Cell-surface sensors for real-time probing of cellular environments

Cellular probing using phytoceuticals encapsulated advanced delivery systems in ameliorating lung diseases: Current trends and future prospects

Chronic respiratory diseases such as Chronic Obstructive Pulmonary Disease (COPD) and asthma have posed a significant healthcare and economic cost over a prolonged duration worldwide. At present, available treatments are limited to a range of preventive medicines, such as mono- or multiple-drug therapy, which necessitates daily use and are not considered as viable treatments to reverse the inflammatory processes of airway remodelling which is inclusive of the alteration of intra and extracellular matrix of the airway tract, death of epithelial cells, the increase in smooth muscle cell and the activation of fibroblasts. Hence, with the problem in mind a considerable body of study has been dedicated to comprehending the underlying factors that contribute to inflammation within the framework of these disorders. Hence, adequate literature that has unveiled the necessary cellular probing to reduce inflammation in the respiratory tract by improving the selectivity and precision of a novel treatment. However, through cellular probing cellular mechanisms such as the downregulation of various markers, interleukin 8, (IL-8), Interleukin 6 (IL-6), interleukin 1β (IL-1β) and tumor necrosis factor-α (TNF-α) have been uncovered. Hence, to target such cellular probes implementation of phytoceuticals encapsulated in an advanced drug delivery system has shown potential to be a solution with in vitro and in vivo studies highlighting their anti-inflammatory and antioxidant effects. However, the high costs associated with advanced drug delivery systems and the limited literature focused exclusively on nanoparticles pose significant challenges. Additionally, the biochemical characteristics of phytoceuticals due to poor solubility, limited bioavailability, and difficulties in mass production makes it difficult to implement this product as a treatment for COPD and asthma. This study aims to examine the integration of many critical features in the context of their application for the treatment of chronic inflammation in respiratory disorders.

Quantifying T cell receptor mechanics at membrane junctions using DNA origami tension sensors

The T cell receptor (TCR) is thought to be a mechanosensor, meaning that it transmits mechanical force to its antigen and leverages the force to amplify the specificity and magnitude of TCR signalling. Although a variety of molecular probes have been proposed to quantify TCR mechanics, these probes are immobilized on hard substrates, and thus fail to reveal fluid TCR-antigen interactions in the physiological context of cell membranes. Here we developed DNA origami tension sensors (DOTS) which bear force sensors on a DNA origami breadboard and allow mapping of TCR mechanotransduction at dynamic intermembrane junctions. We quantified the mechanical forces at fluid TCR-antigen bonds and observed their dependence on cell state, antigen mobility, antigen potency, antigen height and F-actin activity. The programmability of DOTS allows us to tether these to microparticles to mechanically screen antigens in high throughput using flow cytometry. Additionally, DOTS were anchored onto live B cells, allowing quantification of TCR mechanics at immune cell-cell junctions.

High-affinity one-step aptamer selection using a non-fouling porous hydrogel

Aptamers, commonly referred to as chemical antibodies, are used in a wide range of applications including drug delivery and biosensing. However, the process of aptamer selection poses a substantial challenge, as it requires numerous cycles of enrichment and involves issues with nonspecific binding. We present a simple, fast instrument-free method for aptamer enrichment and selection based on a diffusion-binding process in a three-dimensional non-fouling porous hydrogel with immobilized target proteins. Low-affinity aptamer candidates can be rapidly released from the hydrogel, whereas high-affinity candidates are restricted due to their strong binding to the immobilized protein targets. Consequently, a one-step enriched aptamer pool can strongly bind the protein targets. This enrichment is consistent across five proteins with isoelectric points in varying ranges. With thrombin as a representative model, the anti-thrombin aptamer identified from an enriched aptamer pool has been found to have a binding affinity that is comparable to those identified over ten cycles of selection using traditional methods.

The Biomedical Applications of Biomolecule Integrated Biosensors for Cell Monitoring

Cell monitoring is essential for understanding the physiological conditions and cell abnormalities induced by various stimuli, such as stress factors, microbial invasion, and diseases. Currently, various techniques for detecting cell abnormalities and metabolites originating from specific cells are employed to obtain information on cells in terms of human health. Although the states of cells have traditionally been accessed using instrument-based analysis, this has been replaced by various sensor systems equipped with new materials and technologies. Various sensor systems have been developed for monitoring cells by recognizing biological markers such as proteins on cell surfaces, components on plasma membranes, secreted metabolites, and DNA sequences. Sensor systems are classified into subclasses, such as chemical sensors and biosensors, based on the components used to recognize the targets. In this review, we aim to outline the fundamental principles of sensor systems used for monitoring cells, encompassing both biosensors and chemical sensors. Specifically, we focus on biosensing systems in terms of the types of sensing and signal-transducing elements and introduce recent advancements and applications of biosensors. Finally, we address the present challenges in biosensor systems and the prospects that should be considered to enhance biosensor performance. Although this review covers the application of biosensors for monitoring cells, we believe that it can provide valuable insights for researchers and general readers interested in the advancements of biosensing and its further applications in biomedical fields.

Biomimetic Vesicles with Designer Phospholipids Can Sense Environmental Redox Cues

Cell-like materials that sense environmental cues can serve as next-generation biosensors and help advance the understanding of intercellular communication. Currently, bottom-up engineering of protocell models from molecular building blocks remains a grand challenge chemists face. Herein, we describe giant unilamellar vesicles (GUVs) with biomimetic lipid membranes capable of sensing environmental redox cues. The GUVs employ activity-based sensing through designer phospholipids that are fluorescently activated in response to specific reductive (hydrogen sulfide) or oxidative (hydrogen peroxide) conditions. These synthetic phospholipids are derived from 1,2-dipalmitoyl-rac-glycero-3-phosphocholine and they possess a headgroup with heterocyclic aromatic motifs. Despite their structural deviation from the phosphocholine headgroup, the designer phospholipids (0.5-1.0 mol %) mixed with natural lipids can vesiculate, and the resulting GUVs (7-20 μm in diameter) remain intact over the course of redox sensing. All-atom molecular dynamics simulations gave insight into how these lipids are positioned within the hydrophobic core of the membrane bilayer and at the membrane-water interface. This work provides a purely chemical method to investigate potential redox signaling and opens up new design opportunities for soft materials that mimic protocells.

