Rational optimization of siRNA to ensure strand bias in the interaction with the RNA-induced silencing complex

Expanding the binding space of argonaute-2: incorporation of either E or Z isomers of 6'-vinylphosphonate at the 5' end of the antisense strand improves RNAi activity

A phosphate or a phosphate mimic at the 5' terminus of the antisense strand of a small interfering RNA (siRNA) is required for efficient loading into the RISC complex through the MID domain binding pocket of Ago2. Introduction of 5'-E-vinylphosphonate improves this binding and siRNA potency, but the Z isomer does not. Here, we demonstrate that both the E and Z isomers of 6'-vinylphosphonate at the 5' ends of antisense strands of siRNAs have equivalent potencies.

Protocol for Controlling the Strand Selectivity of siRNA Using Acyclic Artificial Nucleic Acids

Small interfering RNA (siRNA) has emerged as a promising therapeutic candidate against previously intractable diseases. An effective siRNA must have high on-target activity while off-target effects are minimized. This balance can be achieved by enhancing the selectivity of the antisense strand through sequence optimization and appropriate chemical modifications. Acyclic artificial nucleic acids such as serinol nucleic acids (SNA) have demonstrated on-target activity while suppressing off-target effects. This article provides guidelines for designing SNA-modified siRNA and outlines a method for the experimental evaluation of the on-target and off-target activities of siRNAs, ensuring accurate functional validation in cell systems. These protocols benefit researchers developing siRNA-based therapeutics to optimize siRNA selectivity and efficacy while minimizing off-target effects through innovative design strategies. © 2025 Wiley Periodicals LLC. Basic Protocol 1: Design of SNA-modified siRNA Basic Protocol 2: Design and preparation of vector plasmids using inverse PCR Alternate Protocol: Design and preparation of vector plasmid using restriction enzymes and ligase Basic Protocol 3: Evaluation of the on- and off-target effects of siRNAs using the dual-luciferase assay Support Protocol 1: Agarose gel electrophoresis and protocol for purifying DNA from gels Support Protocol 2: Transformation and amplification of plasmids.

Improved In Vivo Metabolic Stability and Silencing Efficacy of siRNAs with Phosphorothioate Linkage-Free, GalNAc-Conjugated Sense Strands Containing Morpholino-LNA Modifications

To ensure specificity, loading of the sense strand of small interfering RNAs (siRNAs) into RISC must be inhibited. We show here that siRNAs with 5'- and 6'-morpholino LNA residues or 6'-OH-LNA at the 5' terminus of a fully phosphodiester sense strand resulted in metabolically stable siRNAs with a potency and a duration of action in mice that were greater than those of an siRNA in which the 5' terminus of the sense strand has two terminal phosphorothioate linkages and regular LNA.

Advances in structural-guided modifications of siRNA

To date, the US Food and Drug Administration (FDA) has approved six small interfering RNA (siRNA) drugs: patisiran, givosiran, lumasiran, inclisiran, vutrisiran, and nedosiran, serving as compelling evidence of the promising potential of RNA interference (RNAi) therapeutics. The successful implementation of siRNA therapeutics is improved through a combination of various chemical modifications and diverse delivery approaches. The utilization of chemically modified siRNA at specific sites on either the sense strand (SS) or antisense strand (AS) has the potential to enhance resistance to ribozyme degradation, improve stability and specificity, and prolong the efficacy of drugs. Herein, we provide comprehensive analyses concerning the correlation between chemical modifications and structure-guided siRNA design. Various modifications, such as 2'-modifications, 2',4'-dual modifications, non-canonical sugar modifications, and phosphonate mimics, are crucial for the activity of siRNA. We also emphasize the essential strategies for enhancing overhang stability, improving RISC loading efficacy and strand selection, reducing off-target effects, and discussing the future of targeted delivery.

Structure and Stability of Ago2 MID-Nucleotide Complexes: All-in-One (Drop) His6-SUMO Tag Removal, Nucleotide Binding, and Crystal Growth

The middle (MID) domain of eukaryotic Argonaute (Ago) proteins and archaeal and bacterial homologues mediates the interaction with the 5'-terminal nucleotide of miRNA and siRNA guide strands. The MID domain of human Ago2 (hAgo2) is comprised of 139 amino acids with a molecular weight of 15.56 kDa. MID adopts a Rossman-like beta1-alpha1-beta2-alpha2-beta3-alpha3-beta4-alpha4 fold with a nucleotide specificity loop between beta3 and alpha3. Multiple crystal structures of nucleotides bound to hAgo2 MID have been reported, whereby complexes were obtained by soaking ligands into crystals of MID domain alone. This protocol describes a simplified one-step approach to grow well-diffracting crystals of hAgo2 MID-nucleotide complexes by mixing purified His6-SUMO-MID fusion protein, Ulp1 protease, and excess nucleotide in the presence of buffer and precipitant. The crystal structures of MID complexes with UMP, UTP and 2'-3' linked α-L-threofuranosyl thymidine-3'-triphosphate (tTTP) are presented. This article also describes fluorescence-based assays to measure dissociation constants (Kd) of MID-nucleotide interactions for nucleoside 5'-monophosphates and nucleoside 3',5'-bisphosphates. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Crystallization of Ago2 MID-nucleotide complexes Basic Protocol 2: Measurement of dissociation constant Kd between Ago2 MID and nucleotides.

RNAi-based drug design: considerations and future directions

More than 25 years after its discovery, the post-transcriptional gene regulation mechanism termed RNAi is now transforming pharmaceutical development, proved by the recent FDA approval of multiple small interfering RNA (siRNA) drugs that target the liver. Synthetic siRNAs that trigger RNAi have the potential to specifically silence virtually any therapeutic target with unprecedented potency and durability. Bringing this innovative class of medicines to patients, however, has been riddled with substantial challenges, with delivery issues at the forefront. Several classes of siRNA drug are under clinical evaluation, but their utility in treating extrahepatic diseases remains limited, demanding continued innovation. In this Review, we discuss principal considerations and future directions in the design of therapeutic siRNAs, with a particular emphasis on chemistry, the application of informatics, delivery strategies and the importance of careful target selection, which together influence therapeutic success.