Conditional Deoxyribozyme-Nanoparticle Conjugates for miRNA-Triggered Gene Regulation

Nucleic acid-responsive smart systems for controlled cargo delivery

Stimulus-responsive delivery systems allow controlled, highly regulated, and efficient delivery of various cargos while minimizing side effects. Owing to the unique properties of nucleic acids, including the ability to adopt complex structures by base pairing, their easy synthesis, high specificity, shape memory, and configurability, they have been employed in autonomous molecular motors, logic circuits, reconfigurable nanoplatforms, and catalytic amplifiers. Moreover, the development of nucleic acid (NA)-responsive intelligent delivery vehicles is a rapidly growing field. These vehicles have attracted much attention in recent years due to their programmable, controllable, and reversible properties. In this work, we review several types of NA-responsive controlled delivery vehicles based on locks and keys, including DNA/RNA-responsive, aptamer-responsive, and CRISPR-responsive, and summarize their advantages and limitations.

DNA mechanocapsules for programmable piconewton responsive drug delivery

The mechanical dysregulation of cells is associated with a number of disease states, that spans from fibrosis to tumorigenesis. Hence, it is highly desirable to develop strategies to deliver drugs based on the "mechanical phenotype" of a cell. To achieve this goal, we report the development of DNA mechanocapsules (DMC) comprised of DNA tetrahedrons that are force responsive. Modeling shows the trajectory of force-induced DMC rupture and predicts how applied force spatial position and orientation tunes the force-response threshold. DMCs functionalized with adhesion ligands mechanically denature in vitro as a result of cell receptor forces. DMCs are designed to encapsulate macromolecular cargos such as dextran and oligonucleotide drugs with minimal cargo leakage and high nuclease resistance. Force-induced release and uptake of DMC cargo is validated using flow cytometry. Finally, we demonstrate force-induced mRNA knockdown of HIF-1α in a manner that is dependent on the magnitude of cellular traction forces. These results show that DMCs can be effectively used to target biophysical phenotypes which may find useful applications in immunology and cancer biology.

Nanodiscoidal Nucleic Acids for Gene Regulation

Therapeutic nucleic acids represent a powerful class of drug molecules to control gene expression and protein synthesis. A major challenge in this field is that soluble oligonucleotides have limited serum stability, and the majority of nucleic acids that enter the cells are trapped within endosomes. Delivery efficiency can be improved using lipid scaffolds. One such example is the nanodisc (ND), a self-assembled nanostructure composed of phospholipids and peptides and modeled after high density lipoproteins (HDLs). Herein, we describe the development of the nanodiscoidal nucleic acid (NNA) which is a ND covalently modified with nucleic acids on the top and bottom lipid faces as well as the lateral peptide belt. The 13 nm ND was doped with thiolated phospholipids and thiol-containing peptides and coupled in a one-pot reaction with oligonucleotides to achieve ∼30 DNA/NNA nucleic acid density. NNAs showed superior nuclease resistance and enhanced cellular uptake that was mediated through the scavenger receptor B1. Time-dependent Förster resonance energy transfer (FRET) analysis of internalized NNA confirmed that NNAs display increased stability. NNAs modified with clinically validated antisense oligonucleotides (ASOs) that target hypoxia inducible factor 1-α (HIF-1-α) mRNA showed enhanced activity compared with that of the soluble DNA across multiple cell lines as well as a 3D cancer spheroid model. Lastly, in vivo experiments show that ASO-modified NNAs are primarily localized into livers and kidneys, and NNAs were potent in downregulating HIF-1-α using 5-fold lower doses than previously reported. Collectively, our results highlight the therapeutic potential for NNAs.

The role of Na+ in catalysis by the 8-17 DNAzyme

The 8-17 DNAzyme is the most studied deoxyribozyme in terms of its molecular mechanism; hence it has become a model system to understand the basis behind DNA catalysis. New functional studies and the recent attainment of high-resolution X-ray structures, in addition to theoretical calculations have offered a great opportunity to gain a broader comprehension of its mechanism; however many aspects are unclear yet, especially regarding the precise role of metal ions in catalysis. Recently, molecular dynamics simulations have suggested for the first time a specific and dynamical participation of Na⁺ in the mechanism through the reaction pathway, besides the roles proposed for divalent metal cofactors. Herein, we present experimental evidence of a cooperative role of the monovalent cation Na⁺ in catalysis that is in line with these theoretical suggestions. Our findings show a clear influence of the concentration of Na⁺ on the activity of the 8-17 DNAzyme when Pb²⁺ is used as the cofactor. Interestingly, this effect is not noticed with Mg²⁺, indicating a particular contribution of the monovalent ion to catalysis that would operate preferentially with Pb²⁺. We have also found that Na⁺ affects the pK_a of the general base and the general acid, indicating its influence on general acid-base catalysis, already identified as part of the mechanism of the 8-17 DNAzyme. Finally, our results emphasize the need to consider Na⁺ carefully in the design and analysis of functional studies of catalytic DNAs and its possible specific role in their mechanisms.