DNA nanostructures for exploring cell-cell communication

The process of coordinating between the same or multiple types of cells to jointly execute various instructions in a controlled and carefully regulated environment is a very appealing field. In order to provide clearer insight into the role of cell-cell interactions and the cellular communication of this process in their local communities, several interdisciplinary approaches have been employed to enhance the core understanding of this phenomenon. DNA nanostructures have emerged in recent years as one of the most promising tools in exploring cell-cell communication and interactions due to their programmability and addressability. Herein, this review is dedicated to offering a new perspective on using DNA nanostructures to explore the progress of cell-cell communication. After briefly outlining the anchoring strategy of DNA nanostructures on cell membranes and the subsequent dynamic regulation of DNA nanostructures, this paper highlights the significant contribution of DNA nanostructures in monitoring cell-cell communication and regulating its interactions. Finally, we provide a quick overview of the current challenges and potential directions for the application of DNA nanostructures in cellular communication and interactions.

Identification of druggable regulators of cell secretion via a kinome-wide screen and high-throughput immunomagnetic cell sorting

The identification of genetic regulators of cell secretions is challenging because it requires the sorting of a large number of cells according to their secretion patterns. Here we report the development and applicability of a high-throughput microfluidic method for the analysis of the secretion levels of large populations of immune cells. The method is linked with a kinome-wide loss-of-function CRISPR screen, immunomagnetically sorting the cells according to their secretion levels, and the sequencing of their genomes to identify key genetic modifiers of cell secretion. We used the method, which we validated against flow cytometry for cytokines secreted from primary mouse CD4+ (cluster of differentiation 4-positive) T cells, to discover a subgroup of highly co-expressed kinase-coding genes that regulate interferon-gamma secretion by these cells. We validated the function of the kinases identified using RNA interference, CRISPR knockouts and kinase inhibitors and confirmed the druggability of selected kinases via the administration of a kinase inhibitor in an animal model of colitis. The technique may facilitate the discovery of regulatory mechanisms for immune-cell activation and of therapeutic targets for autoimmune diseases.

Biomimetic Bacterial Capsule for Enhanced Aptamer Display and Cell Recognition

Great effort has been made to encapsulate or coat living mammalian cells for a variety of applications ranging from diabetes treatment to three-dimensional printing. However, no study has reported the synthesis of a biomimetic bacterial capsule to display high-affinity aptamers on the cell surface for enhanced cell recognition. Therefore, we synthesized an ultrathin alginate-polylysine coating to display aptamers on the surface of living cells with natural killer (NK) cells as a model. The results show that this coating-mediated aptamer display is more stable than direct cholesterol insertion into the lipid bilayer. The half-life of the aptamer on the cell surface can be increased from less than 1.5 to over 20 h. NK cells coated with the biomimetic bacterial capsule exhibit a high efficiency in recognizing and killing target cells. Therefore, this work has demonstrated a promising cell coating method for the display of aptamers for enhanced cell recognition.

Cell Surface Engineering Tools for Programming Living Assemblies

Breakthroughs in precision cell surface engineering tools are supporting the rapid development of programmable living assemblies with valuable features for tackling complex biological problems. Herein, the authors overview the most recent technological advances in chemically- and biologically-driven toolboxes for engineering mammalian cell surfaces and triggering their assembly into living architectures. A particular focus is given to surface engineering technologies for enabling biomimetic cell-cell social interactions and multicellular cell-sorting events. Further advancements in cell surface modification technologies may expand the currently available bioengineering toolset and unlock a new generation of personalized cell therapeutics with clinically relevant biofunctionalities. The combination of state-of-the-art cell surface modifications with advanced biofabrication technologies is envisioned to contribute toward generating living materials with increasing tissue/organ-mimetic bioactivities and therapeutic potential.

Advantages of Material Biofunctionalization Using Nucleic Acid Aptamers in Tissue Engineering and Regenerative Medicine

Material engineering is a fundamental issue in the applications of materials in the medical field. One of the aspects of material engineering is incorporating recognition sites on the surface of biomaterials, which plays an essential role in increasing the efficiency of tissue engineering scaffolds in various aspects. The application of peptides and antibodies to establish the recognition and adhesion sites has limitations, such as fragility and instability under physical and chemical processes. Therefore, synthetic ligands such as nucleic acid aptamers have received much attention for easy synthesis, minimal immunogenicity, high specificity, and stability under processing. Due to the effective role of these ligands in increasing the efficiency of engineered constructs in this study, the advantages of nucleic acid aptamers in tissue engineering will be reviewed. Aptamer-functionalized biomaterials can attract endogenous stem cells to wounded areas and organize their actions to facilitate tissue regeneration. This approach harnesses the body's inherent regeneration potential to treat many diseases. Also, increased efficacy in controlled release, slow and targeted drug delivery are important issues in drug delivery for tissue engineering approaches which can be achieved by incorporating aptamers in drug delivery systems. Aptamer-functionalized scaffolds have very applications, such as diagnosis of cancer, hematological infections, narcotics, heavy metals, toxins, controlled release from the scaffolds, and in vivo cell tracing. Aptasensors, as a result of many advantages over other traditional assay methods, can replace older methods. Furthermore, their unique targeting mechanism also targets compounds with no particular receptors. Targeting cell homing, local and targeted drug delivery, cell adhesion efficacy, cytocompatibility and bioactivity of scaffolds, aptamer-based biosensor, and aptamer-functionalized scaffolds are the topics that will be examined in this review study.

