Aptamer-coded DNA nanoparticles for targeted doxorubicin delivery using pH-sensitive spacer

In vitro selection of a trans aptamer complex for target-responsive fluorescence activation

BACKGROUND

Most biological molecular complexes consist of multiple functional domains, yet rationally constructing such multifunctional complexes is challenging. Aptamers, the nucleic acid-based functional molecules, can perform multiple tasks including target recognition, conformational changes, and enzymatic activities, while being chemically synthesizable and tunable, and thus provide a basis for engineering enhanced functionalities through combination of multiple units. However, the conventional approach of simply combining aptamer units in a serial manner is susceptible to undesired crosstalk or interference between the aptamer units and to false interactions with non-target molecules; besides, the approach would require additional mechanisms to separate the units if they are desired to function independently. It is clearly a challenge to develop multi-aptamer complexes that preserve independent functions of each unit while avoiding undesired interference and non-specific interactions.

RESULTS

By directly in vitro selecting a 'trans' aptamer complex, we demonstrate that one aptamer unit ('utility module') can remain hidden or 'inactive' until a target analyte triggers the other unit ('sensing module') and separates the two aptamers. Since the operation of the utility module occurs free from the sensing module, unnecessary crosstalk between the two units can be avoided. Because the utility module is kept inactive until separated from the complex, non-specific interactions of the hidden module with noncognate targets can be naturally prevented. In our demonstration, the sensing module was selected to detect serotonin, a clinically important neurotransmitter, and the target-binding-induced structure-switching of the sensing module reveals and activates the utility module that turns on a fluorescence signal. The aptamer complex exhibited a moderately high affinity and an excellent specificity for serotonin with ∼16-fold discrimination against common neurotransmitter molecules, and displayed strong robustness to perturbations in the design, disallowing nonspecific reactions against various challenges.

SIGNIFICANCE

This work represents the first example of a trans aptamer complex that was in vitro selected de novo. The trans aptamer complex selected by our strategy does not require chemical modifications or immediate optimization processes to function, because the complex is directly selected to perform desired functions. This strategy should be applicable to a wide range of functional nucleic acid moieties, which will open up diverse applications in biosensing and molecular therapeutics.

Targeted cancer treatment using folate-conjugated sponge-like ZIF-8 nanoparticles: a review

ZIF-8 (zeolitic imidazolate framework-8) is a potential drug delivery system because of its unique properties, which include a large surface area, a large pore capacity, a large loading capacity, and outstanding stability under physiological conditions. ZIF-8 nanoparticles may be readily functionalized with targeting ligands for the identification and absorption of particular cancer cells, enhancing the efficacy of chemotherapeutic medicines and reducing adverse effects. ZIF-8 is also pH-responsive, allowing medication release in the acidic milieu of cancer cells. Because of its tunable structure, it can be easily functionalized to design cancer-specific targeted medicines. The delivery of ZIF-8 to cancer cells can be facilitated by folic acid-conjugation. Hence, it can bind to overexpressed folate receptors on the surface of cancer cells, which holds the promise of reducing unwanted deliveries. As a result of its importance in cancer treatment, the folate-conjugated ZIF-8 was the major focus of this review.

Aptamer-based targeted delivery systems for cancer treatment using DNA origami and DNA nanostructures

Due to the limitations of conventional cancer treatment methods, nanomedicine has appeared as a promising alternative, allowing improved drug targeting and decreased drug toxicity. In the development of cancer nanomedicines, among various nanoparticles (NPs), DNA nanostructures are more attractive because of their precisely controllable size, shape, excellent biocompatibility, programmability, biodegradability, and facile functionalization. Aptamers are introduced as single-stranded RNA or DNA molecules with recognize their corresponding targets. So, incorporating aptamers into DNA nanostructures led to influential vehicles for bioimaging and biosensing as well as targeted cancer therapy. In this review, the recent developments in the application of aptamer-based DNA origami and DNA nanostructures in advanced cancer treatment have been highlighted. Some of the main methods of cancer treatment are classified as chemo-, gene-, photodynamic- and combined therapy. Finally, the opportunities and problems for targeted DNA aptamer-based nanocarriers for medicinal applications have also been discussed.