Gene Regulation Using Nanodiscs Modified with HIF-1-α Antisense Oligonucleotides

Delivery of nucleic acids can be hindered by multiple factors including nuclease susceptibility, endosome trapping, and clearance. Multiple nanotechnology scaffolds have offered promising solutions, and among these, lipid-based systems are advantageous because of their high biocompatibility and low toxicity. However, many lipid nanoparticle systems still have issues regarding stability, rapid clearance, and cargo leakage. Herein, we demonstrate the use of a synthetic nanodisc (ND) scaffold functionalized with an anti-HIF-1-α antisense oligonucleotide (ASO) to reduce HIF-1-α mRNA transcript levels. We prepared ND conjugates by using a mixture of phosphoglycerolipids with phosphocholine and phosphothioethanol headgroups that self-assemble into a ∼13 × 5 nm discoidal structure upon addition of a 22-amino-acid ApoA1 mimetic peptide. Optimized reaction conditions yield 15 copies of the anti-HIF-1-α ASO DNA covalently conjugated to the thiolated phospholipids using maleimide-thiol chemistry. We show that DNA-ND conjugates are active, nuclease resistant, and rapidly internalized into cells to regulate HIF-1-α mRNA levels without the use of transfection agents. DNA-ND uptake is partially mediated through Scavenger Receptor B1 and the ND conjugates show enhanced knockdown of HIF-1-α compared to that of the soluble ASOs in multiple cell lines. Our results demonstrate that covalently functionalized NDs may offer an improved platform for ASO therapeutics.

Recent Advances on DNAzyme-Based Sensing

DNAzymes are functional nucleic acid with catalytic activity. Owing to the high sensitivity, excellent programmability, and flexible obtainment through in vitro selection, RNA-cleaving DNAzymes have attracted increasing interest in developing DNAzyme-based sensors. In this review, we summarize the recent advances on DNAzyme-based sensing applications. We initially conclude two general strategies to expand the library of DNAzymes, in vitro selection to discover new DNAzymes towards different targets of interest and chemical modifications to endue the existing DNAzymes with new function or properties. We then discuss the recent applications of DNAzyme-based sensors for the detection of a variety of important biomolecules both in vitro and in vivo . Finally, perspectives on the challenges and future directions in the development of DNAzyme-based sensors are provided.

Conditional Antisense Oligonucleotides Triggered by miRNA

Antisense oligonucleotides (ASOs) are single-stranded short nucleic acids that silence the expression of target mRNAs and show increasing therapeutic potential. Since ASOs are internalized by many cell types, both normal and diseased cells, gene silencing in unwanted cells is a significant challenge for their therapeutic use. To address this challenge, we created conditional ASOs that become active only upon detecting transcripts unique to the target cell. As a proof-of-concept, we modified an HIF1α ASO (EZN2968) to generate miRNA-specific conditional ASOs, which can inhibit HIF1α in the presence of a hepatocyte-specific miRNA, miR-122, via a toehold exchange reaction. We characterized a library of nucleic acids, testing how the conformation, thermostability, and chemical composition of the conditional ASO impact the specificity and efficacy in response to miR-122 as a trigger signal. Optimally designed conditional ASOs demonstrated knockdown of HIF1α in cells transfected with exogenous miR-122 and in hepatocytes expressing endogenous miR-122. We confirmed that conditional ASO activity was mediated by toehold exchange between miR-122 and the conditional ASO duplex, and the magnitude of the knockdown depended on the toehold length and miR-122 levels. Using the same concept, we further generated another conditional ASO that can be triggered by miR-21. Our results suggest that conditional ASOs can be custom-designed with any miRNA to control ASO activation in targeted cells while reducing unwanted effects in nontargeted cells.

Hydrated metal ion as a general acid in the catalytic mechanism of the 8-17 DNAzyme

The RNA-cleaving 8-17 DNAzyme, which is a metalloenzyme that depends on divalent metal ions for its function, is the most studied catalytic DNA in terms of its mechanism. By the end of 2017, a report of the crystal structure of the enzyme-substrate complex in the presence of Pb²⁺ probed some of the previous findings and opened new questions, especially around the participation of the metal ion in the catalytic mechanism and the promiscuity exhibited by the enzyme in terms of the metal cofactor required for catalysis. In this article we explore the role of the divalent metal ion in the mechanism of the 8-17 DNAzyme as a general acid, by measuring the influence of pH over the activity of a slower variant of the enzyme in the presence of Pb²⁺. We replaced G14, which has been identified as a general base in the mechanism of the enzyme, by the unnatural analog 2-aminopurine, with a lower pK_a value of the N1 group. With this approach, we obtained a bell-shaped pH-rate profile with experimental pK_a values of 5.4 and 7.0. Comparing these results with previous pH-rate profiles in the presence of Mg²⁺, our findings suggest the stabilization of the 5'-O leaving group by the hydrated metal ion acting as a general acid, in addition to the activation of the 2'-OH nucleophile by the general base G14.

Smart Nucleic Acids as Future Therapeutics

Nucleic acid therapeutics (NATs) hold promise in treating undruggable diseases and are recognized as the third major category of therapeutics in addition to small molecules and antibodies. Despite the milestones that NATs have made in clinical translation over the past decade, one important challenge pertains to increasing the specificity of this class of drugs. Activating NATs exclusively in disease-causing cells is highly desirable because it will safely broaden the application of NATs to a wider range of clinical indications. Smart NATs are triggered through a photo-uncaging reaction or a specific molecular input such as a transcript, protein, or small molecule, thus complementing the current strategy of targeting cells and tissues with receptor-specific ligands to enhance specificity. This review summarizes the programmable modalities that have been incorporated into NATs to build in responsive behaviors. We discuss the various inputs, transduction mechanisms, and output response functions that have been demonstrated to date.