A Telomerase-Assisted Strategy for Regeneration of DNA Nanomachines in Living Cells

DNA nanomachines have been engineered into diverse personalized devices for diagnostic imaging of biomarkers; however, the regeneration of DNA nanomachines in living cells remains challenging. Here, we report an ingenious DNA nanomachine that can implement telomerase (TE)-activated regeneration in living cells. Upon apurinic/apyrimidinic endonuclease 1 (APE1)-responsive initiation of the nanomachine, the walker of the nanomachine moves along tracks regenerated by TE, generating multiply amplified signals through which APE1 can be imaged in situ. Additionally, augmentation of the signal due to the regeneration of the nanomachines could reveal differential expression of TE in different cell lines. To the best of our knowledge, this is the first proof-of-concept demonstration of the use of biomarkers to assist in the regeneration of nanomachines in living cells. This study offers a new paradigm for the development of more applicable and efficient DNA nanomachines.

Simultaneous detection of foodborne pathogenic bacteria in milk by fluorescence immunoassay

Rapid, sensitive and simultaneous detection of multiple bacteria in foodborne is still a major challenge in public health field. Here, a fluorescence immunoassay that can achieve high-throughput detection of three Gram-positive foodborne pathogenic bacteria simultaneously was proposed. Vancomycin and bovine serum albumin conjugate (Van-BSA) was immobilized on a polycarbonate chip to capture three Gram-positive foodborne pathogenic bacteria, Staphylococcus aureus (S. aureus), Bacillus cereus (B. cereus) and Listeria monocytogenes (L. monocytogenes). CdSe/ZnS quantum dot modified antibodies (Ab-QD) were prepared by carbodiimide coupling chemistry. Due to the affinity reaction between antibodies and proteins on the bacterial surface, the simultaneous detection of multiple Gram-positive bacteria was achieved by monitoring the fluorescence signal of quantum dot by a portable microfluidic chip analyzer. Under optimal conditions, low detection limits was 18 CFU/well, 3 CFU/well and 36 CFU/well for S. aureus, B. cereus and L. monocytogenes, respectively. With satisfactory accuracy and precision, the proposed fluorescence immunoassay holds good prospects to detect pathogens in real food samples.

Highly Efficient Quadruped DNA Walker Guided by Ordered DNA Tracks for Rapid and Ultrasensitive Electrochemical Detection of miRNA-21

Herein, a long period liner DNA tandem (Lr-DNT) was intelligently designed as DNA track for quadruped DNA walker (q-walker) to run in an orderly and efficient manner, which could be applied to construct an electrochemical biosensor for rapid and ultrasensitive detection of microRNA-21 (miRNA-21). Impressively, benefiting from the orderliness and equidistance of Lr-DNT, the q-walker could be endowed with a high controllability, directionality as well as a quite short reaction time down to 20 min compared with those of traditional DNA walkers walked on the stochastic tracks. Once the target miRNA-21 interacted with the locked q-walker, the q-walker could be activated to expeditiously cleave Lr-DNT for releasing amounts of signal probes ferrocene (Fc) with the assistance of the Nt.BbvCI enzyme. This way, the developed q-walker could not only readily overcome the problem of low reaction efficiency but also address the drawback of time consumption in a previous strategy. As a proof of concept, the prepared biosensor could accomplish sensitive detection of target miRNA-21 with a detection limit down to 31 aM. As a result, this tactic gave impetus to design high-performance sensing platform with ultimate application in clinical sample analysis and nucleic acid based cancer diagnostics.

Spatially Resolved, Error-Robust Multiplexed MicroRNA Profiling in Single Living Cells

Simultaneous imaging of multiple microRNAs (miRNAs) in individual living cells is challenging due to the lack of spectrally distinct encoded fluorophores and non-cytotoxic methods. We describe a multiplexed error-robust combinatorial fluorescent label-encoding method, termed fluorophores encoded error-corrected labels (FluoELs), enabling multiplexed miRNA imaging in living cells with error-correcting capability. The FluoELs comprise proportional dual fluorophores for encoding and a constant quantitative single fluorophore for error-corrected quantification. Both are embedded in 260 nm core-shell silica nanoparticles modified with molecular beacon detection probes. The FluoELs are low cytotoxic and could accurately quantify and spatially resolve nine breast-cancer-related miRNAs and evaluate their coordination. The FluoELs enabled a single-cell analysis platform to evaluate miRNA expression profiles and the molecular mechanisms underlying miRNA-associated diseases.