Improving aptamer performance: key factors and strategies

Aptamers are functional single-stranded oligonucleotide fragments isolated from randomized libraries by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), exhibiting excellent affinity and specificity toward targets. Compared with traditional antibody reagents, aptamers display many desirable properties, such as low variation and high flexibility, and they are suitable for artificial and large-scale synthesis. These advantages make aptamers have a broad application potential ranging from biosensors, bioimaging to therapeutics and other areas of application. However, the overall performance of aptamer pre-selected by SELEX screening is far from being satisfactory. To improve aptamer performance and applicability, various post-SELEX optimization methods have been developed in the last decade. In this review, we first discuss the key factors that influence the performance or properties of aptamers, and then we summarize the key strategies of post-SELEX optimization which have been successfully used to improve aptamer performance, such as truncation, extension, mutagenesis and modification, splitting, and multivalent integration. This review shall provide a comprehensive summary and discussion of post-SELEX optimization methods developed in recent years. Moreover, by discussing the mechanism of each approach, we highlight the importance of choosing the proper method to perform post-SELEX optimization.

Delivery of Chemotherapy Agents and Nucleic Acids with pH-Dependent Nanoparticles

With less than one percent of systemically injected nanoparticles accumulating in tumors, several novel approaches have been spurred to direct and release the therapy in or near tumors. One such approach depends on the acidic pH of the extracellular matrix and endosomes of the tumor. With an average pH of 6.8, the extracellular tumor matrix provides a gradient for pH-responsive particles to accumulate, enabling greater specificity. Upon uptake by tumor cells, nanoparticles are further exposed to lower pHs, reaching a pH of 5 in late endosomes. Based on these two acidic environments in the tumor, various pH-dependent targeting strategies have been employed to release chemotherapy or the combination of chemotherapy and nucleic acids from macromolecules such as the keratin protein or polymeric nanoparticles. We will review these release strategies, including pH-sensitive linkages between the carrier and hydrophobic chemotherapy agent, the protonation and disruption of polymeric nanoparticles, an amalgam of these first two approaches, and the release of polymers shielding drug-loaded nanoparticles. While several pH-sensitive strategies have demonstrated marked antitumor efficacy in preclinical trials, many studies are early in their development with several obstacles that may limit their clinical use.

Multivalent Aptamer Approach: Designs, Strategies, and Applications

Aptamers are short and single-stranded DNA or RNA molecules with highly programmable structures that give them the ability to interact specifically with a large variety of targets, including proteins, cells, and small molecules. Multivalent aptamers refer to molecular constructs that combine two or more identical or different types of aptamers. Multivalency increases the avidity of aptamers, a particularly advantageous feature that allows for significantly increased binding affinities in comparison with aptamer monomers. Another advantage of multivalency is increased aptamer stabilities that confer improved performances under physiological conditions for various applications in clinical settings. The current study aims to review the most recent developments in multivalent aptamer research. The review will first discuss structures of multivalent aptamers. This is followed by detailed discussions on design strategies of multivalent aptamer approaches. Finally, recent developments of the multivalent aptamer approach in biosensing and biomedical applications are highlighted.

Nanotechnology as a Platform for the Development of Injectable Parenteral Formulations: A Comprehensive Review of the Know-Hows and State of the Art

Within recent decades, the development of nanotechnology has made a significant contribution to the progress of various fields of study, including the domains of medical and pharmaceutical sciences. A substantially transformed arena within the context of the latter is the development and production of various injectable parenteral formulations. Indeed, recent decades have witnessed a rapid growth of the marketed and pipeline nanotechnology-based injectable products, which is a testimony to the remarkability of the aforementioned contribution. Adjunct to the ability of nanomaterials to deliver the incorporated payloads to many different targets of interest, nanotechnology has substantially assisted to the development of many further facets of the art. Such contributions include the enhancement of the drug solubility, development of long-acting locally and systemically injectable formulations, tuning the onset of the drug’s release through the endowment of sensitivity to various internal or external stimuli, as well as adjuvancy and immune activation, which is a desirable component for injectable vaccines and immunotherapeutic formulations. The current work seeks to provide a comprehensive review of all the abovementioned contributions, along with the most recent advances made within each domain. Furthermore, recent developments within the domains of passive and active targeting will be briefly debated.

