Smart Drug Delivery Systems Based on DNA Nanotechnology

Antithrombotic Effect of a Bivalent DNA Aptamer of Thrombin

Thrombin plays a critical role in both coagulation and platelet activation, and its interaction with thrombin-protease-activated receptor 1 (PAR1) on platelets and vascular smooth muscle cells (VSMCs) leads to a series of pathological processes such as thrombosis, restenosis, and atherosclerosis. This study investigated the antithrombotic properties of a bivalent DNA aptamer (bApt) with phosphorothioate backbone modification designed to inhibit thrombin, with a specific focus on its ability to regulate the thrombin-PAR1 signaling pathway. The results showed that bApt modulated the thrombin-PAR1 pathway, effectively reduced thrombus formation, platelet aggregation, and VSMC proliferation. Key findings from the study highlight that bApt successfully prolonged coagulation reaction time (R value), coagulation time (K value), maximum amplitude (MA) and reduced coagulation angle (α value), and also prolonged thrombin time (TT) and activated partial thromboplastin time (APTT), in a dose-dependent manner. Moreover, in an arterial injury model, bApt reduced thrombus formation significantly, supporting its potential as a therapeutic agent for thrombotic diseases.

Folding an RCA Scaffold into an Intelligent Coiled Nanosnake for Precise/Synergistic RNAi-/Chemotherapy of Cancer

An RCA product is a promising scaffold for the construction of DNA nanostructures, but so far, there is no RCA scaffold-based dynamic reconfigurable nanorobot for biological applications. In this contribution, we develop an intracellular stimuli-responsive reconfigurable coiled DNA nanosnake (N-Snake) by using incomplete aptamer-functionalized (A) DNA tetrahedrons (T) to fold a long tandemly repetitive DNA strand synthesized by rolling circle amplification reaction (R) with the help of palindromic fragment (P). A DNA-assembled product, ARTP, including spiked aptamers, can retain the structural integrity even if exposed to fetal bovine serum (FBS) for 24 h and displays substantially enhanced target molecule-dependent cellular internalization efficiency. ARTP contains tetrahedral containers and linear containers, so that there are 500 doxorubicins (DOXs) and 12.5 siRNAs per ARTP. Moreover, ARTP can precisely transport anticancer drugs to cancerous sites and controllably release via the structural reconfiguration upon intracellular stimuli, almost 100% inhibiting tumor growth without detectable systemic toxicity owing to the synergistic RNAi-/Chemotherapy. Apparently, coiled N-snake, DOX/siPlk1-loaded ARTP, can specifically enter tumor cells, uncoil upon intracellular stimuli, and attack the cells from the inside, exerting precise cancer therapy.

Structural Basis for C2'-methoxy Recognition by DNA Polymerases and Function Improvement

DNA modified with C2'-methoxy (C2'-OMe) greatly enhances its resistance to nucleases, which is beneficial for the half-life of aptamers and DNA nanomaterials. Although the unnatural DNA polymerases capable of incorporating C2'-OMe modified nucleoside monophosphates (C2'-OMe-NMPs) were engineered via directed evolution, the detailed molecular mechanism by which an evolved DNA polymerase recognizes C2'-OMe-NTPs remains poorly understood. Here, we present the crystal structures of the evolved Stoffel fragment of Taq DNA polymerase SFM4-3 processing the C2'-OMe-GTP in different states. Our results reveal the structural basis for recognition of C2'-methoxy by SFM4-3. Based on the analysis of other mutated residues in SFM4-3, a new Stoffel fragment variant with faster catalytic rate and stronger inhibitor-resistance was obtained. In addition, the capture of a novel pre-insertion co-existing with template 5'-overhang stacking conformation provides insight into the catalytic mechanism of Taq DNA polymerase.

Construction of Smart DNA-Based Drug Delivery Systems for Cancer Therapy

Due to the disadvantages of poor targeting, slow action, and low effectiveness of current commonly used cancer treatments, including surgery, chemotherapy, and radiotherapy, researchers have turned to DNA as a biomaterial for constructing drug delivery nanocarriers. DNA is favored for its biocompatibility and programmability. In order to overcome the limitations associated with traditional drug delivery systems (DDSs), researchers have developed smart-responsive DNA DDSs that can control drug release in response to specific physical or chemical stimuli at targeted sites. In this review, a summary of multiple targeted ligand structures is provided, various shapes of stable DNA nanomaterials, and different stimuli-responsive drug release strategies in DNA DDSs. Specifically, targeted cell recognition, in vivo stable transport, and controlled drug release of smart DDSs are focused. Finally, the further development prospects and challenges of clinical application of DNA nanomaterials in the field of smart drug delivery are discussed. The objective of this review is to enhance researchers' comprehension regarding the potential application of DNA nanomaterials in precision drug delivery, with the aim of expediting the clinical implementation of intelligent DDSs.

