Enhancing the Sensitivity of DNA and Aptamer Probes in the Dextran/PEG Aqueous Two-Phase System

Marangoni Droplets of Dextran in PEG Solution and Its Motile Change Due to Coil-Globule Transition of Coexisting DNA

Motile droplets using Marangoni convection are attracting attention for their potential as cell-mimicking small robots. However, the motion of droplets relative to the internal and external environments that generate Marangoni convection has not been quantitatively described. In this study, we used an aqueous two-phase system [poly(ethylene glycol) (PEG) and dextran] in an elongated chamber to generate motile dextran droplets in a constant PEG concentration gradient. We demonstrated that dextran droplets move by Marangoni convection, resulting from the PEG concentration gradient and the active transport of PEG and dextran into and out of the motile dextran droplet. Furthermore, by spontaneously incorporating long DNA into the dextran droplets, we achieved cell-like motility changes controlled by coexisting environment-sensing molecules. The DNA changes its position within the droplet and motile speed in response to external conditions. In the presence of Mg2+, the coil-globule transition of DNA inside the droplet accelerates the motile speed due to the decrease in the droplet's dynamic viscosity. Globule DNA condenses at the rear part of the droplet along the convection, while coil DNA moves away from the droplet's central axis, separating the dipole convections. These results provide a blueprint for designing autonomous small robots using phase-separated droplets, which change the mobility and molecular distribution within the droplet in reaction with the environment. It will also open unexplored areas of self-assembly mechanisms through phase separation under convections, such as intracellular phase separation.

Reconfigurable aqueous 3D printing with adaptive dual locks

Using aqueous two-phase systems (ATPSs) for three-dimensional (3D) printed complex structures has attracted considerable attention in the field of biomedicine. In this study, we present an unusual approach to constructing reconfigurable 3D printed structures within an aqueous environment. Inspired by biological systems, we introduce both specific and nonspecific interactions to anchor functionalized nanoparticles to the water-water interface, thereby imparting adaptive dual locks of structural integrity and permeability to the 3D printed liquid structures. Using state-of-the-art in situ liquid-liquid interfacial atomic force microscopy imaging, we successfully demonstrate various morphologies of interfacial films formed at the ATPS interface. In addition, by incorporating d-glucose or sodium alginate into the systems, the dual locks can be easily manipulated. Our study paves a pathway for 3D printing multiresponsive all-aqueous systems with controllable structures and permeability, showing promising implications for the development of smart drug delivery systems and in vivo reactions.

Integrated phase separation in microliter droplets for ultratrace-enriching biomarker analysis

Ultratrace-enriching biomarker analysis is an effective method for achieving highly accurate and enhanced sensitive detection. In this study, we have developed an enrichment detection platform by combining a minipillar array with an aqueous two-phase system (ATPS) for ultratrace enriching biomarker analysis. After optimizing the enrichment conditions of ATPS, target miRNAs at ultratrace levels specifically accumulate in the DEX-rich phase, which significantly increases the target miRNA concentration-related fluorescence intensity. Compared to non-enriched miRNA in the single-phase PEG solution, the detection limit of ATPS-enriched miRNA had improved more than 200-fold. The ATPS-based enrichment detection strategy offers a novel and convenient approach for the simultaneous detection of biomarkers with ultratrace.

Quencher-free fluorescent assays by controlled DNA partitioning in the aqueous two-phase system with crowding-enhanced kinetics

Fluorescent DNA assays are promising in disease diagnosis, environmental monitoring, and drug screening, encompassing both heterogeneous and homogeneous assay types. Nevertheless, heterogeneous assays suffer from tedious washing steps and slow reaction kinetics, whereas homogenous assays require well-designed fluorophore pairs to modulate signal off/on. Herein, we developed a cost-effective and efficient quencher-free fluorescent DNA assay using an aqueous two-phase system (ATPS). Using a strand-displacement reaction, we showed that similar sensing performance could be achieved at a much lower cost. Furthermore, the unique crowding environment in ATPS accelerated strand-displacement reactions by up to six-fold and reduced DNA amplification time from 120 min to 30 min. Our assay demonstrated robust sensing in serum environments and successful detection of miRNA extracted from cells. This innovative assay format has the potential for biosensor development with both heterogeneous readout and rapid reaction kinetics in various applications.