A collagen-immobilized nanodevice for in situ ratiometric imaging of cancer biomarkers in the tumor microenvironment

Monitoring the spatiotemporal dynamics of cancer biomarkers within the tumor microenvironment (TME) is critical to understanding their roles in tumorigenesis. Here, we reported a multifunctional fusion protein (collagen-binding domain and duck circovirus tag fused to mCherry, CBD-mCherry-DCV) capable of binding collagen with high affinity and covalently binding specific nucleic acids with exceptional efficiency. We then constructed a chimeric protein-nucleic acid nanodevice (CPNN) using CBD-mCherry-DCV and an aptamer-based sensing module to enable spatially controlled ratiometric imaging of cancer biomarkers in the TME. The collagen-anchoring module CBD-mCherry-DCV allowed specific immobilization of CPNN on 3D multicellular tumor spheroids, enabling the sensing module to achieve "off-on" fluorescence imaging of cancer biomarkers upon specific target recognition by an aptamer. Taking advantage of the constant fluorescence signal of mCherry and the activatable fluorescence response of Cy5 to specific cancer biomarkers, the detection sensitivity and reliability of CPNN were improved by self-calibrating the signal intensity. Specifically, CPNN enabled ratiometric fluorescence imaging of varying concentrations of exogenous PDGF-BB and ATP in tumor spheroids with a high signal-to-background ratio. Furthermore, it allowed the visual monitoring of endogenous PDGF-BB and ATP released from cells. Overall, this study demonstrates the potential of the nanodevice as a versatile approach for the visualization and imaging of cancer biomarkers in the TME.

DNA tetrahedron-mediated triplex molecular switch for extracellular pH monitoring

This study aimed to construct a novel DNA triplex molecular switch modified with DNA tetrahedron (DTMS-DT) with sensitive response to extracellular pH using a DNA tetrahedron as the anchoring unit and DNA triplex as the response unit. The results showed that the DTMS-DT had desirable pH sensitivity, excellent reversibility, outstanding anti-interference ability, and good biocompatibility. Confocal laser scanning microscopy suggested that the DTMS-DT could not only be stably anchored on the cell membrane but also be employed to dynamically monitor the change in extracellular pH. Compared with the reported probes for extracellular pH monitoring, the designed DNA tetrahedron-mediated triplex molecular switch exhibited higher cell surface stability and brought the pH-responsive unit closer to the cell membrane surface, making the results more reliable. In general, developing the DNA tetrahedron-based DNA triplex molecular switch is helpful for understanding and illustrating the pH dependent cell behaviors and disease diagnostics.

DNA Origami Tension Sensors (DOTS) to study T cell receptor mechanics at membrane junctions

The T cell receptor (TCR) is thought to be a mechanosensor, meaning that it transmits mechanical force to its antigen and leverages the force to amplify the specificity and magnitude of TCR signaling. The past decade has witnessed the development of molecular probes which have revealed many aspects of receptor mechanotransduction. However, most force probes are immobilized on hard substrates, thus failing to reveal mechanics in the physiological context of cell membranes. In this report, we developed DNA origami tension sensors (DOTS) which bear force sensors on a DNA origami breadboard and allow mapping of TCR mechanotransduction at dynamic intermembrane junctions. We demonstrate that TCR-antigen bonds experience 5-10 pN forces, and the mechanical events are dependent on cell state, antigen mobility, antigen potency, antigen height and F-actin activity. We tethered DOTS onto a microparticle to mechanically screen antigen in high throughput using flow cytometry. Finally, DOTS were anchored onto live B cell membranes thus producing the first quantification of TCR mechanics at authentic immune cell-cell junctions.

A cell-surface-anchored DNA probe coupled with hybridization chain reaction enzyme-free dual signal amplification for sensitive electrochemical detection of the cellular microenvironment

The cellular microenvironment plays key roles in regulating physiological processes. However, it is still a challenge to detect it with quantification. Here, a simple, biocompatible, and universal strategy based on cell surface-anchored specific DNAzymes and hybridization chain reaction enzyme-free signal amplification for cellular microenvironment electrochemical detection is presented. In this strategy, the cell could be captured on the surface of the electrode via aptamer-target recognition. On the other hand, the DNAzyme hybridized with the substrate strand as a metal ion probe was anchored on the surface of the cell. In the presence of metal ions, the substrate strand could be cleaved into two fragments by the DNAzyme and released from the cell surface. Then, the DNA modified gold nanoparticles (AuNPs) could be captured on the electrode. Subsequently, an alternative hybridization reaction of two hairpin probes was triggered by the carried initiators forming nicked double helices. For signal readout, hemin could be inserted into the double-helix DNA long chain via electrostatic interaction, which could electro-reduce hydrogen peroxide to generate an electrochemical signal. Based on the intrinsic advantages of DNAzymes, including rapid kinetics, high sensitivity, and high selectivity, and the signal amplification strategy, this method should be able to monitor and semi-quantify target metal ions in the cellular microenvironment. Furthermore, this method shows potential for various targets by employing different DNA probes in the cellular microenvironment, providing a platform for bioanalysis.

Multiplexed Detection of Molecular Interactions with DNA Origami Engineered Cells in 3D Collagen Matrices

The interactions of cells with signaling molecules present in their local microenvironment maintain cell proliferation, differentiation, and spatial organization and mediate progression of diseases such as metabolic disorders and cancer. Real-time monitoring of the interactions between cells and their extracellular ligands in a three-dimensional (3D) microenvironment can inform detection and understanding of cell processes and the development of effective therapeutic agents. DNA origami technology allows for the design and fabrication of biocompatible and 3D functional nanodevices via molecular self-assembly for various applications including molecular sensing. Here, we report a robust method to monitor live cell interactions with molecules in their surrounding environment in a 3D tissue model using a microfluidic device. We used a DNA origami cell sensing platform (CSP) to detect two specific nucleic acid sequences on the membrane of B cells and dendritic cells. We further demonstrated real-time detection of biomolecules with the DNA sensing platform on the surface of dendritic cells in a 3D microfluidic tissue model. Our results establish the integration of live cells with membranes engineered with DNA nanodevices into microfluidic chips as a highly capable biosensor approach to investigate subcellular interactions in physiologically relevant 3D environments under controlled biomolecular transport.

