Controlling lipid micelle stability using oligonucleotide headgroups

Biomolecule-guided co-localization of intermolecular G-rich strands for the construction of a tetramolecular G-quadruplex sensing strategy

We herein introduce the principle of proximity assay into tetramolecular G-quadruplexes guided by various biomolecules for the construction of a sensing strategy. Our strategy is based on the co-localization of intermolecular G-rich strands guided by a recognition event of a specific biomolecule to its corresponding affinity ligand. In such case, the local concentration among intermolecular strands is significantly increased to trigger the following self-assembly that served as the peroxidase-mimicking activity. This strategy is versatile, homogenous and adaptable to different types of biomolecules.

Affibody Modified G-quadruplex DNA Micelles Incorporating Polymeric 5-Fluorodeoxyuridine for Targeted Delivery of Curcumin to Enhance Synergetic Therapy of HER2 Positive Gastric Cancer

Combination chemotherapy is emerging as an important strategy for cancer treatment with decreased side effects. However, chemotherapeutic drugs with different solubility are not easy to realize co-delivery in traditional nanocarriers. Herein, an affibody modified G-quadruplex DNA micellar prodrug (affi-F/GQs) of hydrophilic 5-fluorodeoxyuridine (FUdR) by integrating polymeric FUdRs into DNA strands is developed for the first time. To achieve synergistic efficacy with hydrophobic drugs, curcumin (Cur) is co-loaded into affi-F/GQs micelles to prepare the dual drug-loaded DNA micelles (Cur@affi-F/GQs), in which affibody is employed as a targeting moiety to facilitate HER2 receptor-mediated uptake. Cur@affi-F/GQs have a small size of approximately 130 nm and exhibit excellent stability. The system co-delivers FUdR and Cur in a ratiometric manner, and the drug loading rates are 21.1% and 5.6%, respectively. Compared with the physical combination of FUdR and Cur, Cur@affi-F/GQs show higher cytotoxicity and greater synergistic effect on HER2 positive gastric cancer N87 cells. Surprisingly, Cur@affi-F/GQs significantly enhance the expression and activity of apoptosis-associated proteins in Bcl-2/Bax-caspase 8, 9-caspase 3 apoptotic pathway, which is the main factor in the death of tumor cells induced by FUdR. Overall, this nanoencapsulation is a promising candidate for the targeted co-delivery of drugs with significant differences in solubility.

ssDNA nanotubes for selective targeting of glioblastoma and delivery of doxorubicin for enhanced survival

Effective treatment of glioblastoma remains a daunting challenge. One of the major hurdles in the development of therapeutics is their inability to cross the blood-brain tumor barrier (BBTB). Local delivery is an alternative approach that can still suffer from toxicity in the absence of target selectivity. Here, we show that nanotubes formed from self-assembly of ssDNA-amphiphiles are stable in serum and nucleases. After bilateral brain injections, nanotubes show preferential retention by tumors compared to normal brain and are taken up by glioblastoma cells through scavenger receptor binding and macropinocytosis. After intravenous injection, they cross the BBTB and internalize in glioblastoma cells. In a minimal residual disease model, local delivery of doxorubicin showed signs of toxicity in the spleen and liver. In contrast, delivery of doxorubicin by the nanotubes resulted in no systemic toxicity and enhanced mouse survival. Our results demonstrate that ssDNA nanotubes are a promising drug delivery vehicle to glioblastoma.

An analytical study of lipid-oligonucleotide aggregation properties

Lipid-oligonucleotides (LON) attract great interest as supramolecular scaffolds to improve the intracellular delivery of nucleic acids. Analytical characterization of LON assemblies is critical to formulation development, understanding in-vivo performance, as well as quality control. For this study, we selected LONs featuring different modifications on both oligonucleotide (with or without a G4 prone sequence) and lipid (mono or bis-alkyl chain covalently attached to the oligonucleotide sequence). Size exclusion chromatography (SEC) and, for the first time, capillary electrophoresis (CE) were investigated to study LON supramolecular self-assemblies. Results were correlated to those obtained with conventional physico-chemical characterization techniques i.e. gel electrophoresis, dynamic light scattering, and circular dichroism. In SEC, a separation between LON monomers and micelles was achieved in 5min on a TSK-gel G3000PW column at 70°C with 100% water, as mobile phase. CE conditions were optimized using a fused-silica capillary length of 10.0cm effective length at 15°C. Different background electrolytes were tested by varying the nature and the concentration of salts added. A sodium tetraborate buffer with 75mM NaCl appeared suitable to promote LON assembly. CE offers benefits to LON micelle analysis in terms of speed of analysis, high resolution, and low quantity of sample injected. Moreover, CE provides an appropriate tool to assess the impact of media of biological relevance on LON self-assembly. In this work, the key role of lipophilic tails and the formation of tetramolecular G-quadruplexes on the stability of LON micelles was confirmed.

