Effect of 2'-5'/3'-5' phosphodiester linkage heterogeneity on RNA interference

Enhancing Gene Delivery to Breast Cancer with Highly Efficient siRNA Loading and pH-Responsive Small Extracellular Vesicles

Small extracellular vesicles (sEVs) are promising nanocarriers for drug delivery to treat a wide range of diseases due to their natural origin and innate homing properties. However, suboptimal therapeutic effects, attributed to ineffective targeting, limited lysosomal escape, and insufficient delivery, remain challenges in effectively delivering therapeutic cargo. Despite advances in sEV-based drug delivery systems, conventional approaches need improvement to address low drug-loading efficiency and to develop surface functionalization techniques for precise targeting of cells of interest, all while preserving the membrane integrity of sEVs. We report an enhanced gene delivery system using multifunctional sEVs for highly efficient siRNA loading and delivery. The integration of chiral graphene quantum dots enhanced the loading capacity while preserving the structural integrity of the sEVs. Additionally, lysosomal escape is facilitated by functionalizing sEVs with pH-responsive peptides, fully harnessing the inherent homing effect of sEVs for targeted and precise delivery. These sEVs achieved a 1.74-fold increase in cytosolic cargo delivery compared to unmodified sEVs, resulting in substantial gene silencing of around 73%. Our approach has significant potential to advance sEV-based gene delivery in order to accelerate clinical progress.

2'-O-Alkyl-N 3-Methyluridine Functionalized Passenger Strand Improves RNAi Activity by Modulating the Thermal Stability

Herein, we have demonstrated that the siRNA activity could be enhanced by incorporating the guide strand in the RISC complex through thermodynamic asymmetry caused by m3U-based destabilizing modifications. A nuclease stability study revealed that 2'-OMe-m3U and 2'-OEt-m3U modifications slightly improved the half-lives of siRNA strands in human serum. In the in vitro gene silencing assay, 2'-OMe-m3U modification at the 3'-overhang and cleavage site of the passenger strand in anti-renilla and anti-Bcl-2 siRNA duplexes were well-tolerated and exhibited improved gene silencing activity. However, gene silencing activity was attenuated when these modifications were incorporated at position 3 in the seed region of the antisense strand. The molecular modeling studies using these modifications at the seed region with the MID domain of hAGO2 explained that the 2'-alkoxy group makes steric interactions with the amino acid residues of the hAGO2 protein.

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.

cGAS-STING pathway agonists are promising vaccine adjuvants

Adjuvants are of critical value in vaccine development as they act on enhancing immunogenicity of antigen and inducing long-lasting immunity. However, there are only a few adjuvants that have been approved for clinical use, which highlights the need for exploring and developing new adjuvants to meet the growing demand for vaccination. Recently, emerging evidence demonstrates that the cGAS-STING pathway orchestrates innate and adaptive immunity by generating type I interferon responses. Many cGAS-STING pathway agonists have been developed and tested in preclinical research for the treatment of cancer or infectious diseases with promising results. As adjuvants, cGAS-STING agonists have demonstrated their potential to activate robust defense immunity in various diseases, including COVID-19 infection. This review summarized the current developments in the field of cGAS-STING agonists with a special focus on the latest applications of cGAS-STING agonists as adjuvants in vaccination. Potential challenges were also discussed in the hope of sparking future research interests to further the development of cGAS-STING as vaccine adjuvants.

CRISPR/Cas and Argonaute-Based Biosensors for Pathogen Detection

Over the past few decades, pathogens have posed a threat to human security, and rapid identification of pathogens should be one of the ideal methods to prevent major public health security outbreaks. Therefore, there is an urgent need for highly sensitive and specific approaches to identify and quantify pathogens. Clustered Regularly Interspaced Short Palindromic Repeats CRISPR/Cas systems and Argonaute (Ago) belong to the Microbial Defense Systems (MDS). The guided, programmable, and targeted activation of nucleases by both of them is leading the way to a new generation of pathogens detection. We compare these two nucleases in terms of similarities and differences. In addition, we discuss future challenges and prospects for the development of the CRISPR/Cas systems and Argonaute (Ago) biosensors, especially electrochemical biosensors. This review is expected to afford researchers entering this multidisciplinary field useful guidance and to provide inspiration for the development of more innovative electrochemical biosensors for pathogens detection.