Strategies to bioengineer aptamer-driven nanovehicles as exceptional molecular tools for targeted therapeutics: A review

Aptamers are a class of folded nucleic acid strands capable of binding to different target molecules with high affinity and selectivity. Over the years, they have gained a substantial amount of interest as promising molecular tools for numerous medical applications, particularly in targeted therapeutics. However, only the different treatment approaches and current developments of aptamer-drug therapies have been discussed so far, ignoring the crucial technical and functional aspects of constructing a therapeutically effective aptamer-driven drug delivery system that translates to improved in-vivo performance. Hence, this paper provides a comprehensive review of the strategies used to improve the therapeutic performance of aptamer-guided delivery systems. We focus on the different functional features such as drug deployment, payload capacity, in-vivo stability and targeting efficiency to further our knowledge in enhancing the cell-specific delivery of aptamer-drug conjugates. Each reported strategy is critically discussed to emphasize both the benefits provided in comparison with other similar techniques and to outline their potential drawbacks with respect to the molecular properties of the aptamers, the drug and the system to be designed. The molecular architecture and design considerations for an efficient aptamer-based delivery system are also briefly elaborated.

Design strategies for programmable oligonucleotide nanotherapeutics

A systematic review on how to design different programmable nanotherapeutics using oligonucleotides as building blocks or as surface and matrix modifiers for controlled and targeted delivery of various therapeutic agents in presented.

Multifunctional REDV-G-TAT-G-NLS-Cys peptide sequence conjugated gene carriers to enhance gene transfection efficiency in endothelial cells

Rapid endothelialization on small diameter artificial blood vessels is an effective strategy to facilitate long-term patency and inhibit thrombosis. The gene delivery can enhance the proliferation and migration of endothelial cells (ECs), which is beneficial for rapid endothelialization. REDV-G-TAT-G-NLS-Cys (abbreviated as TP-G) peptide could weakly condense pEGFP-ZNF580 (pZNF580) and transfect ECs, but its transfection efficiency was still very low because of its low positive charge, low stability and weak endosome escape ability. In order to develop more stable and efficient gene carriers with low cytotoxicity, in the present study, we conjugated different amounts of TP-G peptide onto poly(lactide-co-glycolide)-g-polyethylenimine (PLGA-g-PEI) amphiphilic copolymers via a hetero-poly(ethylene glycol) spacer (OPSS-PEG-NHS). The TP-G peptide and PEI could cooperatively and strongly condense pZNF580. The carrier's cytotoxicity was reduced by the introduction of poly(ethylene glycol) spacer. They condensed pZNF580 to form gene complexes (PPP-TP-G/pZNF580) with suitable size and positive zeta potential for gene delivery. The transfected ECs promoted their migration ability as demonstrated by cell migration assay. The results of cellular uptake and confocal laser scanning microscopy showed significantly high internalization efficiency, endosomal/lysosomal escape and nucleus location of pZNF580 by this multifunctional TP-G peptide sequence conjugated gene delivery system. Furthermore, several inhibitors were used to study the cellular uptake pathways of PPP-TP-G/pZNF580 complexes. The results showed that PPP-TP-G2/Cy5-oligonucleotide complexes exhibited the optimized endocytosis pathways which facilitated for cellular uptake. In conclusion, the multifunctional TP-G peptide conjugated gene carriers could promote the transfection efficiency due to the multifunction of REDV, cell-penetrating peptide and nuclear localization signal in the peptide sequence, which could be a suitable gene carrier for endothelialization.