Recent Advances in DNA-Based Cell Surface Engineering for Biological Applications

Due to its excellent programmability and biocompatibility, DNA molecule has unique advantages in cell surface engineering. Recent progresses provide a reliable and feasible way to engineer cell surfaces with diverse DNA molecules and DNA nanostructures. The abundant form of DNA nanostructures has greatly expanded the toolbox of DNA-based cell surface engineering and gave rise to a variety of novel and fascinating applications. In this review, we summarize recent advances in DNA-based cell surface engineering and its biological applications. We first introduce some widely used methods of immobilizing DNA molecules on cell surfaces and their application features. Then we discuss the approaches of employing DNA nanostructures and dynamic DNA nanotechnology as elements for creating functional cell surfaces. Finally, we review the extensive biological applications of DNA-based cell surface engineering and discuss the challenges and prospects of DNA-based cell surface engineering.

Cell pairing for biological analysis in microfluidic devices

Cell pairing at the single-cell level usually allows a few cells to contact or seal in a single chamber and provides high-resolution imaging. It is pivotal for biological research, including understanding basic cell functions, creating cancer treatment technologies, developing drugs, and more. Laboratory chips based on microfluidics have been widely used to trap, immobilize, and analyze cells due to their high efficiency, high throughput, and good biocompatibility properties. Cell pairing technology in microfluidic devices provides spatiotemporal research on cellular interactions and a highly controlled approach for cell heterogeneity studies. In the last few decades, many researchers have emphasized cell pairing research based on microfluidics. They designed various microfluidic device structures for different biological applications. Herein, we describe the current physical methods of microfluidic devices to trap cell pairs. We emphatically summarize the practical applications of cell pairing in microfluidic devices, including cell fusion, cell immunity, gap junction intercellular communication, cell co-culture, and other applications. Finally, we review the advances and existing challenges of the presented devices and then discuss the possible development directions to promote medical and biological research.

Screening T-Cell Activity via a Photodetachable DNA-Copolymer Nanocage and Its Therapeutic Application

Screening T-cell activity and selecting active ones from large ex vivo-expanded populations before reinfusion is important for the success of T-cell therapy. Cytokine secretion is the evaluation criterion of cell immune activity. Cell membrane-anchored probes and microchamber-based techniques have been used to screen cytokine secretion at the single-cell level. However, they are either easily affected by nearby cells' secretion or lack of single-cell encapsulation efficiency. Here, we design a photodetachable DNA-copolymer nanocage on the cell membrane for screening the activities of ex vivo-expanded T cells by in-situ monitoring cytokine interferon-gamma (IFN-γ) secretion. The ones with good immune activity are selected for therapeutic application. DNA-copolymer nanocage is self-assembled on a cell membrane to encapsulate a single T cell. A self-quenched IFN-γ recognition aptamer is contained in the DNA-copolymer nanocage, which recovers fluorescence in response to IFN-γ secretion to indicate individual T-cell activity. The active T cells are collected after fluorescence-activated cell sorting, irradiated with 5 min UV light to detach nanocage from the cell membrane, and continuously cocultured with downstream cells. The selected Jurkat cells and CD19 CAR-T cells showed improved capabilities for downstream cell activation and cancer cell killing. The cell membrane-detachable DNA-copolymer nanocage-based T-cell activity screening and selection would have promising applications in T-cell therapy.

Calcium-Differentiated Cellular Internalization of Allosteric Framework Nucleic Acids for Targeted Payload Delivery

Target delivery systems have extensively shown promising applications in cancer therapy, and many of them function smartly by responding to the cancer cell microenvironment. Here, we for the first time report Ca²⁺-differentiated cellular internalization of 2D/3D framework nucleic acids (FNAs), enabling the engineering of a conceptually new target delivery system using an allosteric FNA nanovehicle. The FNA vehicle is subject to a 2D-to-3D transformation on the cancer cell surface via G-quadruplexes responding to environmental K⁺ and thereby allows its cell entry to be more efficiently promoted by Ca²⁺. This design enables the FNA vehicle to target cancer cells and selectively deliver an antisense strand-containing cargo for live-cell mRNA imaging. It would open new avenues toward targeted drug delivery and find extensive applications in precise disease treatment.

Analysis of cell-nanoparticle interactions and imaging of in vitro labeled cells showing barcorded endosomes using fluorescent thiol-organosilica nanoparticles surface-functionalized with polyethyleneimine

Biomedical imaging using cell labeling is an important technique to visualize cell dynamics in the body. To label cells, thiol-organosilica nanoparticles (thiol-OS) containing fluorescein (thiol-OS/Flu) and rhodamine B (thiol-OS/Rho) were surface-functionalized with polyethyleneimine (PEI) (OS/Flu-PEI and OS/Rho-PEI) with 4 molecular weights (MWs). We hypothesized PEI structures such as brush, bent brush, bent lie-down, and coiled types on the surface depending on MWs based on dynamic light scattering and thermal gravimetric analyses. The labeling efficacy of OS/Flu-PEIs was dependent on the PEI MW and the cell type. A dual-particle administration study using thiol-OS and OS-PEIs revealed differential endosomal sorting of the particles depending on the surface of the NPs. The endosomes in the labeled cells using OS/Flu-PEI and thiol-OS/Rho revealed various patterns of fluorescence termed barcoded endosomes. The cells labeled with OS-PEI in vitro were administrated to mice intraperitoneally after in situ labeling of peritoneal cells using thiol-OS/Rho. The in vitro labeled cells were detected and identified in cell aggregates in vivo seamlessly. The labeled cells with barcoded endosomes were also identified in cell aggregates. Biomedical imaging of in vitro OS-PEI-labeled cells combined with in situ labeled cells showed high potential for observation of cell dynamics.

