DNA Micelles Research Articles

Localized hybridization chain reaction amplifier utilizing three-dimensional DNA nanostructures for efficient and reliable microRNA imaging in living cells

MicroRNAs (miRNAs) are pivotal in regulating biological processes such as cell proliferation and disease progression. Traditional miRNA detection methods like qRT-PCR and Northern blotting do not allow for monitoring dynamic changes in living cells and typically require invasive sample collection. This research presents a robust, non-enzymatic technique known as the Localized Hybridization Chain Reaction Amplifier (LHCRA), designed for real-time, in vivo miRNA imaging. This method addresses these limitations by providing rapid and sensitive detection of miRNAs, crucial for progressing clinical diagnostics and research. The LHCRA utilizes hairpin chain reaction probes embedded within self-assembled DNA micelles (DM), significantly amplifying miRNA signals. LHCRA demonstrated exceptional performance, with a detection limit of 100 pM and a response time of 10 min. Importantly, it effectively differentiated between cancerous and normal cells using clinical peripheral blood samples, showcasing high specificity and stability under physiological conditions. Additionally, LHCRA maintained consistent performance in complex biological media, including 10 % serum and 2 U/mL DNase I, confirming its broad applicability in various diagnostic scenarios. This performance highlights LHCRA's potential as a transformative tool in miRNA-based diagnostics. The introduction of LHCRA marks a significant advancement in miRNA detection technology. By enabling accurate, non-invasive, and real-time monitoring of miRNA dynamics within living cells, this method offers substantial potential to enhance diagnostic accuracy and deepen our understanding of disease mechanisms, particularly in cancer. Thus, it could greatly improve therapeutic strategies and patient outcomes in clinical environment.

Enzymatic interlocking aptamer-micelles for enhanced cellular internalization and nucleus-targeted cancer phototherapy

Multifunctional micelles that permit both diagnosis and treatment present enormous advantage and potential for precision medicine. However, the inherent complexities and structural instability of these systems often cause unsatisfactory targeting and therapeutic performances. Herein, by ingenious design of a 2,5-bis(2-thienyl)pyrrole (SNS) modifier to covalently link with AS1411 aptamer and lipid segment, a simple strategy is proposed for one-step enzymatic preparation of interlocked aptamer-micelle (IApM) under bio-friendly conditions. The interlocked poly(SNS) skeleton in IApM can not only stabilize the micelle structure but also enhance near-infrared (NIR) absorption ability, thus further enhancing cellular internalization and photothermal therapy. In addition, the multivalent AS1411 aptamers tethered in the hydrophilic shell can simultaneously increase the specific binding affinity of DNA micelles and induce nucleus-targeted accumulation for DNA damage-triggered apoptosis. This DNA micelle achieves “best of both worlds” with enhanced biostability for cellular internalization and improved NIR photothermal conversion efficiency for nucleus-targeted therapy, which provides a promising formulation strategy for precision cancer treatment.

Determining the Role of Surfactant on the Cytosolic Delivery of DNA Cross-Linked Micelles.

Nucleic Acid Nanocapsules (NANs) are nucleic acid nanostructures that radially display oligonucleotides on the surface of cross-linked surfactant micelles. Their chemical makeup affords the stimuli-responsive release of therapeutically active DNA-surfactant conjugates into the cells. While NANs have so far demonstrated the effective cytosolic delivery of their nucleic acid cargo, as seen indirectly by their gene regulation capabilities, there remain gaps in the molecular understanding of how this process happens. Herein, we examine the enzymatic degradation of NANs and confirm the identity of the DNA-surfactant conjugates formed by using mass spectrometry (MS). With surface enhanced (resonance) Raman spectroscopy (SE(R)RS), we also provide evidence that the energy-independent translocation of such DNA-surfactant conjugates is contingent upon their release from the NAN structure, which, when intact, otherwise buries the hydrophobic surfactant tail in its interior. Such information suggests a critical role of the surfactant in the lipid disruption capability of the DNA surfactant conjugates generated from degradation of the NANs. Using NANs made with different tail lengths (C12 and C10), we show that this mechanism likely holds true despite significant differences in the physical properties (i.e., critical micelle concentration (CMC), surfactants per micelle, Nagg) of the resultant particles (C12 and C10 NANs). While the total cellular uptake efficiencies of C12 and C10 NANs are similar, there were differences observed in their cellular distribution and localized trafficking, even after ensuring that the total concentration of DNA was the same for both particles. Ultimately, C10 NANs appeared less diffuse within cells and colocalized less with lysosomes over time, achieving more significant knockdown of the target gene investigated, suggesting more effective endosomal escape. These differences indicate that the surfactant assembly and disassembly properties, including the number of surfactants per particle and the CMC can have important implications for the cellular delivery efficacy of DNA micelles and surfactant conjugates.