RNA-protein complexes and force field polarizability

Molecular dynamic (MD) simulations offer a way to study biomolecular interactions and their dynamics at the atomistic level. There are only a few studies of RNA-protein complexes in MD simulations, and here we wanted to study how force fields differ when simulating RNA-protein complexes: 1) argonaute 2 with bound guide RNA and a target RNA, 2) CasPhi-2 bound to CRISPR RNA and 3) Retinoic acid-inducible gene I C268F variant in complex with double-stranded RNA. We tested three non-polarizable force fields: Amber protein force fields ff14SB and ff19SB with RNA force field OL3, and the all-atom OPLS4 force field. Due to the highly charged and polar nature of RNA, we also tested the polarizable AMOEBA force field and the ff19SB and OL3 force fields with a polarizable water model O3P. Our results show that the non-polarizable force fields lead to compact and stable complexes. The polarizability in the force field or in the water model allows significantly more movement from the complex, but in some cases, this results in the disintegration of the complex structure, especially if the protein contains longer loop regions. Thus, one should be cautious when running long-scale simulations with polarizability. As a conclusion, all the tested force fields can be used to simulate RNA-protein complexes and the choice of the optimal force field depends on the studied system and research question.

Unlike RNA-TBA (rTBA), iso-rTBA, the 2'-5'-linked RNA-thrombin-binding aptamer, is a functional equivalent of TBA

An antiparallel, functional RNA G-quadruplex of the 2'-5'-linked thrombin-binding aptamer (iso-rTBA) is reported for the first time. It can inhibit clotting and is remarkably stable to nuclease-degradation, besides having high thermal stability. It is thus, a superior candidate to TBA, rTBA or isoTBA, for further development as an anticoagulant.

From bench to bedside: Improving the clinical safety of GalNAc-siRNA conjugates using seed-pairing destabilization

Preclinical mechanistic studies have pointed towards RNA interference-mediated off-target effects as a major driver of hepatotoxicity for GalNAc-siRNA conjugates. Here, we demonstrate that a single glycol nucleic acid or 2'-5'-RNA modification can substantially reduce small interfering RNA (siRNA) seed-mediated binding to off-target transcripts while maintaining on-target activity. In siRNAs with established hepatotoxicity driven by off-target effects, these novel designs with seed-pairing destabilization, termed enhanced stabilization chemistry plus (ESC+), demonstrated a substantially improved therapeutic window in rats. In contrast, siRNAs thermally destabilized to a similar extent by the incorporation of multiple DNA nucleotides in the seed region showed little to no improvement in rat safety suggesting that factors in addition to global thermodynamics play a role in off-target mitigation. We utilized the ESC+ strategy to improve the safety of ALN-HBV, which exhibited dose-dependent, transient and asymptomatic alanine aminotransferase elevations in healthy volunteers. The redesigned ALN-HBV02 (VIR-2218) showed improved specificity with comparable on-target activity and the program was reintroduced into clinical development.

Inhaled siRNA Formulations for Respiratory Diseases: From Basic Research to Clinical Application

The development of siRNA technology has provided new opportunities for gene-specific inhibition and knockdown, as well as new ideas for the treatment of disease. Four siRNA drugs have already been approved for marketing. However, the instability of siRNA in vivo makes systemic delivery ineffective. Inhaled siRNA formulations can deliver drugs directly to the lung, showing great potential for treating respiratory diseases. The clinical applications of inhaled siRNA formulations still face challenges because effective delivery of siRNA to the lung requires overcoming the pulmonary and cellular barriers. This paper reviews the research progress for siRNA inhalation formulations for the treatment of various respiratory diseases and summarizes the chemical structural modifications and the various delivery systems for siRNA. Finally, we conclude the latest clinical application research for inhaled siRNA formulations and discuss the potential difficulty in efficient clinical application.

Nucleoside Analogues with a Seven-Membered Sugar Ring: Synthesis and Structural Compatibility in DNA-RNA Hybrids