Intraparticle and Interparticle Transferable DNA Walker Supported by DNA Micelles for Rapid Detection of MicroRNA

Synthetic DNA walkers are artificially designed DNA self-assemblies with the capability of performing quasi-mechanical movement at the micro/nanoscale and have shown extensive promise in biosensing, intracellular imaging, and drug delivery. However, DNA walkers are usually constructed by covalently or coordinately binding DNA strands specifically to hard surfaces, thereby greatly limiting their movement efficiency. Herein, we report an intraparticle and interparticle transferable DNA walker (dynamic micelle-supported DNA walker, DM-walker) constructed by immobilizing walking tracks and walking arms onto the corona of DNA micelles according to the principle of Watson-Crick base pairing. The DNAzyme-powered walking arm can drive the intraparticle and interparticle movements of the DM-walker due to the fact that the dynamic structure of the DNA micelle helps overcome the spatial barrier between the arms and tracks in the system, resulting in high walking efficiency. Moreover, the whole DM-walker can be constructed by self-assembly, getting rid of the tedious process and low efficiency of fixing DNA strands on hard surfaces. Taking miRNA-10b as a model target, the DM-walker demonstrates high walking efficiency (reaction duration of 20 min) and high sensitivity (LOD of 87 pM). The proposed DM-walker provides an avenue to develop novel DNA walkers on dynamic interfaces and holds great potential in clinical diagnosis.

Tuning G-Quadruplex Nanostructures with Lipids. Towards Designing Hybrid Scaffolds for Oligonucleotide Delivery

Two G-quadruplex forming oligonucleotides [d(TG₄T)₄ and d(TG₆T)₄] were selected as two tetramolecular quadruplex nanostructures because of their demonstrated ability to be modified with hydrophobic molecules. This allowed us to synthesize two series of G-quadruplex conjugates that differed in the number of G-tetrads, as well as in the terminal position of the lipid modification. Both solution and solid-phase syntheses were carried out to yield the corresponding lipid oligonucleotide conjugates modified at their 3′- and 5′-termini, respectively. Biophysical studies confirmed that the presence of saturated alkyl chains with different lengths did not affect the G-quadruplex integrity, but increased the stability. Next, the G-quadruplex domain was added to an 18-mer antisense oligonucleotide. Gene silencing studies confirmed the ability of such G-rich oligonucleotides to facilitate the inhibition of target Renilla luciferase without showing signs of toxicity in tumor cell lines.

Amphiphilic "Like-a-Brush" Oligonucleotide Conjugates with Three Dodecyl Chains: Self-Assembly Features of Novel Scaffold Compounds for Nucleic Acids Delivery

The conjugation of lipophilic groups to oligonucleotides is a promising approach for improving nucleic acid-based therapeutics' intracellular delivery. Lipid oligonucleotide conjugates can self-aggregate in aqueous solution, which gains much attention due to the formation of micellar particles suitable for cell endocytosis. Here, we describe self-association features of novel "like-a-brush" oligonucleotide conjugates bearing three dodecyl chains. The self-assembly of the conjugates into 30-170 nm micellar particles with a high tendency to aggregate was shown using dynamic light scattering (DLS), atomic force (AFM), and transmission electron (TEM) microscopies. Fluorescently labeled conjugates demonstrated significant quenching of fluorescence intensity (up to 90%) under micelle formation conditions. The conjugates possess increased binding affinity to serum albumin as compared with free oligonucleotides. The dodecyl oligonucleotide conjugate and its duplex efficiently internalized and accumulated into HepG2 cells' cytoplasm without any transfection agent. It was shown that the addition of serum albumin or fetal bovine serum to the medium decreased oligonucleotide uptake efficacy (by 22.5-36%) but did not completely inhibit cell penetration. The obtained results allow considering dodecyl-containing oligonucleotides as scaffold compounds for engineering nucleic acid delivery vehicles.