Plasmonic nano-bowls for monitoring intra-membrane changes in liposomes, and DNA-based nanocarriers in suspension.

Programmable nanoscale carriers, such as liposomes and DNA, are readily being explored for personalized medicine or disease prediction and diagnostics. The characterization of these nanocarriers is limited and challenging due to their complex chemical composition. Here, we demonstrate the utilization of surface-enhanced Raman spectroscopy (SERS), which provides a unique molecular fingerprint of the analytes while reducing the detection limit. In this paper, we utilize a silver coated nano-bowl shaped polydimethylsiloxane (PDMS) SERS substrate. The utilization of nano-bowl surface topology enabled the passive trapping of particles by reducing mobility, which results in reproducible SERS signal enhancement. The biological nanoparticles' dwell time in the nano-trap was in the order of minutes, thus allowing SERS spectra to remain in their natural aqueous medium without the need for drying. First, the geometry of the nano-traps was designed considering nanosized bioparticles of 50-150 nm diameter. Further, the systematic investigation of maximum SERS activity was performed using rhodamine 6 G as a probe molecule. The potential of the optimized SERS nano-bowl is shown through distinct spectral features following surface- (polyethylene glycol) and bilayer- (cholesterol) modification of empty liposomes of around 140 nm diameter. Apart from liposomes, the characterization of the highly crosslinked DNA specimens of only 60 nm in diameter was performed. The modification of DNA gel by liposome coating exhibited unique signatures for nitrogenous bases, sugar, and phosphate groups. Further, the unique sensitivity of the proposed SERS substrate displayed distinct spectral signatures for DNA micelles and drug-loaded DNA micelles, carrying valuable information to monitor drug release. In conclusion, the findings of the spectral signatures of a wide range of molecular complexes and chemical morphology of intra-membranes in their natural state highlight the possibilities of using SERS as a sensitive and instantaneous characterization alternative.

3D dynamic DNA walker traveling on DNA micelles coupled CRISPR-Cas12a nucleases to recover electrochemiluminescence signal for microcystin-LR detection

3D dynamic DNA walker traveling on DNA micelles coupled CRISPR-Cas12a nucleases sensor was proposed to recover electrochemiluminescence (ECL) signal for microcystin-LR (MC-LR) detection. The 3D DNA walker was anchored in DNA micelles, self-assembled from amphiphilic DNA by the hydrophobicity of cholesterol and the electrostatic repulsion of the phosphate backbone. By the MC-LR stimulus, the released swing arm DNA hybridized with the track DNA while cleaving the hairpin structure to obtain the track DNA fragments. The track DNA fragments hybridized with the H1 hairpin structure to form a double-helix structure with PAM sequences, which could activate the Cas12a nucleases for trans-cleavage of the Fc probe-labeled ssDNA to induce ECL signal recovery. The DNA micelles maintained the morphological stability and free diffusion ability of the 3D DNA walker in the biofluidic state and overcome the collisional hindrance for facilitating efficient intraparticle and interparticle walking motions. Meanwhile, the coupled trans-cleavage activity of Cas12a nucleases improved the signal-amplification performance and achieved higher sensitivity with a detection limit of 0.015 pM. Acceptable results confirmed the ability of DNA micelles to stabilize 3D DNA walkers and the validated cleavage activity of Cas12a nucleases.

Controlled Release of a Dual Zinc-sensing and Gene Regulating Small Molecule from DNA Micelles.