A progressively targeted gene delivery system with a pH triggered surface charge-switching ability to drive angiogenesis in vivo

For clinical application of therapeutic gene delivery, it is urgent to develop safe and in vivo efficient delivery systems. Nowadays, gene delivery carriers based on functional peptides have attracted much attention due to their excellent biocompatibility, biodegradability and biological multifunctionality. In the present study, a star-shaped integrated functional peptide, polyhedral oligomeric silsesquioxane (POSS-(C-G-NLS-G-TAT)16, abbreviated as PP1), was synthesized through "thiol-ene" click chemistry between the TAT-G-NLS-G-C multifunctional peptide sequence and inorganic octa-diallyl POSS. Cationic PP1 was mixed with the pZNF580 plasmid to obtain stable binary gene complexes (BCPs) with membrane penetrating and nucleus targeting functions. In order to improve BCPs' biocompatibility, cellular uptake, and endosome escape, they were further modified using an anionic polymer of PLL-g-CAGW21%-g-Acon (n = 47%, 57% and 64%) having an EC targeting ligand (CAGW peptide) and a charge reversal moiety (cis-aconitic amide) through electrostatic absorption to obtain ternary gene complexes (TCPs). By adjusting the weight ratio of PP1/pZNF580 plasmid/PLL-g-CAGW21%-g-Acon to 5/1/1.25, TCPs-1 with n = 47%, TCPs-2 with n = 57% and TCPs-3 with n = 64% exhibited a neutral zeta potential and suitable particle size; thus they were used for further biological evaluation. Compared with BCPs (5/1 weight ratio of PP1/pZNF580 plasmid), TCPs exhibited high hemocompatibility and cytocompatibility; more interestingly, they also showed significantly enhanced gene delivery efficiency. The TCP groups achieved perfect transfection effects in the proliferation and migration of human umbilical vein endothelial cells (HUVECs), and especially high neovascularization in vitro and in vivo. Our results demonstrated that the high graft ratio of cis-aconitic amide provided benefits of high biocompatibility and gene delivery efficiency, and the TCPs-3 group showed the optimized transfection efficiency among the three groups. Importantly, HUVECs transfected with TCPs-3 exhibited an outstanding ability to enhance angiogenesis in vivo. In brief, this multifunctional ternary gene system with the EC targeting ligand and membrane penetrating, charge reversal and nucleus targeting functions is a promising platform for the transfection of HUVECs, and may be useful for the treatment of cardiovascular diseases in clinical applications.

Enhanced tumor uptake and activity of nanoplex-loaded doxorubicin

Doxorubicin (Dox) has widespread use as a cancer chemotherapeutic agent, but Dox is limited by several side effects including irreversible cardiomyopathy. Although liposomal Dox formulations, such as Doxil, mitigate side effects, they do not prolong survival in many patients. As a result, efforts have continued to discover improved formulations of Dox. We previously found that a peptide-based nanoplex delivered plasmid DNA efficiently to tumors in murine models. Unlike the majority of nanoparticles that depend solely on enhanced permeability and retention (EPR) for their transport into the tumor, our peptide-based nanoplex has a potential advantage in that its uptake primarily depends on neuropilin-1 receptor targeting. Because Dox binds to DNA, we tested whether this delivery platform could effectively deliver Dox to tumors and reduce their size. The nanoplexes increased the levels of Dox in tumors by about 5.5-fold compared to aqueous (free) Dox controls. Consistent with enhanced levels in the tumor, the nanoplex-Dox treatment had significantly greater anti-tumor activity. Whereas low dose free Dox did not reduce the size of tumors compared to untreated controls, the low dose nanoplex-Dox reduced the size of tumors by nearly 55% (p < 0.001). The high dose nanoplex-Dox also inhibited the size of tumor significantly more than the comparable high-dose free Dox (p < 0.001). Furthermore, apoptosis and proliferation markers (Ki67) of tumors observed in the different treatment groups correlated with their ability to inhibit tumor size. This study shows the efficacy of an NRP-1 targeted nanoplexes to deliver Dox to tumors in vivo and lays the groundwork for more complex and effective formulations.