Conformational Conversion Enhances Cellular Uptake of F Base Double-Strand-Conjugated Oligonucleotides

Artificial bases have emerged as a useful tool to expand genetic alphabets and biomedical applications of oligonucleotides. Herein, we reported that the conformation conversion enhances cellular uptake of hydrophobic 3,5-bis(trifluoromethyl)benzene (F) base double-strand-conjugated oligonucleotides. The formation of the F base double-strand caged the hydrophobic F base in the duplex strand, thus preventing F base from interacting with cells to some extent. However, upon conversion of F base double-strand-conjugated oligonucleotide to F base single-strand-conjugated oligonucleotide, F bases then were allowed to interact with cells by stronger hydrophobic interactions, followed by cellular uptake. The results were concluded as a pairing-induced cage effect of F base and have the potential for the construction of stimuli-responsive cellular uptake of functional nucleic acids.

Human serum albumin as an intrinsic signal amplification amplifier for ultrasensitive assays of the prostate-specific antigen in human plasma

Endogenous human serum albumin is used as an intrinsic signal amplification amplifier for ultrasensitive assays of disease biomarkers in blood tests.

ssDNA-amphiphile architecture used to control dimensions of DNA nanotubes

Controlling the dimensions of DNA nanotubes is of great interest as they can be used in different applications ranging from functional elements in nanodevices to carriers for drug delivery. ssDNA-amphiphiles composed of a ssDNA headgroup, a hydrophobic dialkyl tail and a polycarbon spacer between the tail and the headgroup, self-assemble into hollow DNA nanotubes by forming bilayer nanotapes that transition from twisted nanotapes, to helical nanotapes, to nanotubes. The presence of the DNA nanotubes is verified via cryo-TEM and SAXS. We further explore the effect of the ssDNA secondary structure and tail length on the assembly of the ssDNA-amphiphiles. We demonstrate that the presence of intermolecular G-quadruplexes in the ssDNA sequence dictates the nanotube length. The nanotube diameter is controlled by the hydrophobic tail length, and coarse-grained molecular dynamics simulations are employed to elucidate the tail design impact on assembly.

Traditional Chinese medicine combined with hepatic targeted drug delivery systems: A new strategy for the treatment of liver diseases

Liver diseases are clinically common and present a substantial public health issue. Many of the currently available drugs for the treatment of liver diseases suffer from limitations that include low hepatic distribution, lack of target effects, poor in vivo stability and adverse effects on other organs. Consequently, conventional treatment of hepatic diseases is ineffective. TCM is commonly used in the treatment of liver diseases worldwide, particularly in China, and has advantages over conventional therapy. HTDDS can be designed to enhance clinical efficacy in the treatment of liver diseases. We have conducted an extensive review of 335 studies reported since 1964. These included about 166 references involving the treatment of liver diseases with TCM (covering active components of TCM, single TCM and Chinese medicine formulas), 169 reports on HTDDS and background studies on liver-related diseases. Here we review the long history of TCM in the treatment of liver diseases.We have also reviewed the status of studies on active components of TCM using nanotechnology-based targeted delivery systems to provide support for further research and development of TCM-based targeted preparations for the treatment of liver disease.

Dynamic Nanostructures from DNA-Coupled Molecules, Polymers, and Nanoparticles

Dynamic and reconfigurable systems that can sense and react to physical and chemical signals are ubiquitous in nature and are of great interest in diverse areas of science and technology. DNA is a powerful tool for fabricating such smart materials and devices due to its programmable and responsive molecular recognition properties. For the past couple of decades, DNA-based self-assembly is actively explored to fabricate various DNA-organic and DNA-inorganic hybrid nanostructures with high-precision structural control. Building upon past development, researchers have recently begun to design and assemble dynamic nanostructures that can undergo an on-demand transformation in the structure, properties, and motion in response to various external stimuli. In this Review, recent advances in dynamic DNA nanostructures, focusing on hybrid structures fabricated from DNA-conjugated molecules, polymers, and nanoparticles, are introduced, and their potential applications and future perspectives are discussed.

DNA Quadruple Helices in Nanotechnology

DNA has played an early and powerful role in the development of bottom-up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs. However, in addition to the above components underlying the iconic double helix, a number of alternative pairing schemes of nucleobases are known. This review focuses on two of these noncanonical classes of DNA helices: G-quadruplexes and the i-motif. The unique properties of these two classes of DNA helix have been utilized toward some remarkable constructions and applications: G-wires; nanostructures such as DNA origami; reconfigurable structures and nanodevices; the formation and utilization of hemin-utilizing DNAzymes, capable of generating varied outputs from biosensing nanostructures; composite nanostructures made up of DNA as well as inorganic materials; and the construction of nanocarriers that show promise for the therapeutics of diseases.

