building blocks with different 2'-tethered modifications like aminoethyl and guanidinoethyl and show that they are compatible with RNAi function. They enhance the half life of the siRNA in serum suggesting that these modifications can enhance the pharmacokinetic properties and knock down activity of siRNAs in vivo.

Expanding functionality of RNA: synthesis and properties of RNA containing imidazole modified tandem G-U wobble base pairs.

Imidazole modification at C-5 of uridine that is part of tandem G-U wobble base pairs causes slight reduction of thermal stability (DeltaDeltaG(0)(310) < 0.4 kcal mol(-1)) and relatively small change in hydration of short RNA helices.

Synthesis and anti-inflammatory activity of derivatives of 5-[(2-disubstitutedamino-6-methyl-pyrimidin-4-yl)-sulfanylmethyl]-3H-1,3,4-oxadiazole-2-thiones.

Synthesis and results of anti-inflammatory activity in vivo of 5-[(2-disubstitutedamino-6-methyl-pyrimidin-4-yl)-sulfanylmethyl]-3H-1,3,4-oxadiazole-2-thiones and their S-alkyl-, N(3)-acyl- and N(3)-aminomethyl derivatives are described. All the tested compounds possess anti-inflammatory activity comparable to that of acetylsalicylic acid and some derivatives of 5-[(6-methyl-2-piperidin-1-yl-pyrimidin-4-yl)-sulfanylmethyl]-3H-1,3,4-oxadiazole-2-thione were found to be much more active than ibuprofen.

Chemical synthesis of 2'-O-alkylated siRNAs.

Chemical synthesis has been a major endeavor to create active siRNAs. The downregulation of mRNA by 21-mer double-stranded siRNAs can be improved by using modified nucleotides, especially 2'-O-alkylated ones. Besides the commercially available 2 cent-O-methyl ribosides, 2'-alkyl groups bearing positive charges are especially promising candidates. We have shown that in a proper formulation they are superior to unmodified siRNAs. This may be due to enhanced stability and most probably to a better uptake into the cells.