Aqueous two-phase system based on pH-responsive polymeric deep eutectic solvent for efficient extraction of aromatic amino acids

Recently, more and more attention has been paid to the construction of stimulus-responsive aqueous two-phase systems (ATPSs) for the extraction and separation of various bioactive compounds. In this work, an ATPS based on a pH-responsive polymeric deep eutectic solvent (PDES) and phosphate salt was constructed for the first time. The pH-response properties of the PDES were studied through a series of experiments. Additionally, the phase formation mechanism was studied through experiments and simulations. This novel PDES-based ATPS was used to extract aromatic amino acids (AAAs). The extraction efficiencies for tyrosine (Tyr), phenylalanine (Phe), and tryptophan (Trp) reached 95.25%, 99.05%, and 99.10%, respectively. By adjusting pH, PDES was recycled and reused. This novel and recyclable PDES-based ATPS could be an efficient method for the extraction of AAAs, which could also be applied used as a versatile and sustainable method for the extraction of other bioactive compounds in the future.

A flash signal amplification approach for ultrasensitive and rapid detection of single nucleotide polymorphisms in tuberculosis

In recent years, the demand for rapid, sensitive, and simple methods for diagnosing deoxyribonucleic acid (DNA) has grown due to the increase in the variation of infectious diseases. This work aimed to develop a flash signal amplification method coupled with electrochemical detection for polymerase chain reaction (PCR)-free tuberculosis (TB) molecular diagnosis. We exploited the slightly miscible properties of butanol and water to instantly concentrate a capture probe DNA, a single-stranded mismatch DNA, and gold nanoparticles (AuNPs) to a small volume to reduce the diffusion and reaction time in the solution. In addition, the electrochemical signal was enhanced once two strands of DNA were hybridized and bound to the surface of the gold nanoparticle at an ultra-high density. To eliminate non-specific adsorption and identify mismatched DNA, the self-assembled monolayers (SAMs) and Muts proteins were sequentially modified on the working electrode. This sensitive and specific approach can detect as low as attomolar levels of DNA targets (18 aM) and is successfully applied to detecting tuberculosis-associated single nucleotide polymorphisms (SNPs) in synovial fluid. More importantly, as this biosensing strategy can amplify the signal in only a few seconds, it possesses a great potential for point-of-care and molecular diagnosis applications.

Partitioning-Induced Isolation of Analyte and Analysis via Multiscaled Aqueous Two-Phase System

Most fluorescence-based bioanalytical applications need labeling of analytes. Conventional labeling requires washing to remove the excess fluorescent labels and reduce the noise signals. These pretreatments are labor intensive and need specialized equipment, hindering portable applications in resource-limited areas. Herein, we use the aqueous two-phase system (ATPS) to realize the partitioning-induced isolation of labeled analytes from background signals without extra processing steps. ATPS is formed by mixing two polymers at sufficiently high concentrations. ATPS-based isolation is driven by intrinsic affinity differences between analytes and excess labels. To demonstrate the partitioning-induced isolation and analysis, fluorescein isothiocyanate (FITC) is selected as the interfering fluorophore, and a monoclonal antibody (IgG) is used as the analyte. To optimize ATPS compositions, different molecular weights and mass fractions of polyethylene glycol (PEG) and dextran and different phosphate-buffered saline (PBS) concentrations are investigated. Various operational scales of our approach are demonstrated, suggesting its compatibility with various bioanalytical applications. In centimeter-scale ATPS, the optimized distribution ratios of IgG and FITC are 91.682 and 0.998 using PEG 6000 Da and dextran 10,000 Da in 10 mM PBS. In millimeter-scale ATPS, the analyte is enriched to 6.067 fold using 15 wt % PEG 35,000 Da and 5 wt % dextran 500,000 Da in 10 mM PBS. In microscale ATPS, analyte dilutions are isolated into picoliter droplets, and the measured fluorescence intensities linearly correlated with the analyte concentrations (R² = 0.982).

Up/Down Tuning of Poly(ionic liquid)s in Aqueous Two-Phase Systems

Thermally induced reversible up/down migration of poly(ionic liquid)s (PILs) in aqueous two-phase systems (ATPSs) was achieved for the first time in this study. Novel ATPSs were fabricated using azobenzene (Azo)- and benzyl (Bn)-modified PILs, and their upper and lower phases could be easily tuned using the grafting degree (GD) of the Azo and Bn groups. Bn-PIL with higher GD_Bn could go up into the upper phase and Azo-PIL come down to the lower phase when the temperature increased (>65 °C); this behavior was reversed at lower temperatures. Moreover, a reversible two-phase/single-phase transition was realized under UV irradiation. Experimental and simulation results revealed that the difference in the hydration capacity between Bn-PIL and Azo-PIL accounted for their unique phase-separation behavior. A versatile platform for fabricating ATPSs with tunable stimuli-responsive behavior can be realized based on our findings, which can broaden their applications in the fields of smart separation systems and functional material development.