Intracellular zinc ions are essential for various biological cell processes and are often dysregulated in many diseases de-pending on their location, protein binding affinity, and concentration in the cell. Due to their prevalence in diseases, it is important to not only effectively sense but chelate the often excess amount of zinc in a cell to alleviate further disease progression. N, N, N', N'-tetrakis (2-pyridinylmethyl)-1,2-ethanediamine (TPEN) is a selective zinc chelator but its water-insoluble nature and general cytotoxicity limit its therapeutic potential. To address these challenges, TPEN loaded nucleic acid nanocapsules (TL-NANs) were synthesized, and its dual ability to sense and suppress zinc levels intracellularly were evaluated. Additionally, TL-NANs were incubated in lung cells and shown to down regulate Eotaxin, a protein up-regulated during asthma, at significantly reduced concentrations of TPEN showcasing the potential therapeutic potential of this drug for asthma.

Suppression of Lung Cancer Malignancy by Micellized siRNA through Cell Cycle Arrest (Adv. Healthcare Mater. 11/2023)

Gene Therapy In article 2202358, Minseok Kwak, Peter Chang-Whan Lee, and co-workers show effective tumor suppression using RNAi with just three DNA and RNA strands. This transfection reagent-free technique self-assembles siRNAs and covers DNA micelles to create nanomedicine for lung cancer. Raw data files are used to create a montage background, recognizing the work of graduate students.

A General Signal Amplifier of Self-Assembled DNA Micelles for Sensitive Quantification of Biomarkers.

Owing to the excellent structural rigidity and programmable reaction sites, DNA nanostructures are more and more widely used, but they are limited by high cost, strict sequence requirements, and time-consuming preparation. Herein, a general signal amplifier based on a micelle-supported entropy-driven circuit (MEDC) was designed and prepared for sensitive quantification of biomarkers. By modifying a hydrophobic cholesterol molecule onto a hydrophilic DNA strand, the amphiphilic DNA strand was first prepared and then self-assembled into DNA micelles (DMs) driven by hydrophobic effects. The as-developed DM showed unique advantages of sequence-independence, easy preparation, and low cost. Subsequently, amplifier units DMF and DMTD were successfully fabricated by connecting fuel strands and three-strand duplexes (TDs) to DMs, respectively. Finally, the MEDC was triggered by microRNA-155 (miR-155), which herein acted as a model analyte, resulting in dynamic self-assembly of poly-DNA micelles (PDMs) and causing the recovery of cyanine 3 (Cy3) fluorescence as the DMTD dissociated. Benefiting from the "diffusion effect", the MEDC herein had a nearly 2.9-fold increase in sensitivity and a nearly 97-fold reduction in detection limit compared to conventional EDC. This amplifier exhibited excellent sensitivity of microRNAs, such as miR-155 detection in a dynamic range from 0.05 to 4 nM with a detection limit of 3.1 pM, and demonstrated outstanding selectivity with the distinguishing ability of a single-base mismatched sequence of microRNAs. Overall, the proposed strategy demonstrated that this sequence-independent DNA nanostructure improved the performance of traditional DNA probes and provided a versatile method for the development of DNA nanotechnology in biosensing.

Polymyxin B stabilized DNA micelles for sustained antibacterial and antibiofilm activity against P. aeruginosa.

Nucleic acid-based materials showcase an increasing potential for antimicrobial drug delivery. Although numerous reports on drug-loaded DNA nanoparticles outline their pivotal antibacterial activities, their potential as drug delivery systems against bacterial biofilms awaits further studies. Among different oligonucleotide structures, micellar nanocarriers derived from amphiphilic DNA strands are of particular interest due to their spontaneous self-assembly and high biocompatibility. However, their clinical use is hampered by structural instability upon cation depletion. In this work, we used a cationic amphiphilic antibiotic (polymyxin B) to stabilize DNA micelles destined to penetrate P. aeruginosa biofilms and exhibit antibacterial/antibiofilm properties. Our study highlights how the strong affinity of this antibiotic enhances the stability of the micelles and confirms that antibacterial activity of the novel micelles remains intact. Additionally, we show that PMB micelles can penetrate P. aeruginosa biofilms and impact their metabolic activity. Finally, PMB micelles were highly safe and biocompatible, highlighting their possible application against P. aeruginosa biofilm-colonized skin wounds.

DNA micelle-templated copper nanoclusters for fluorescent imaging of MUC1-positive cancer cells.