Molecular vessels from preorganised natural building blocks

Supramolecular vessels emerged as tools to mimic and better understand compartmentalisation, a central aspect of living matter. However, many more applications that go beyond those initial goals have been documented in recent years, including new sensory systems, artificial transmembrane transporters, catalysis, and targeted drug or gene delivery. Peptides, carbohydrates, nucleobases, and steroids bear great potential as building blocks for the construction of supramolecular vessels, possessing complexity that is still difficult to attain with synthetic methods - they are rich in functional groups and well-defined stereogenic centers, ready for noncovalent interactions and further functions. One of the options to tame the functional and dynamic complexity of natural building blocks is to place them at spatially designed positions using synthetic scaffolds. In this review, we summarise the historical and recent advances in the construction of molecular-sized vessels by the strategy that couples synthetic predictability and durability of various scaffolds (cyclodextrins, porphyrins, crown ethers, calix[n]arenes, resorcin[n]arenes, pillar[n]arenes, cyclotriveratrylenes, coordination frameworks and multivalent high-symmetry molecules) with functionality originating from natural building blocks to obtain nanocontainers, cages, capsules, cavitands, carcerands or coordination cages by covalent chemistry, self-assembly, or dynamic covalent chemistry with the ultimate goal to apply them in sensing, transport, or catalysis.

Molecular circuit for exponentiation based on the domain coding strategy

DNA strand displacement (DSD) is an efficient technology for constructing molecular circuits. However, system computing speed and the scale of logical gate circuits remain a huge challenge. In this paper, a new method of coding DNA domains is proposed to carry out logic computation. The structure of DNA strands is designed regularly, and the rules of domain coding are described. Based on this, multiple-input and one-output logic computing modules are built, which are the basic components forming digital circuits. If the module has n inputs, it can implement 2n logic functions, which reduces the difficulty of designing and simplifies the structure of molecular logic circuits. In order to verify the superiority of this method for developing large-scale complex circuits, the square root and exponentiation molecular circuits are built. Under the same experimental conditions, compared with the dual-track circuits, the simulation results show that the molecular circuits designed based on the domain coding strategy have faster response time, simpler circuit structure, and better parallelism and scalability. The method of forming digital circuits based on domain coding provides a more effective way to realize intricate molecular control systems and promotes the development of DNA computing.

NICE-FF: A non-empirical, intermolecular, consistent, and extensible force field for nucleic acids and beyond

A new non-empirical ab initio intermolecular force field (NICE-FF in buffered 14-7 potential form) has been developed for nucleic acids and beyond based on the dimer interaction energies (IEs) calculated at the spin component scaled-MI-second order Møller-Plesset perturbation theory. A fully automatic framework has been implemented for this purpose, capable of generating well-polished computational grids, performing the necessary ab initio calculations, conducting machine learning (ML) assisted force field (FF) parametrization, and extending existing FF parameters by incorporating new atom types. For the ML-assisted parametrization of NICE-FF, interaction energies of ∼18 000 dimer geometries (with IE < 0) were used, and the best fit gave a mean square deviation of about 0.46 kcal/mol. During this parametrization, atom types apparent in four deoxyribonucleic acid (DNA) bases have been first trained using the generated DNA base datasets. Both uracil and hypoxanthine, which contain the same atom types found in DNA bases, have been considered as test molecules. Three new atom types have been added to the DNA atom types by using IE datasets of both pyrazinamide and 9-methylhypoxanthine. Finally, the last test molecule, theophylline, has been selected, which contains already-fitted atom-type parameters. The performance of NICE-FF has been investigated on the S22 dataset, and it has been found that NICE-FF outperforms the well-known FFs by generating the most consistent IEs with the high-level ab initio ones. Moreover, NICE-FF has been integrated into our in-house developed crystal structure prediction (CSP) tool [called FFCASP (Fast and Flexible CrystAl Structure Predictor)], aiming to find the experimental crystal structures of all considered molecules. CSPs, which were performed up to 4 formula units (Z), resulted in NICE-FF being able to locate almost all the known experimental crystal structures with sufficiently low RMSD20 values to provide good starting points for density functional theory optimizations.