Droplet microfluidics on analysis of pathogenic microbes for wastewater-based epidemiology

Infectious diseases caused by pathogenic microbes have posed a major health issue for the public, such as the ongoing COVID-19 global pandemic. In recent years, wastewater-based epidemiology (WBE) is emerging as an effective and unbiased method for monitoring public health. Despite its increasing importance, the advancement of WBE requires more competent and streamlined analytical platforms. Herein we discuss the interactions between WBE and droplet microfluidics, focusing on the analysis of pathogens in droplets, which is hard to be tackled by traditional analytical tools. We highlight research works from three aspects, namely, quantitation of pathogen biomarkers in droplets, single-cell analysis in droplets, and living cell biosensors in droplets, as well as providing future perspectives on the synergy between WBE and droplet microfluidics.

A DNA Molecular Robot that Autonomously Walks on the Cell Membrane to Drive Cell Motility

Synthetic molecular robots can execute sophisticated molecular tasks at nanometer resolution. However, a molecular robot capable of controlling cellular behavior remains unexplored. Herein, we report a self-propelled DNA robot operating on the cell membrane to control the migration of a cell. Driven by DNAzyme catalytic activity, the DNA robot could autonomously and stepwise move on the membrane-floating cell-surface receptors in a stochastic manner and simultaneously trigger the receptor-dimerization to activate downstream signaling for cell motility. The cell membrane-associated continuous motion and operation of a DNA robot allowed for the ultrasensitive regulation of MET/AKT signaling and cytoskeleton remodeling to enhance cell migration. Finally, we designed distinct conditional DNA robots to orthogonally manipulate the cell migration in a coculture of mixed cell populations. We have developed a novel strategy to engineer a cell-driving molecular robot, representing a promising avenue for precise cell manipulation with nanoscale resolution.

Flap Endonuclease 1-Assisted DNA Walkers for Sensitively and Specifically Sensing ctDNAs

DNA walkers have shown superior performance in biosensing due to their programmability to design molecular walking behaviors with specific responses to different biological targets. However, it is still challenging to make DNA walkers capable of distinguishing DNA targets with single-base differences, so that DNA walkers that can be used for circulating tumor DNA sensing are rarely reported. Herein, a flap endonuclease 1 (FEN 1)-assisted DNA walker has been proposed to achieve mutant biosensing. The target DNA is captured on a gold nanoparticle (AuNP) as a walking strand to walk by hybridizing to the track strands on the surface of the AuNP. FEN 1 is employed to report the walking events by cleaving the track strands that must form a three-base overlapping structure recognized by FEN 1 after hybridizing with the captured target DNA. Owing to the high specificity of FEN 1 for structure recognition, the one-base mutant DNA target can be discriminated from wild-type DNA. By constructing a sensitivity-enhanced DNA walker system, as low as 1 fM DNA targets and 0.1% mutation abundance can be sensed, and the theoretical detection limits for detecting the DNA target and mutation abundance achieve 0.22 fM and 0.01%, respectively. The results of epidermal growth factor receptor (EGFR) L858R mutation detection on cell-free DNA samples from 15 patients with nonsmall cell lung cancer were completely consistent with that of next-generation sequencing, indicating that our DNA walker has potential for liquid biopsy.

DNA pom-pom nanostructure as a multifunctional platform for pathogenic bacteria determination and inactivation

Pathogenic bacteria levels are significantly related with disease control, clinical diagnosis, and even environmental monitoring. It is becoming highly urgent to achieve ultrasensitive detection of pathogenic bacteria and efficient combat of bacterial infection. Toward this end, we have assembled a DNA Pom-Pom nanostructure (PP-N) based multifunctional platform for pathogenic bacteria determination and inactivation. In particular, one DNA oligonucleotide probe that serve as a trigger was specifically designed for the autonomous cross-opening of metastable DNA hairpin probes and long dsDNA structure formation, achieving a catalytic self-assembly of DNA nanostructure. Numerous DNA strands in this PP-N assembly provide sufficient interaction sites for functional domains and connector, showing high programmability, excellent biostability, as well as selective target recognition. With these properties, the fluorescence dyes modified PP-N platform showed excellent bacteria analysis with both excellent selectivity and ultrasensitive determination limit as low as 2.0 CFU/mL. Furthermore, the aptamer-functionalized and antibiotics loaded PP-N platform demonstrate excellent merits of high antibiotics-loading capacity and negligible cytotoxicity to targets. Therefore, this DNA PP-N assembly based multifunctional platform promise its great application in targeted sensing, combating bacterial infection, and potential clinic therapy.