DNA micelles formed by hydrophobic, self-assembly of amphiphilic DNA monomers have enormous potential in biological imaging owing to its unique and programmable, three-dimensional nanostructure. Herein, we rationally design double-stranded DNA oligonucleotides with two cholesterols that can spontaneously form the lipid-mediated DNA micelles and generate the high fluorescence signal after the formation of DNA-templated copper nanoclusters (CuNCs). Furthermore, the DNA aptamer specific to MUC1 protein, aberrantly overexpressed on the surface of cancer cells, is attached to lipid-mediated DNA micelles to confer the selectivity towards the target cancer cells. With the well-defined DNA nanostructures, the cell membrane of MUC1-positive cancer cells are stained by CuNCs exhibiting an intense, red fluorescence signal, which are clearly distinguished from MUC1-negative cancer cells. This approach may not only expand the application scope of both DNA micells and CuNCs, especially in the area of cellular imaging, but also provides a basis for developing other types of DNA nanostructures to detect target biomarkers.

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.

Multi-layered stimuli responsive DNA micelles for the stepwise controlled release of small molecules.

Controllable release of multiple distinct cargoes from a nanomaterial is crucial to a variety of therapeutic and catalytic applications. In this study, we describe a DNA functionalized multi-layered surface crosslinked micelle (mlSCM) consisting of individually degradable layers. The DNA modified mlSCM has the ability to encapsulate separate small molecule cargo in distinct compartments within the nanocapsule, separated by chemical crosslinkers. Through a multistep self-assembly process, we show physical separation of internalized cargo as evidenced by electron microscopy, along with observation of chemical control over release, and chemical reaction conditions, as seen by fluorescence spectroscopy and a high-performance liquid chromatography mass spectrometry assay. Additionally, we evaluated the ability of these DNA crosslinked micelles to co-release two separate cargoes into the same cellular environment through an in vitro confocal microscopy assay. We show individualized targeting of two distinct but related dyes for the detection of ATP and mitochondria. The colocalization of these dyes indicates that unique locations and signals related to cellular respiration can be identified using a single mlSCM. Through these studies we ultimately show that the mlSCM has a tailorable design with the potential to be applied to numerous applications, ranging from sensing to drug delivery.

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.

Phototheranostic DNA micelles from the self-assembly of DNA-BODIPY amphiphiles for the thermal ablation of cancer cells.

Design of phototheranostic agents in a single step approach is one of the challenges in cancer therapy. Herein, a one-step strategy based on amphiphilicity-driven self-assembly of DNA-BODIPY amphiphiles for the design of a new class of micelles, which offer all three phototheranostic functions, is reported. These include (i) strong emission at NIR (φf = 30%) for imaging, (ii) high photothermal conversion (η = 52%) for PTT and (iii) an ssDNA-based shell for the integration of cell targeting moieties. Selective uptake of DNA micelles into a target cancer cell and its killing by laser irradiation (635 nm) are also demonstrated. Furthermore, the excellent biocompatibility, ultrasmall nanosize and high stability of DNA micelles are promising for in vivo applications.

Rapid self-disassembly of DNA diblock copolymer micelles via target induced hydrophilic-hydrophobic regulation for sensitive MiRNA detection.

In this work, a novel DNA nanostructure with a shorter assembly time and larger loading capacity was constructed using amphiphilic DNA-alkane group (Spacer C12)10 conjugates encapsulating plentiful fat-soluble fluorescent dyes into the hydrophobic core to form the DNA micelles, which could be rapidly self-disassembled via target induced hydrophilic-hydrophobic regulation to release fluorescent dyes from micelles to the organic phase, realizing the fast and sensitive detection of microRNA.

Spherically Directed Synthesis and Enhanced Cellular Internalization of Metal-Crosslinked DNA Micelles

Using spherically directed reduction of metal ions, a facile and universal method for in situ crosslinking of DNA micelles is described. By incorporating a series of specific template domains into lipid-DNA monomers, copper-, silver-, and gold-crosslinked DNA micelles are formed. By combining characterization results and simulation algorithms, accurate structural profiling of DNA micelles is achieved for the first time. The prepared metal-crosslinked DNA micelles show obvious merits, including one-step formation of core structure and ligand corona, facile size tunability, monodispersity, stability against salt-induced aggregation, high utilization of DNA ligand, mild synthesis conditions, and less time consumption and better internalization. Based on our spherically directed synthesis, metal-crosslinked DNA micelle flares were further prepared for effective intracellular imaging by integrating an aptamer-toehold strategy. In addition, we extended the strategy to cholesterol-based double-stranded DNA micelles, giving strong evidence that our method is not only universal but also flexible.