Multivalent Engineering of Exosomes with Activatable Aptamer Probes for Specific Regulation and Monitoring of Cell Targeting

Reconstituting and probing exosome-cell interactions is critical for elucidating exosome-related cell biology and advancing their diagnostic and therapeutic potential. We report here an exosomal engineering strategy to achieve controlled regulation of exosome-cell interactions with activatable sensing capability. The approach relies on membrane-protein directed, programmable DNA self-assembly to construct a DNA polymeric scaffold with multivalent display of structure-switchable aptamer sensing probes on exosome surfaces. The engineered exosomes exhibit enhanced cancer cell targeting ability compared to exosomes modified with monovalent aptamers. Furthermore, the anchored aptamer probes could be activated by specific membrane protein targeting, followed by structural switching to report an output fluorescence signal, thus allowing dynamic monitoring of exosome-cell interactions both in vitro and in vivo. We envision this will provide a complementary tool for specific regulation and monitoring of exosome-cell docking interactions and will advance the development of exosome-based biomedical applications.

DNA-Based Molecular Engineering of the Cell Membrane

The cell membrane serves as a barrier and gatekeeper to regulate the cellular transportation of substances and information. It plays a significant role in protecting the cell from the extracellular environment, maintaining intracellular homeostasis, and regulating cellular function and behaviors. The capability to engineer the cell membrane with functional modules that enable dynamic monitoring and manipulating the cell-surface microenvironment would be critical for studying molecular mechanisms underlying various biological processes. To meet this goal, DNA, with intrinsic advantages of high versatility, programmability, and biocompatibility, has gained intense attention as a molecular tool for cell-surface engineering. The past three decades have witnessed the rapid advances of diverse nucleic acid materials, including functional nucleic acids (FNAs), dynamic DNA circuits, and exquisite DNA nanostructures. In this mini review, we have summarized the recent progress of DNA technology for cell membrane engineering, particularly focused on their applications for molecular sensing and imaging, precise cell identification, receptor activity regulation, and artificial membrane structures. Furthermore, we discussed the challenge and outlook on using nucleic acid materials in this specific research area.

Recent Advances in Aptamer-Based Liquid Biopsy

Liquid biopsy capable of noninvasive and real-time molecular profiling is considered as a breakthrough technology, endowing an opportunity for precise diagnosis of individual patients. Extracellular vesicles (EVs) and circulating tumor cells (CTCs) consisting of substantial disease-related molecular information play an important role in liquid biopsy. Therefore, it is critically significant to exploit high-performance recognition ligands for efficient isolation and analysis of EVs and CTCs from complex body fluids. Aptamers exhibit extraordinary merits of high specificity and affinity, which are considered as superior recognition ligands for liquid biopsy. In this review, we first summarize recent advanced strategies for the evolution of high-performance aptamers and the construction of various aptamer-based recognition elements. Subsequently, we mainly discuss the isolation and analysis of EVs and CTCs based on the aptamer functioned biomaterials/biointerface. Ultimately, we envision major challenges and future direction of aptamer-based liquid biopsy for clinical utilities.

Construction and bioapplications of aptamer-based dual recognition strategy

Aptamer-based dual recognition strategy, using dual aptamers or the cooperation of aptamers with other recognition elements, can better utilize the advantages of each recognition molecule and increase the design flexibility to effectively overcome the limitations of a single molecule recognition strategy, thereby improving the sensitivity and selectivity and facilitating the regulation of biological process. Hence, this review systematically tracks the construction and application of dual aptamers recognition strategy in the versatile detection of protein biomarkers, pathogenic microorganisms, cancer cells, and the treatment of some diseases and, more importantly, in functional regulation and imaging of cell-surface protein receptors. Then, the cooperation of aptamers with other recognition elements are briefly introduced. Potential challenges facing this field have been highlighted, aiming to expand bioanalytical applications of aptamer-based dual or multiple recognition strategies and meet the growing demand for precision medicine.

Cancer diagnosis and analysis devices based on multimolecular crowding

The study of the multimolecular crowding around cancer cells has opened up the possibility of developing new devices for cancer diagnosis and analysis through the measurement of intercellular communication related to cell proliferation and invasive metastasis associated with cancer malignancy. In particular, cells and extracellular vesicles that flow into the bloodstream contain metabolites and secreted products of the cancer microenvironment. These are positioned as targets for the development of new devices for the understanding and application of multimolecular crowding around cancer cells. Examples include the separation analysis of cancer cells in blood for the next generation of less invasive testing techniques, and mapping analysis using Raman scattering to detect cancer cells without staining. Another example is the evaluation of the relationship between exosomes and cancer traits for the exploration of new anti-cancer drugs, and the commercialization of exosome separation devices for ultra-early cancer diagnosis. The development of nanobiodevice engineering, which applies multimolecular crowding to conventional nanobioscience, is expected to contribute to the diagnosis and analysis of various diseases in the future.

Synthetic nanosensors for imaging neuromodulators

Neuromodulation plays a critical role in regulating brain function and its dysregulation is implicated in the pathogenesis of numerous neurological and psychiatric disorders. However, only in the last few years have optical tools become available to probe the spatial and temporal profiles of neuromodulator signaling, including dopamine, with the requisite resolution to uncover mechanisms of neuromodulation. In this review, we summarize the current state of synthetic nanomaterial-based optical nanosensors for monitoring neurotransmission with high spatial and temporal resolution. Specifically, we highlight how synthetic nanosensors can elucidate the spatial distribution of neuromodulator release sites and report the temporal dynamics and spatial diffusion of neuromodulator release. Next, we outline advantages and limitations of currently available nanosensors and their recent application to imaging endogenous dopamine release in brain tissue. Finally, we discuss strategies to improve nanosensors for in vivo use, with implications for translational applications.