Cross-Linked Aptamer-Lipid Micelles for Excellent Stability and Specificity in Target-Cell Recognition

The specific binding ability of DNA-lipid micelles (DLMs) can be increased by the introduction of an aptamer. However, supramolecular micellar structures based on self-assemblies of amphiphilic DLMs are expected to demonstrate low stability when interacting with cell membranes under certain conditions, which could lead to a reduction in selectivity for targeting cancer cells. We herein report a straightforward cross-linking strategy that relies on a methacrylamide branch to link aptamer and lipid segments. By an efficient photoinduced polymerization process, covalently linked aptamer-lipid units help stabilize the micelle structure and enhance aptamer probe stability, further improving the targeting ability of the resulting nanoassembly. Besides the development of a facile cross-linking method, this study clarifies the relationship between aptamer-lipid concentration and the corresponding binding ability.

DNA quadruplexes as molecular scaffolds for controlled assembly of fluorogens with aggregation-induced emission

Aggregation-induced emission (AIE) can be generated due to the restriction of intramolecular motions. The controllable assembly of fluorogens with AIE properties (AIEgens) is able to provide a new opportunity for precise manipulation of fluorescent signal transduction. Here, a tetrapod DNA quadruplex (TP-G4) was designed as a molecular scaffold for assembly and precise modulation of light emission of an oligonucleotide-grafted fluorogen with aggregation-induced emission (Oligo-AIEgen). The Oligo-AIEgen was synthesized by attaching the AIEgen to the 3'-terminus of the oligonucleotide through a dibenzylcyclooctyne mediated coupling reaction. The AIEgen emitted no detectable fluorescence in the context of a double-stranded structure. When hybridized to the parallel-stranded TP-G4, several AIEgens were located in close proximity to generate fluorescence. The fluorescence intensity has been precisely regulated by manipulation of the spacer length between the core structure of the scaffold and AIEgen, as well as by altering the quartet number of the G-quadruplex. Similar control of fluorescence was also demonstrated using tetramolecular and bimolecular i-motif quadruplex structures as the scaffolds. These scaffolds provide a proof of concept on the manipulation of molecular interactions, which forms a universal molecular tool for the design of new biosensing strategies.

Responsive DNA G-quadruplex micelles

A novel and versatile design of DNA-lipid conjugates is presented. The assembly of the DNA headgroups into G-quadruplex structures is essential for the formation of micelles and their stability. By hybridization with a complementary oligonucleotide the micelles were destabilized, resulting in cargo release. In combination with a hairpin DNA aptamer as complementary strand, the release is obtained selectively by the presence of ATP.

Biotin-functionalized targeted polydiacetylene micelles

Polydiacetylene micelles were functionalized with controlled amounts of biotin using bioorthogonal click chemistry.

Engineering Stability-Tunable DNA Micelles Using Photocontrollable Dissociation of an Intermolecular G-Quadruplex

Because of their facile preparation, small size (<100 nm), programmable design, and biocompatibility, lipid-based DNA micelles show enormous potential as a tool to monitor biological events and treat human diseases. However, their structural stability in biological matrices suffers from spatiotemporal variability, thus limiting their in vivo use. Herein, we have engineered stability-tunable DNA micelle flares using photocontrollable dissociation of intermolecular G-quadruplexes, which confers DNA micelle flares with robust structural stability against disruption by serum albumin. However, once exposed to light, the G-quadruplex formation is blocked by strand hybridization, resulting in the loss of stability in the presence of serum albumin and subsequent cellular uptake. This programmable regulation to stabilize lipid-based micelles in the presence of fatty-acid-binding serum albumin should further the development of biocompatible DNA micelles for in vivo applications.

Aptamer micelles targeting fractalkine-expressing cancer cells in vitro and in vivo

In this work we hypothesized that the chemokine fractalkine can serve as a cancer molecular target. We engineered aptamer micelles functionalized with an outer poly(ethylene glycol) (PEG) corona, and investigated the extent and efficacy of using them as a targeting tool against fractalkine-expressing colon adenocarcinoma cells. In vitro cell binding results showed that aptamer micelles bound and internalized to fractalkine-expressing cancer cells with the majority of the micelles found free in the cytoplasm. Minimal surface binding was observed by healthy cells. Even though partial PEGylation did not prevent serum adsorption, micelles were highly resistant to endonuclease and exonuclease degradation. In vivo biodistribution studies and confocal studies demonstrated that even though both aptamer and control micelles showed tumor accumulation, only the aptamer micelles internalized into fractalkine-expressing cancer cells, thus demonstrating the potential of the approach and showing that fractalkine may serve as a specific target for nanoparticle delivery to cancer cells.

Controlling G-quadruplex formation via lipid modification of oligonucleotide sequences

G-quadruplexes (G4) represent attractive supramolecular scaffolds.