Computable structured aptamer for targeted treatment of ovarian cancer

Nucleolin protein expression is higher on the ovarian cancer cell surface. AS1411, a DNA aptamer, can bind with nucleolin protein specifically. In this study, we developed HA and ST DNA tiles to assemble six AS1411 aptamers to deliver doxorubicin. In addition, to superior serum stability and drug loading, HA-6AS and ST-6AS outperformed TDN-AS in cellular uptake. HA-6AS and ST-6AS exhibited satisfactory targeted cytotoxicity and achieved resounding lysosomal escape. Moreover, when injected into nude mice subcutaneous xenograft models, HA-6AS reached the peak in tumor more quickly than ST-6AS, and better expressed the active targeting ability of AS1411. Our study suggests that designing appropriate DNA tiles to assemble different aptamers to deliver different chemotherapeutic drugs is a promising treatment for ovarian cancer.

DNA nanotubes in coacervate microdroplets as biomimetic cytoskeletons modulate the liquid fluidic properties of protocells

Coacervate microdroplets, formed via liquid-liquid phase separation, have been proposed as a compartment model for the construction of artificial cells or organelles. However, these microsystems are very fragile and demonstrate liquid-like fluidity. Here, an artificial cytoskeleton based on DNA nanotubes was constructed in coacervate microdroplets to modulate the liquid fluidic properties of the microdroplets. The coacervate microdroplets were obtained from the association of oppositely charged polyelectrolytes through liquid-liquid phase separation, and DNA nanotubes were constructed by molecular tile self-assembly from six clip sequences. The DNA nanotubes were efficiently sequestered in the liquid coacervate microdroplets, and the rigid structure of the DNA nanotubes was capable of modulating the liquid fluidic properties of the coacervate protocell models, as indicated by coalescence imaging and atomic force microscopy analysis. Therefore, artificial cytoskeletons made from DNA nanotubes worked in modulating the liquid fluidic properties of coacervate microdroplets, in a manner akin to the cytoskeleton in the cell. DNA cytoskeletons have the potential to become an ideal platform with which how the liquid fluidic properties of cells are modulated by their cytoskeletons can be investigated, and the cell-sized coacervate microdroplets containing artificial cytoskeletons might be critical in developing a stable liquid-phase protocell model.

Electrochemical Aptamer Biosensor Based on ATP-Induced 2D DNA Structure Switching for Rapid and Ultrasensitive Detection of ATP

Herein, a two-dimensional (2D) DNA structure with multiple ATP aptamers was elegantly designed to establish an electrochemical biosensor for rapid and sensitive detection of ATP based on ATP-induced structure switching. Concretely, the prepared 2D DNA structure containing numerous ATP aptamers as ATP-specific toehold switches could not only immobilize a large number of methylene blue (MB) for generating a remarkable electrochemical signal, but also greatly increase the local concentration of ATP aptamers to obviously enhance the capture efficiency of ATP. Once the target ATP interacted with the toehold switches, the 2D DNA structure could be sharply collapsed to trigger the burst release of MB from the electrode surface, ultimately resulting in a significantly decreased electrochemical signal for ultrasensitive detection of target ATP over a short period of time. Impressively, by dexterously adjusting the length of the ATP-specific toehold switches to 15-base, optimization of the binding affinity between ATP and the toehold switches was achieved for cutting down the detection time to 30 min and achieving a low detection limit of 0.3 pM, which addressed the shortcoming of time-consuming and poor sensitivity in the previous sensors with a small quantity of ATP aptamers and deficient binding affinity to ATP. Consequently, this strategy opened a promising avenue for ultrasensitive and rapid detection of various biomolecules in biomedical application and disease diagnosis.