Herein we describe results on the pairing properties of synthetic DNA and RNA oligonucleotides that contain nucleotide analogues with a 7-membered sugar ring (oxepane nucleotides). Specifically, we describe the stereoselective synthesis of a set of three oxepane thymine nucleosides (OxT), their conversion to phosphoramidite derivatives, and their use in solid-phase synthesis to yield chimeric OxT-DNA and OxT-RNA strands. The different regioisomeric OxT phosphoramidites allowed for positional variations of the phosphate bridge and assessment of duplex stability when the oxepane nucleotides were incorporated in dsDNA, dsRNA, and DNA-RNA hybrids. Little to no destabilization was observed when two of the three regioisomeric OxT units were incorporated in the DNA strand of DNA-RNA hybrids, a remarkable result considering the dramatically different structure of oxepanes in comparison to 2'-deoxynucleosides. Extensive molecular modeling and dynamics studies further revealed the various structural features responsible for the tolerance of both OxT modifications in DNA-RNA duplexes, such as base-base stacking and sugar-phosphate H-bond interactions. These studies suggest that oxepane nucleotide analogues may find applications in synthetic biology, where synthetic oligonucleotides can be used to create new tools for biotechnology and medicine.

Gene editing with CRISPR-Cas12a guides possessing ribose-modified pseudoknot handles

CRISPR-Cas12a is a leading technology for development of model organisms, therapeutics, and diagnostics. These applications could benefit from chemical modifications that stabilize or tune enzyme properties. Here we chemically modify ribonucleotides of the AsCas12a CRISPR RNA 5' handle, a pseudoknot structure that mediates binding to Cas12a. Gene editing in human cells required retention of several native RNA residues corresponding to predicted 2'-hydroxyl contacts. Replacing these RNA residues with a variety of ribose-modified nucleotides revealed 2'-hydroxyl sensitivity. Modified 5' pseudoknots with as little as six out of nineteen RNA residues, with phosphorothioate linkages at remaining RNA positions, yielded heavily modified pseudoknots with robust cell-based editing. High trans activity was usually preserved with cis activity. We show that the 5' pseudoknot can tolerate near complete modification when design is guided by structural and chemical compatibility. Rules for modification of the 5' pseudoknot should accelerate therapeutic development and be valuable for CRISPR-Cas12a diagnostics.

Site-specific Incorporation of 2',5'-Linked Nucleic Acids Enhances Therapeutic Profile of Antisense Oligonucleotides

Site-specific incorporation of 2'-modifications and neutral linkages in the deoxynucleotide gap region of toxic phosphorothioate (PS) gapmer ASOs can enhance therapeutic index and safety. In this manuscript, we determined the effect of introducing 2',5'-linked RNA in the deoxynucleotide gap region on toxicity and potency of PS ASOs. Our results demonstrate that incorporation of 2',5'-linked RNA in the gap region dramatically improved hepatotoxicity profile of PS-ASOs without compromising potency and provide a novel alternate chemical approach for improving therapeutic index of ASO drugs.

Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry

This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.

Chemical strategies for strand selection in short-interfering RNAs

Therapeutic small interfering RNAs (siRNAs) are double stranded RNAs capable of potent and specific gene silencing through activation of the RNA interference (RNAi) pathway. The potential of siRNA drugs has recently been highlighted by the approval of multiple siRNA therapeutics. These successes relied heavily on chemically modified nucleic acids and their impact on stability, delivery, potency, and off-target effects. Despite remarkable progress, clinical trials still face failure due to off-target effects such as off-target gene dysregulation. Each siRNA strand can downregulate numerous gene targets while also contributing towards saturation of the RNAi machinery, leading to the upregulation of miRNA-repressed genes. Eliminating sense strand uptake effectively reduces off-target gene silencing and helps limit the disruption to endogenous regulatory mechanisms. Therefore, our understanding of strand selection has a direct impact on the success of future siRNA therapeutics. In this review, the approaches used to improve strand uptake are discussed and effective methods are summarized.

Hybrid DNA/RNA nanostructures with 2'-5' linkages

Nucleic acid nanostructures with different chemical compositions have shown utility in biological applications as they provide additional assembly parameters and enhanced stability. The naturally occurring 2'-5' linkage in RNA is thought to be a prebiotic analogue and has potential use in antisense therapeutics. Here, we report the first instance of DNA/RNA motifs containing 2'-5' linkages. We synthesized and incorporated RNA strands with 2'-5' linkages into different DNA motifs with varying number of branch points (a duplex, four arm junction, double crossover motif and tensegrity triangle motif). Using experimental characterization and molecular dynamics simulations, we show that hybrid DNA/RNA nanostructures can accommodate interspersed 2'-5' linkages with relatively minor effect on the formation of these structures. Further, the modified nanostructures showed improved resistance to ribonuclease cleavage, indicating their potential use in the construction of robust drug delivery vehicles with prolonged stability in physiological conditions.