An enzyme-powered, three-dimensional lame DNA walker

Molecular machines constructed by three-dimensional (3-D) DNA walker have emerged as a hot topic in applications such as novel biosensors, cargo delivery platforms and intracellular imaging. Herein, we first propose a lame DNA walker that can randomly and autonomously move on microsphere-based 3-D track. The stochastic lame walker has a long leg mainly responsible for persistent movement and a short leg cutting substrates rapidly. Its motion is propelled by a nicking endonuclease cleavage of hybridized DNA tracks. Kinetic and persistent study show that the lame DNA walker enables reaction equilibrium at 30 min, need a cleat domain of at least 14 nucleotides and can persistently move on 3-D tracks with an average rate of 6.467 × 10^-11 M s^-1. We also demonstrate that the lame walker can be used to detect target DNA in the detection range of 10 pM-5 nM with high specificity by toehold exchange mechanism. This work will further expand the performance of 3-D DNA walkers and substantially contributes to the improved understanding of DNA walking systems.

Fabrication of 3D concentric amphiphilic microparticles to form uniform nanoliter reaction volumes for amplified affinity assays

Reactions performed in uniform microscale volumes have enabled numerous applications in the analysis of rare entities (e.g. cells and molecules). Here, highly monodisperse aqueous droplets are formed by simply mixing microscale multi-material particles, consisting of concentric hydrophobic outer and hydrophilic inner layers, with oil and water. The particles are manufactured in batch using a 3D printed device to co-flow four concentric streams of polymer precursors which are polymerized with UV light. The cross-sectional shapes of the particles are altered by microfluidic nozzle design in the 3D printed device. Once a particle encapsulates an aqueous volume, each "dropicle" provides uniform compartmentalization and customizable shape-coding for each sample volume to enable multiplexing of uniform reactions in a scalable manner. We implement an enzymatically-amplified immunoassay using the dropicle system, yielding a detection limit of <1 pM with a dynamic range of at least 3 orders of magnitude. Multiplexing using two types of shape-coded particles was demonstrated without cross talk, laying a foundation for democratized single-entity assays.

High-throughput screening by droplet microfluidics: perspective into key challenges and future prospects

In two decades of development, impressive strides have been made for automating basic laboratory operations in droplet-based microfluidics, allowing the emergence of a new form of high-throughput screening and experimentation in nanoliter to femtoliter volumes. Despite advancements in droplet storage, manipulation, and analysis, the field has not yet been widely adapted for many high-throughput screening (HTS) applications. Broad adoption and commercial development of these techniques require robust implementation of strategies for the stable storage, chemical containment, generation of libraries, sample tracking, and chemical analysis of these small samples. We discuss these challenges for implementing droplet HTS and highlight key strategies that have begun to address these concerns. Recent advances in the field leave us optimistic about the future prospects of this rapidly developing technology.

Poly-adenine regulated DNA density on AuNPs to construct efficient DNA walker for microRNA-21 detection

DNA-modified gold nanoparticles (AuNPs) are useful nanomaterials for detecting multiple molecules. However, their performance is greatly dependent on the density of probe DNA on the surface of AuNPs. Here, we used Poly-adenine (PolyA) to regulate the surface density of probe DNA to achieve a highly efficient DNA walking biosensor system to detection miRNA-21. The movement track of the biosensor system consists of PolyA-DNA probe was connected to AuNPs, and exonuclease III (Exo III) acted as a motor driving the walker movement to achieve signal amplification. By optimizing the length of PolyA, the surface density of probe DNA was changed, thereby affecting the target binding and enzymatic processing of the bound probes, which ultimately enhanced the sensitivity and reduced timeliness of the DNA walker. Furthermore, the designed PolyA-DNA probe exhibits an outstanding sensitivity, due to the effect of density regulation, which is 7.9 times and 11.1 times lower than those of the SH-DNA and the free-DNA, respectively. In addition, the hairpin structure of DNA probe locates fluorophore at a zone adjacent to AuNPs surface, which reduces the background signal by 1.1 times compared with traditional straight probe. In this work, the biosensor system shows a high selectivity towards miRNA-21. Moreover, the biosensor system has been demonstrated to be potentially useful for the miRNA-21 detection in human serum with the recoveries of 93.2%-110.0% and has high repeatability. Considering these advantages, this PolyA-regulated DNA walking biosensor system has great potential as a routine tool for miRNA detection and has wide applications in the field of biomedical analysis.