Target-Dependent Protection of DNA Aptamers against Nucleolytic Digestion Enables Signal-On Biosensing with Toehold-Mediated Rolling Circle Amplification

We report a generalizable strategy for biosensing that takes advantage of the resistance of DNA aptamers against nuclease digestion when bound with their targets, coupled with toehold mediated strand displacement (TMSD) and rolling circle amplification (RCA). A DNA aptamer containing a toehold extension at its 5'-end protects it from 3'-exonuclease digestion by phi29 DNA polymerase (phi29 DP) in a concentration-dependent manner. The protected aptamer can participate in RCA in the presence of a circular template that is designed to free the aptamer from its target via TMSD. The absence of the target leads to aptamer digestion, and thus no RCA product is produced, resulting in a turn-on sensor. Using two different DNA aptamers, we demonstrate rapid and quantitative real-time fluorescence detection of two human proteins: platelet-derived growth factor (PDGF) and thrombin. Sensitive detection of PDGF was also achieved in human serum and human plasma, demonstrating the selectivity of the assay.

A SERS-Active Electrospun Polymer Mesh for Spatially Localized pH Measurements of the Cellular Microenvironment

Extracellular pH (pHe) is an important chemical factor in many cellular processes and disease pathologies. The routine sampling of pHe in vitro could lead to innovative advances in therapeutics. To this end, we have fabricated a novel gold-coated polymer mesh, which facilitates the real-time measurement of pHe via surface-enhanced Raman scattering (SERS). In this proof of concept study, we apply our SERS sensor to measure metabolically induced changes in the pHe of carcinoma-derived cell line HepG2/C3A. We demonstrate that gold-coated polyurethane electrospun nanofibers (AuNF) have strong and reproducible SERS spectra of surface-adsorbed analytes. By functionalizing AuNF with pH-responsive reporter 4-mercaptobenzoic acid (MBA), we have developed an accurate pH SERS sensor for the extracellular microenvironment. We cultured HepG2/C3A on the surface of MBA-AuNF and measured an acidic shift in pHe at the cell-fiber interface. Following exposure to staurosporine, an apoptosis-inducing drug, we observed changes in the HepG2/C3A cellular morphology indicative of controlled cell death, and detected an increase in the pHe of HepG2/C3A. These results demonstrate how subtle changes in pHe, induced by the metabolic activity of cells, can be measured with our novel SERS sensor MBA-AuNF. The excellent pH measurement performance of MBA-AuNF provides a unique platform to study extracellular pH on the microscale and will help to deepen our understanding of pHe in disease pathology.

Deoxyribonucleic acid anchored on cell membranes for biomedical application

Engineering cellular membranes with functional molecules provides an attractive strategy to manipulate cellular behaviors and functionalities. Currently, synthetic deoxyribonucleic acid (DNA) has emerged as a promising molecular tool to engineer cellular membranes for biomedical applications due to its molecular recognition and programmable properties. In this review, we summarized the recent advances in anchoring DNA on the cellular membranes and their applications. The strategies for anchoring DNA on cell membranes were summarized. Then their applications, such as immune response activation, receptor oligomerization regulation, membrane structure mimicking, cell-surface biosensing, and construction of cell clusters, were listed. The DNA-enabled intelligent systems which were able to sense stimuli such as DNA strands, light, and metal ions were highlighted. Finally, insights regarding the remaining challenges and possible future directions were provided.

A Biomimetic Approach for Spatially Controlled Cell Membrane Engineering Using Fusogenic Spherical Nucleic Acid

Engineering of the cell plasma membrane using functional DNA is important for studying and controlling cellular behaviors. However, most efforts to apply artificial DNA interactions on cells are limited to external membrane surface due to the lack of suitable synthetic tools to engineer the intracellular side, which impedes many applications in cell biology. Inspired by the natural extracellular vesicle-cell fusion process, we have developed a fusogenic spherical nucleic acid construct to realize robust DNA functionalization on both external and internal cell surfaces via liposome fusion-based transport (LiFT) strategy, which enables applications including the construction of heterotypic cell assembly for programmed signaling pathway and detection of intracellular metabolites. This approach can engineer cell membranes in a highly efficient and spatially controlled manner, allowing one to build anisotropic membrane structures with two orthogonal DNA functionalities.

Growth and site-specific organization of micron-scale biomolecular devices on living mammalian cells

Mesoscale molecular assemblies on the cell surface, such as cilia and filopodia, integrate information, control transport and amplify signals. Designer cell-surface assemblies could control these cellular functions. Such assemblies could be constructed from synthetic components ex vivo, making it possible to form such structures using modern nanoscale self-assembly and fabrication techniques, and then oriented on the cell surface. Here we integrate synthetic devices, micron-scale DNA nanotubes, with mammalian cells by anchoring them by their ends to specific cell surface receptors. These filaments can measure shear stresses between 0-2 dyn/cm², a regime important for cell signaling. Nanotubes can also grow while anchored to cells, thus acting as dynamic cell components. This approach to cell surface engineering, in which synthetic biomolecular assemblies are organized with existing cellular architecture, could make it possible to build new types of sensors, machines and scaffolds that can interface with, control and measure properties of cells.

Mesoscale molecular assemblies on the cell surface integrate information and amplify signals. Here the authors integrate DNA nanotubes in a controlled manner with mammalian cells to act as sheer stress meters.

Logic-Gated Proximity Aptasensing for Cell-Surface Real-Time Monitoring of Apoptosis

In nature, intact apoptotic cells release ATP as a signaling molecule to trigger prompt phagocytic clearance, even at the earliest stage of apoptosis. Inspired by this, here we introduce a straightforward strategy for real-time monitoring ATP exocytosis and drug-stimulated apoptosis in the cancer cell surroundings. Triplex-boosted G-quadruplexes (tb-G4s) responding to cell environmental factors (H⁺ and K⁺ ) are engineered to construct a DNA logic-gated nanoplatform for proximity ATP aptasensing on the cell surface. It enables the real-time monitoring of cell apoptosis by capturing released endogenous ATP during chemotherapy drug stimulation, providing a sensitive approach for dynamically evaluating drug-induced apoptosis and therapeutic efficacy.