Advancements in Nanogels for Enhanced Ocular Drug Delivery: Cutting-Edge Strategies to Overcome Eye Barriers

Nanomedicine in gel or particle formation holds considerable potential for enhancing passive and active targeting within ocular drug delivery systems. The complex barriers of the eye, exemplified by the intricate network of closely connected tissue structures, pose significant challenges for drug administration. Leveraging the capability of engineered nanomedicine offers a promising approach to enhance drug penetration, particularly through active targeting agents such as protein peptides and aptamers, which facilitate targeted release and heightened bioavailability. Simultaneously, DNA carriers have emerged as a cutting-edge class of active-targeting structures, connecting active targeting agents and illustrating their potential in ocular drug delivery applications. This review aims to consolidate recent findings regarding the optimization of various nanoparticles, i.e., hydrogel-based systems, incorporating both passive and active targeting agents for ocular drug delivery, thereby identifying novel mechanisms and strategies. Furthermore, the review delves into the potential application of DNA nanostructures, exploring their role in the development of targeted drug delivery approaches within the field of ocular therapy.

Poloxamer-based nanogels as delivery systems: how structural requirements can drive their biological performance?

Poloxamers or Pluronics®-based nanogels are one of the most used matrices for developing delivery systems. Due to their thermoresponsive and flexible mechanical properties, they allowed the incorporation of several molecules including drugs, biomacromolecules, lipid-derivatives, polymers, and metallic, polymeric, or lipid nanocarriers. The thermogelling mechanism is driven by micelles formation and their self-assembly as phase organizations (lamellar, hexagonal, cubic) in response to microenvironmental conditions such as temperature, osmolarity, and additives incorporated. Then, different biophysical techniques have been used for investigating those structural transitions from the mechanisms to the preferential component's orientation and organization. Since the design of PL-based pharmaceutical formulations is driven by the choice of the polymer type, considering its physico-chemical properties, it is also relevant to highlight that factors inherent to the polymeric matrix can be strongly influenced by the presence of additives and how they are able to determine the nanogels biopharmaceuticals properties such as bioadhesion, drug loading, surface interaction behavior, dissolution, and release rate control. In this review, we discuss the general applicability of three of the main biophysical techniques used to characterize those systems, scattering techniques (small-angle X-ray and neutron scattering), rheology and Fourier transform infrared absorption spectroscopy (FTIR), connecting their supramolecular structure and insights for formulating effective therapeutic delivery systems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12551-023-01093-2.

Tools and techniques for the discovery of therapeutic aptamers: recent advances

INTRODUCTION

The pursuit of novel therapeutic agents for serious diseases such as cancer has been a global endeavor. Aptamers characteristic of high affinity, programmability, low immunogenicity, and rapid permeability hold great promise for the treatment of diseases. Yet obtaining the approval for therapeutic aptamers remains challenging. Consequently, researchers are increasingly devoted to exploring innovative strategies and technologies to advance the development of these therapeutic aptamers.

AREAS COVERED

The authors provide a comprehensive summary of the recent progress of the SELEX (Systematic Evolution of Ligands by EXponential enrichment) technique, and how the integration of modern tools has facilitated the identification of therapeutic aptamers. Additionally, the engineering of aptamers to enhance their functional attributes, such as inhibiting and targeting, is discussed, demonstrating the potential to broaden their scope of utility.

EXPERT OPINION

The grand potential of aptamers and the insufficient development of relevant drugs have spurred countless efforts for stimulating their discovery and application in the therapeutic field. While SELEX techniques have undergone significant developments with the aid of advanced analysis instruments and ingeniously updated aptameric engineering strategies, several challenges still impede their clinical translation. A key challenge lies in the insufficient understanding of binding conformation and susceptibility to degradation under physiological conditions. Despite the hurdles, our opinion is optimistic. With continued progress in overcoming these obstacles, the widespread utilization of aptamers for clinical therapy is envisioned to become a reality soon.