β-Cyclodextrin Polymer-Based Host-Guest Interaction and Fluorescence Enhancement of Pyrene for Sensitive Isocarbophos Detection

The extensive use of organophosphorus pesticides in agriculture poses a high risk to human health and has boosted the demands for developing sensitive monitoring methods. Herein, we developed a facile and sensitive method for isocarbophos detection based on the remarkable fluorescence enhancement of pyrene during host-guest interaction of β-cyclodextrin polymer (β-CDP) and pyrene. The 3'-pyrene-labeled isocarbophos aptamer could be cleaved by exonuclease I to obtain free pyrene that was tagged on mononucleotides, which could enter the hydrophobic cavity of β-CDP, resulting in a prominent fluorescence enhancement. While the target isocarbophos was added, aptamer could undergo a conformational change into a hairpin complex, which prevented the cleavage and host-guest interaction because of the steric hindrance, leading to a weak fluorescence. The isocarbophos has been sensitively and selectively analyzed by detecting the system fluorescence intensity with a detection limit as low as 1.2 μg/L. In addition, we have verified the ability of our proposed method in real sample detection from fruit extract.

Microfluidic Control of Coexisting Chemical Microenvironments within Multiphase Water-in-Fluorocarbon Droplets

The use of aqueous polymer-based phase separation within water-in-oil emulsion droplets provides a powerful platform for exploring the impact of compartmentalization and preferential partitioning on biologically relevant solutes. By forming an emulsion, a bulk solution is converted into a large number of chemically isolated microscale droplets. Microfluidic techniques provide an additional level of control over the formation of such systems. This enables the selective production of multiphase droplets with desired solution compositions and specific characteristics, such as solute partitioning. Here, we demonstrate control over the chemical microenvironment by adjusting the composition to increase tie line length for poly(ethylene glycol) (PEG)-dextran aqueous two-phase systems (ATPS) encapsulated within multiphase water-in-fluorocarbon oil emulsion droplets. Through rational adjustment of microfluidic parameters alone, ATPS droplets containing differing compositions could be produced during the course of a single experiment, with the produced droplets demonstrating a controllable range of tie line lengths. This provided control over partitioning behavior for biologically relevant macromolecules such that the difference in local protein concentration between adjacent phases could be rationally tuned. This work illustrates a broadly applicable technique to rationally create emulsified multiphase aqueous systems of desired compositions through the adjustment of microfluidic parameters alone, allowing for easy and rapid screening of various chemical microenvironments.

Ultrafast Ratiometric Detection of Aflatoxin B1 Based on Fluorescent β-CD@Cu Nanoparticles and Pt2+ Ions

Rapid detection of aflatoxin B1 (AFB1) is a very important task in food safety monitoring. However, it is still challenging to achieve highly sensitive detection without antibody or aptamer biomolecules. In this work, a rapid detection of aflatoxin B1 was achieved using a ratiometric fluorescence probe without antibody or aptamer for the first time. In the ratiometric fluorescence system, the fluorescence emission of AFB1 at 433 nm was significantly enhanced due to the β-cyclodextrin-AFB1 host-guest interaction and the complexation of AFB1 and Pt²⁺. Meanwhile, the inclusion of aflatoxin B1 also quenched the fluorescence emission of β-CD@Cu nanoparticles (NPs) at 650 nm based on inner filter effect mechanism. On the basis of the above effects, the ratiometric detection of aflatoxin B1 was achieved in the range of 0.03-10 ng/mL with a low detection limit of 0.012 ng/mL (3σ/s). In addition, the β-CD@Cu NPs based nanoprobe could achieve stable response within 1 min to AFB1. The above ratiometric detection also demonstrated excellent application potential in the rapid on-site detection of AFB1 in food due to the advantages of convenience, rapidness, and high accuracy.

Modulation of DNAzyme Activity via Butanol Dehydration

Understanding the activity of biomolecules in cosolvent systems is important for catalysis, separation and developing biosensors. The majority of previously studied solvents are either phase separated with water or miscible with water. Butanol was recently used to extract water for the conjugation of DNA to gold nanoparticles. In this work, the effect of butanol on the activity of a few RNA-cleaving DNAzymes was studied. A 130-fold improvement in sensitivity for the Na⁺ -specific EtNa DNAzyme was observed, and butanol also improved the activity of another Na⁺ -specific DNAzyme, NaA43T by a few folds. However, when divalent metal ions were used for both EtNa and 17E DNAzymes, the activity was inhibited. A main driven force for enhanced DNAzyme activity is the concentration effect due to butanol dehydration. This study provides insights into the interplay between DNA, metal ions and organic solvents, and such an understanding might be useful for developing sensitive biosensors.