A PEG-b-poly(disulfide-l-lysine) based redox-responsive cationic polymer for efficient gene transfection

Gene therapy is concerned with the transfer of complement genes to functionally defective cells in a safe and directed manner for the treatment of the most challenging diseases. But safety issues and low transfection efficiency of the gene vectors are the major challenges, which need to be overcome. Recently, redox-responsive bioreducible polymers containing disulfide linkages have been considered as efficient gene vectors, owing to the selective degradation of the disulfide bond in the reducing environment of the cells. This enables spatiotemporal release of pDNA with no or minimum toxicity. Herein, we reported a bioreducible poly(ethyleneglycol)-b-poly(disulfide-l-lysine) cationic polymer (denoted as PEG-SSL) via a Michael addition reaction of poly(ethyleneglycol)tetraacrylate PEG(Ac)₄ and the terminal amine group of poly(disulfide-l-lysine). PEG-SSL efficiently condensed the plasmid ZNF580 gene (pZNF580) forming nano-sized polyplexes (155 ± 4 to 285 ± 3 nm) with zeta potentials of 1.9 ± 0.1 to 26.7 ± 0.4 mV. PEG-SSL successfully retarded pZNF580 at a small polymer/pDNA weight ratio of 10/1 and higher. When exposed to a reducing environment of 5 mM DTT, it rapidly released genes even at higher weight ratios of the PEG-SSL polymer in the PEG-SSL/pDNA complexes. The PEG-SSL/pZNF580 complexes exhibited good stability when exposed to DNase I and efficiently protected pDNA from degradation. In vitro transfection and cytotoxicity were investigated in EA.hy926 cells. The results showed that PEG-SSL successfully delivered pZNF580 into the cells with less cytotoxicity compared to PEI25kDa. The flow cytometry and confocal scanning laser microscopy results indicated that PEG-SSL polyplexes exhibited good cellular uptake and nuclear co-localization rates. All these results implied that PEG-SSL had the potential as a non-viral vector for gene transfection.

Multifunctional gene delivery systems with targeting ligand CAGW and charge reversal function for enhanced angiogenesis

A charge reversible polyanion with a targeting peptide was assembled onto binary gene complexes to enhance their endosomal escape and transfection efficiency.

pH-Control in Aptamer-Based Diagnostics, Therapeutics, and Analytical Applications

Aptamer binding has been used effectively for diagnostics, in-vivo targeting of therapeutics, and the construction and control of nanomachines. Nanostructures that respond to pH by releasing or changing affinity to a target have also been used for in vivo delivery, and in the construction of sensors and re-usable nanomachines. There are many applications that use aptamers together with pH-responsive materials, notably the targeted delivery of chemotherapeutics. However, the number of reported applications that directly use pH to control aptamer binding is small. In this review, we first discuss the use of aptamers with pH-responsive nanostructures for chemotherapeutic and other applications. We then discuss applications that use pH to denature or otherwise disrupt the binding of aptamers. Finally, we discuss motifs using non-canonical nucleic acid base pairing that can shift conformation in response to pH, followed by an overview of engineered pH-controlled aptamers designed using those motifs.

Design strategies for physical-stimuli-responsive programmable nanotherapeutics

Nanomaterials that respond to externally applied physical stimuli such as temperature, light, ultrasound, magnetic field and electric field have shown great potential for controlled and targeted delivery of therapeutic agents. However, the body of literature on programming these stimuli-responsive nanomaterials to attain the desired level of pharmacologic responses is still fragmented and has not been systematically reviewed. The purpose of this review is to summarize and synthesize the literature on various design strategies for simple and sophisticated programmable physical-stimuli-responsive nanotherapeutics.