Enhancing the Effectiveness of Oligonucleotide Therapeutics Using Cell-Penetrating Peptide Conjugation, Chemical Modification, and Carrier-Based Delivery Strategies

Oligonucleotide-based therapies are a promising approach for treating a wide range of hard-to-treat diseases, particularly genetic and rare diseases. These therapies involve the use of short synthetic sequences of DNA or RNA that can modulate gene expression or inhibit proteins through various mechanisms. Despite the potential of these therapies, a significant barrier to their widespread use is the difficulty in ensuring their uptake by target cells/tissues. Strategies to overcome this challenge include cell-penetrating peptide conjugation, chemical modification, nanoparticle formulation, and the use of endogenous vesicles, spherical nucleic acids, and smart material-based delivery vehicles. This article provides an overview of these strategies and their potential for the efficient delivery of oligonucleotide drugs, as well as the safety and toxicity considerations, regulatory requirements, and challenges in translating these therapies from the laboratory to the clinic.

Liquid exfoliation of ultrasmall zirconium carbide nanodots as a noninflammatory photothermal agent in the treatment of glioma

Photothermal therapy (PTT), like other clinical translational tumor ablation techniques, requires a temperature increase above 50 °C to cause necrosis and death of tumor cells. Although the tumor can be eliminated rapidly by PTT, the inflammatory response is triggered by the large amounts of released reactive oxygen species (ROS). Therefore, liquid exfoliation was used to create ultrasmall zirconium carbide nanodots (NDs) with an average diameter of approximately 4.5 nm as noninflammatory/anti-inflammatory photosensitizers for PTT of glioma. Ultrasmall ZrC NDs showed excellent photothermal stability and biocompatibility but no obvious toxicity. Moreover, the ultrasmall ZrC NDs effectively ablated glioma at relatively low concentrations and inhibited tumor migration and proliferation in vitro and in vivo. Furthermore, the excellent ROS-scavenging ability of ultrasmall ZrC NDs suppressed the inflammatory response to PTT. Intriguingly, we found that ZrC had the capability of performing CT imaging. We demonstrated that the ultrasmall ZrC NDs created in this study could effectively and safely treat glioma without inflammation.

Calcium Hydride-Based Dressing to Promote Wound Healing

Wound microenvironment with excess reactive oxygen species (ROS) can significantly inhibit wound healing. Encouraged by hydrogen molecules (H₂ ) with effective ROS scavenging and calcium hydride (CaH₂ ) with sufficient H₂ supply, the authors for the first time employed CaH₂ as a therapeutic H₂ donor and starch as a diluent to construct CaH₂ pulvis dressing for wound healing treatment. It has been found that CaH₂ by generating H₂ exhibited excellent ROS scavenging performance, favorable for preserving the oxidative-stress-induced cell death. After being applied onto the skin wound, the CaH₂ pulvis dressing with the unique ROS-scavenging ability can accelerate skin wound healing in healthy/diabetic mice (small animal models) and Bama mini-pigs (large animal model). Such CaH₂ dressing can release H₂ to relieve the inflammation levels, decrease the secretion of pro-inflammatory cytokines, increase the infiltration of inflammation-suppressive immune cells, and promote the regeneration of new blood vessels and collagens, thereby accelerating wound healing. This work highlighted that the integration of anti-oxidation and anti-inflammation functions based on CaH₂ dressing endowed it with a promising possibility for the treatment of inflammatory diseases.

Ultrasmall zirconium carbide nanodots for synergistic photothermal-radiotherapy of glioma

Glioma is characterized by highly invasive, progressive, and lethal features. In addition, conventional treatments have been poorly effective in treating glioma. To overcome this challenge, synergistic therapies combining radiotherapy (RT) with photothermal therapy (PTT) have been proposed and extensively explored as a highly feasible cancer treatment strategy. Herein, ultrasmall zirconium carbide (ZrC) nanodots were successfully synthesized with high near-infrared absorption and strong photon attenuation for synergistic PTT-RT of glioma. ZrC-PVP nanodots with an average size of approximately 4.36 nm were prepared by the liquid exfoliation method and modified with the surfactant polyvinylpyrrolidone (PVP), with a satisfactory absorption and photothermal conversion efficiency (53.4%) in the near-infrared region. Furthermore, ZrC-PVP nanodots can also act as radiosensitizers to kill residual tumor cells after mild PTT due to their excellent photon attenuating ability, thus achieving a significant synergistic therapeutic effect by combining RT and PTT. Most importantly, both in vitro and in vivo experimental results further validate the high biosafety of ZrC-PVP NDs at the injected dose. This work systematically evaluates the feasibility of ZrC-PVP NDs for glioma treatment and provides evidence of the application of zirconium-based nanomaterials in photothermal radiotherapy.