Stochastic DNA Dual-Walkers for Ultrafast Colorimetric Bacteria Detection

Rapid, sensitive, and reliable pathogen detection is growing in importance in human health and safety. In this work, we report a stochastic DNA dual-walker-based colorimetric biosensor for bacterial detection. In the presence of target bacteria, two kinds of released multiple walking strands are allowed for continuous walking on the Au nanoparticle (AuNP)-based 3D track, resulting in destabilized aggregation of AuNP-based probes. The induced color change from red to blue can serve as an analytical signal for colorimetric detection of target bacteria. We demonstrated that this mothed enables sensitive and specific bacterial detection within 15 min due to its ultrafast reaction kinetics and sensitive color change, showing a linear response ranging from 10⁰ to 10⁵ CFU/mL with a limit of detection of 1 CFU/mL. Moreover, we also realized analysis of practical samples using this colorimetric biosensor. Given its features of rapid, sensitive, specific, and reliable analysis, our stochastic dual-walker-based colorimetric biosensor shows much promise in point-of-care testing for bacteria detection.

Differentiated Visualization of Single-Cell 5-Hydroxymethylpyrimidines with Microfluidic Hydrogel Encoding

5-Hydroxymethyluracil ( 5hmU ) is found in the genomes of a diverse range of organisms as another kind of 5-hydroxymethylpyrimidine, with the exception of 5-hydroxymethylcytosine ( 5hmC ). The biological function of 5hmU has not been well explored due to lacking both specific 5hmU recognition and single-cell analysis methods. Here we report differentiated visualization of single-cell 5hmU and 5hmC with microfluidic hydrogel encoding (sc 5hmU / 5hmC -microgel). Single cells and their genomic DNA after cell lysis can be encapsulated in individual agarose microgels. The 5hmU sites are then specifically labeled with thiophosphate for the first time, followed by labeling 5hmC with azide glucose. These labeled bases are each encoded into respective DNA barcode primers by chemical cross-linking. In situ amplification is triggered for single-molecule fluorescence visualization of single-cell 5hmU and 5hmC . On the basis of the sc 5hmU / 5hmC -microgel, we reveal cell type-specific molecular signatures of these two bases with remarkable single-cell heterogeneity. Utilizing machine learning algorithms to decode four-dimensional signatures of 5hmU / 5hmC , we visualize the discrimination of nontumorigenic, carcinoma and highly invasive breast cell lines. This strategy provides a new route to analyze and decode single-cell DNA epigenetic modifications.

A well-directional three-dimensional DNA walking nanomachine that runs in an orderly manner

Herein, we report a three-dimensional (3D) DNA walking nanomachine innovatively constructed from a functionalized 3D DNA track, which runs in an orderly manner with favorable directionality to allow for programming certain pathways of information transduction for some target tasks. The nanomachine was constructed using a departure station of walker (UB + W) and a functionalized 3D track, which was made up of a rolling circle amplification (RCA)-generated backbone chain and numerous triangular rung units with stators (UA + S) assembled into a repeating array along the backbone. A specific domain (SD) was designed at the 5'-end of the backbone to capture the UB + W, and stators with specific RNA substrates were immobilized at the three UA corners for the DNA walker to travel on. Powered by 10-23 DNAzyme, the DNA walker started moving from the SD end to the other end of the track by the autonomous cleavage of RNA substrates. Significantly, the homogeneous distribution of stators in the longitudinal and horizontal extensions paved a specific path for each walker to move along the 3D track. This resulted in random and inactive self-avoiding walking; thus, the nanomachine exhibited good executive ability. These properties allowed the DNA walking nanomachine to program the certain pathways of information transduction for the stepwise and programmed execution of some target tasks, such as the synthesis of specific polyorganics and cargo delivery. We believe that such a 3D DNA walking nanomachine could enrich the concept in the field of dynamic DNA nanotechnology, and may improve the development of novel DNA nanomachines in cargo delivery and composite product synthesis.

Nonlinear Regulation of Enzyme-Free DNA Circuitry with Ultrasensitive Switches

DNA is used to construct synthetic chemical reaction networks (CRNs), such as inorganic oscillators and gene regulatory networks. Nonlinear regulation with a simpler molecular mechanism is particularly important in large-scale CRNs with complex dynamics, such as bistability, adaptation, and oscillation of cellular functions. Here we introduce a new approach based on ultrasensitive switches as modular regulatory elements to nonlinearly regulate DNA-based CRNs. The nonlinear behavior of the systems can be finely tuned by programmable regulation of the linker length and the ligand binding sites, of which the Hill coefficients (n_H) are in the range of 1.00-2.32. By integrating two different strand displacement reactions with low-order nonlinearities (n_H ≈ 1.44 and 1.54), we could construct CRNs exhibiting high-order nonlinearities with Hill coefficients of up to ∼2.70. In addition, this could provide an efficient approach for designing CRNs at will with complex chemical dynamics by incorporating our design with previously developed enzyme-free DNA circuits.