Atomic Scale Interactions between RNA and DNA Aptamers with the TNF-α Protein

Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting the infection biomarker protein TNF-α, as an example of a novel computational workflow for selecting the aptamer candidate with the highest binding strength to a target. We combine information from the binding free energy calculations, molecular docking, and molecular dynamics simulations to investigate the interactions of both aptamers with TNF-α. The results reveal that the RNA aptamer has a more stable structure relative to the DNA aptamer. Interaction of aptamers with TNF-α does not have any negative effect on its structure. The results of molecular docking and molecular dynamics simulations suggest that the RNA aptamer has a stronger interaction with the protein. Also, these findings illustrate that basic residues of TNF-α establish more atomic contacts with the aptamers compared to acidic or pH-neutral ones. Furthermore, binding energy calculations show that the interaction of the RNA aptamer with TNF-α is thermodynamically more favorable. In total, the findings of this study indicate that the RNA aptamer is a more suitable candidate for using as an apta-biosensor of TNF-α and, therefore, of greater potential use for the diagnosis of blood infections. Also, this study provides more information about aptamer-protein interactions and increases our understanding of this phenomenon.

In Situ Protease Secretion Visualization and Metastatic Lymph Nodes Imaging via a Cell Membrane-Anchored Upconversion Nanoprobe

Matrix metalloproteinase (MMP) secretion is highly associated with tumor invasion and metastasis; therefore, monitoring MMP secretion is important for disease progression study and therapy choosing. Though working well for intracellular MMP imaging, the performance of current MMP detection probes is impaired in secretion monitoring due to the diffusion of MMP in an extracellular environment after secretion and low secreted amount. Here, we design a cell membrane-anchored ratiometric upconversion nanoprobe (UCNPs-Cy3/Pep-QSY7/Ab) for in situ MMP secretion visualization. Anti-EGFR is functionalized on the nanoprobe to provide specific recognition to tumor cells and guarantee fast response to MMP2 in the local place of secretion. MMP-responsive cleavage of Pep-QSY7 results in Cy3 luminescence recovery at 580 nm, which is ratioed over an internal standard of UCNP emission at 654 nm for MMP2 detection. The presented cell membrane-anchored ratiometric upconversion nanoprobe demonstrated that satisfactory results for in situ monitoring of MMP2 secretion from MDA-MB-231 cells and MCF-7 cells, as well as in vivo imaging of metastatic lymph nodes, would provide a universal platform for protease secretion study and contribute to tumor invasiveness assessment.

[Controlling Cell Dynamics by Cell-surface Modification]

Although the concept of a drug delivery system (DDS) is usually applied to conventional drug therapy, it is also important for cell-based therapy. The surface manipulation of living cells represents a powerful tool for controlling cell behaviors in the body, such as enhancement of cell-cell interactions, targeted delivery of cells, and protection from immunological rejection. Functional groups, including amines, thiols, and carbonyls, offer excellent opportunities for chemical modification through the formation of covalent bonds with exogenous molecules. Non-natural reactive groups introduced by metabolic labeling were recently utilized for targeted chemical modification. On the other hand, noncovalent strategies are also available; two major examples are electrostatic interaction with a negative charge on the cell surface and hydrophobic insertion or interaction with the cell membrane. In this study, we analyzed factors affecting cell surface modifications using PEG-lipid and succeeded in enhancing the efficacy of modification by cyclodextrin. Then, mesenchymal stem cells (MSCs), whose therapeutic effect has been demonstrated at the clinical stage and which have been clinically used as a drug, were decorated with PEG-lipid conjugates having a targeted ligand such as peptide or scFv, which are recognized by ICAM1. The peptide or scFv decoration enhanced the cell adhesion of MSCs on cytokine treated-endothelial cells. This technique will prompt the targeted delivery of MSCs to intended therapy sites, and underscores the promise of cell surface engineering as a tool for improving cell-based therapy.

Cell surface-localized imaging and sensing

Systematically dissecting the molecular basis of the cell surface as well as its related biological activities is considered as one of the most cutting-edge fields in fundamental sciences. The advent of various advanced cell imaging techniques allows us to gain a glimpse of how the cell surface is structured and coordinated with other cellular components to respond to intracellular signals and environmental stimuli. Nowadays, cell surface-related studies have entered a new era featured by a redirected aim of not just understanding but artificially manipulating/remodeling the cell surface properties. To meet this goal, biologists and chemists are intensely engaged in developing more maneuverable cell surface labeling strategies by exploiting the cell's intrinsic biosynthetic machinery or direct chemical/physical binding methods for imaging, sensing, and biomedical applications. In this review, we summarize the recent advances that focus on the visualization of various cell surface structures/dynamics and accurate monitoring of the microenvironment of the cell surface. Future challenges and opportunities in these fields are discussed, and the importance of cell surface-based studies is highlighted.

Functionalization of Cellular Membranes with DNA Nanotechnology

Due to its versatility and programmability, DNA nanotechnology has greatly expanded the experimental toolbox for biomedical research. Recent advances allow reliable and efficient functionalization of cellular plasma membranes with a variety of synthetic DNA constructs, ranging from single strands to complex 3D DNA origami. The scope for applications, which probe biophysical parameters or equip cells with novel functions, is rapidly increasing. These applications extend from programmed cellular connectivity and tissue engineering to molecular force measurements, controlled receptor-ligand interactions, membrane-anchored biosensors, and artificial transmembrane structures. Here, we give guidance on different strategies to functionalize cellular membranes with DNA nanotechnology and summarize current trends employing membrane-anchored DNA as a tool in biophysics, cell biology, and synthetic biology.