Block Copolymer/Plasmid DNA Micelles Postmodified with Functional Peptides via Thiol-Maleimide Conjugation for Efficient Gene Delivery into Plants.

Introducing exogenous genes into plant cells is essential for a wide range of applications in agriculture and plant biotechnology fields. Cationic peptide carriers with cell-penetrating and DNA-binding domains successfully deliver exogenous genes into plants. However, their cell-penetrating activity may be attenuated by undesired electrostatic interactions between the cell-penetrating peptide (CPP) domain and DNA cargo, resulting in limited gene delivery efficiency. Here, we developed the block copolymer maleimide-conjugated tetra(ethylene glycol) and poly(l-lysine) (MAL-TEG-PLL). Through electrostatic interactions with plasmid DNA (pDNA), MAL-TEG-PLL formed a micelle that presented maleimide groups on its surface. The micelle enabled postmodification with cysteine-containing functional peptides, including a CPP (BP100-Cys) and nuclear localization signal (Cys-NLS) via thiol-maleimide conjugation, thereby avoiding undesired interactions. According to a comparison of gene delivery efficiencies among the peptide-postmodified micelles, the amount of BP100-Cys on the micelle surface was key for efficient gene delivery. The BP100-postmodified micelle showed more efficient delivery compared with that of the BP100-premodified micelle. Thus, postmodification of polymeric micelles with functional peptides opens the door to designing highly efficient plant gene delivery systems.

Fluorinated DNA Micelles: Synthesis and Properties.

Creating new functional building blocks that expand the versatility of nanostructures depends on bottom-up self-assembly of amphiphilic biomolecules. Inspired by the unique physicochemical properties of hydrophobic perfluorocarbons, coupled with the powerful functions of nucleic acids, we herein report the synthesis of a series of diperfluorodecyl-DNA conjugates (PF-DNA) which can efficiently self-assemble into micelles in aqueous solution. On the basis of the micelle structure, both target binding affinity and enzymatic resistance of the DNA probe can be enhanced. In addition, based on the hydrophobic effect, the PF-DNA micelles (PFDM) can actively anchor onto the cell membrane, offering a promising tool for cell-surface engineering. Finally, the PFDM can enter cells, which is significant for designing carriers for intracellular delivery. The combined advantages of the DNA micelle structure and the unique physicochemical properties of perfluorocarbons make these PFDM promising for applications in bioimaging and biomedicine.

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.

Model studies on the interactions of a Cu(II)-quinone complex with surfactant micelles and DNA explore its induction of apoptosis in human MDA-MB-231 breast adenocarcinoma cells

The interactions of copper complex (CuQ2) of 1-amino-4-hydroxy-9,10-anthraquinone (QH) with calf thymus DNA, anionic surfactant sodium dodecyl sulfate (SDS), and cationic surfactant cetyltrimethylammonium bromide (CTAB) were investigated in an aqueous solution at physiological pH (7.4). Affinities of such molecule to DNA and surfactant micelles, a model for a biological membrane, are important in determining its biological action. Using different models, various binding parameters were evaluated in both of molecule–DNA interaction and molecule–surfactant interaction. The study showed that hydrophobic interaction plays a major role in the binding of CuQ2 to surfactant micelles. In addition, the hydrophobic interaction has an important role in the distribution of CuQ2 between micelle-water phases. Gibbs free energy for the binding and distribution of CuQ2 between the bulk aqueous medium and surfactant micelles were calculated. In order to correlate the physicochemical properties deciphered from the aforementioned studies with the biological property of the molecule, CuQ2 was treated with MDA-MB-231 breast adenocarcinoma cells where it was found that the molecule affects the viability of the cancer cells. Fluorescent staining of the treated cells with AO/EB and Hoechst indicated that the CuQ2 induces apoptosis, suggesting its use in the treatment of breast cancer.