Rationally Designed Multivalent Aptamers Targeting Cell Surface for Biomedical Applications

Specific interactions between ligands and receptors on cell surface play an important role in the cell biological process. Nucleic acid aptamers as commonly used ligands enable specific recognition and tight binding to membrane protein receptors for modulation of cell fate. Therefore, molecular probes with aptamers can be applied for cancer diagnosis and targeted therapy by targeting overexpression membrane proteins of cancer cells. However, because of their fast degradation and rapid glomerulus clearance in vivo, the applications of aptamers in physiological conditions remain challenged. Inspired by natural multivalent interactions, many approaches have been developed to construct multivalent aptamers to improve the performance of aptamers in complex matrices with higher binding affinity, more stability, and longer circulation time. In this review, we first introduce the aptamer generation from purified protein-based SELEX and whole cell-based SELEX for targeting the cell surface. We then highlight the approaches to fabricate multivalent aptamers and discuss their properties. By integrating different materials (including inorganic nanomaterials, diacyllipid, polymeric nanoparticles, and DNA nanostructures) as scaffolds with an interface modification technique, we have summarized four kinds of multivalent aptamers. After that, representative applications in biosensing and targeted therapy are illustrated to show the elevated performance of multivalent aptamers. In addition, we analyze the challenges and opportunities for the clinical practices of multivalent aptamers.

Synthetic DNA for Cell-Surface Engineering

The cell membrane is not only a physical barrier, but also a functional organelle that regulates the communication between a cell and its environment. The ability to functionalize the cell membrane with synthetic molecules or nanostructures would advance cellular functions beyond what evolution has provided. The aim of this Minireview is to introduce recent progress in using synthetic DNA and DNA-based nanostructures for cell-surface engineering. We first introduce chemical conjugation and physical binding methods for monovalent and polyvalent surface engineering. We then introduce the application of these methods for either the promotion or inhibition of cell-environment communication in numerous applications, including the promotion of cell-cell recognition, regulation of intracellular pathways, protection of therapeutic cells, and sensing of the intracellular and extracellular microenvironments. Lastly, we summarize current challenges existing in this area and potential solutions to solve these challenges.

Efficient and selective DNA modification on bacterial membranes

With highly precise self-assembly and programmability, DNA has been widely used as a versatile material in nanotechnology and synthetic biology. Recently, DNA-based nanostructures and devices have been engineered onto eukaryotic cell membranes for various exciting applications in the detection and regulation of cell functions. While in contrast, the potential of applying DNA nanotechnology for bacterial membrane studies is still largely underexplored, which is mainly due to the lack of tools to modify DNA on bacterial membranes. Herein, using lipid–DNA conjugates, we have developed a simple, fast, and highly efficient system to engineer bacterial membranes with designer DNA molecules. We have constructed a small library of synthetic lipids, conjugated with DNA oligonucleotides, and characterized their membrane insertion properties on various Gram-negative and Gram-positive bacteria. Simply after incubation, these lipid–DNA conjugates can be rapidly and efficiently inserted onto target bacterial membranes. Based on the membrane selectivity of these conjugates, we have further demonstrated their applications in differentiating bacterial strains and potentially in pathogen detection. These lipid–DNA conjugates are promising tools to facilitate the possibly broad usage of DNA nanotechnology for bacterial membrane analysis, functionalization, and therapy.

A lipid-based approach to effectively modify DNA molecules onto various types of bacterial membranes after simple incubation.

Functional Nucleic Acid-Based Live-Cell Fluorescence Imaging

Cell is the structural and functional unit of organism. It serves as a key research object in various biological processes, such as growth, ontogeny, metabolism and stress. Studying the spatiotemporal distribution and functional activity of specific biological molecules in living cells is crucial for exploring the mechanism governing life. It also facilitates the elucidation of pathogenesis, clinical prevention and disease theranostics. In recent years, the fluorescence imaging technique has been greatly exploited for live-cell imaging. However, the development of molecular probes has lagged far behind. Functional nucleic acids (FNAs), for example, aptamer and DNAzyme, possess special chemical and/or biological functions, hence severing as promising molecular tools for cellular imaging. The current mini review focuses on the applications of FNAs in live-cell fluorescence imaging.

Lipid-oligonucleotide conjugates for bioapplications

Lipid-oligonucleotide conjugates (LONs) are powerful molecular-engineering materials for various applications ranging from biosensors to biomedicine. Their unique amphiphilic structures enable the self-assembly and the conveyance of information with high fidelity. In particular, LONs present remarkable potential in measuring cellular mechanical forces and monitoring cell behaviors. LONs are also essential sensing tools for intracellular imaging and have been employed in developing cell-surface-anchored DNA nanostructures for biomimetic-engineering studies. When incorporating therapeutic oligonucleotides or small-molecule drugs, LONs hold promise for targeted therapy. Moreover, LONs mediate the controllable assembly and fusion of vesicles based on DNA-strand displacements, contributing to nanoreactor construction and macromolecule delivery. In this review, we will summarize the general synthesis strategies of LONs, provide some characterization analysis and emphasize recent advances in bioanalytical and biomedical applications. We will also consider the relevant challenges and suggest future directions for building better functional LONs in nanotechnology and materials-science applications.

Live-Cell Imaging of Neurotransmitter Release with a Cell-Surface-Anchored DNA-Nanoprism Fluorescent Sensor

Neurotransmitters are essential chemical mediators for neuronal communication in variable neuromodulations. However, the progress of neuroscience is hampered by the shortage of suitable sensors to track neurotransmitters with high spatial and temporal resolution. Here, we introduce a self-assembled DNA-nanoprism fluorescent probe capable of nongenetically engineering the cell surface for ultrasensitive imaging of the neurotransmitter release at a single live-cell level. The DNA-nanoprism structure conjugated with three cholesterol tails enables the probe to rapidly and stably anchor on the cell surface within 10 min. The in situ detection of neurotransmitters is achieved by equipping the DNA-nanoprism with an aptamer-based "turn-on" fluorescent sensory module for the transmitter of interest. In a proof-of-concept study, we directly visualized the transient dopamine (DA) release on the cell surface with selective responsivity and high spatiotemporal precision and further explored the dynamic correlation between DA release and calcium influx triggered by high K⁺. This study provides a robust and sensitive tool for cell-surface-targeted imaging of neuromodulations, which might open up a new avenue to improve the understanding of neurochemistry and advance neuroscience research.