DNA-Programed Plasmon Rulers Decrypt Single-Receptor Dimerization on Cell Membrane

Engineered Artificial Nanochannels with Cell Membrane Nanointerface for Ultrasensitive Detection and Discrimination of Multiple Bacterial Infections

Bacterial infection is a major threat to global public health, which urgently require rapid and reliable analytical techniques for complex biological samples but remains a challenge. Herein, we developed an artificial affinity nanochannel with a cell membrane nanointerface, which enables broad-spectrum capture and specifically discriminates multiple pathogens. The macrophage membrane is pre-engineered with azide groups by a biometabolic process and then modified on a porous anodized aluminum oxide substrate via click reactions, preserving dynamic lateral fluidity and broad-spectrum recognition capacity. The macrophage membrane/anodized aluminum oxide membrane is evaluated with remarkable ion current rectification performance with a distinct current response upon bacterial binding, which realizes ultrasensitive detection of bacteria. Moreover, discrimination of bacterial species is achieved by further introducing specific antibodies. The nanochannel-based biosensor allows accurately capturing and quantifying multiple bacteria over a broad linear range, with a detection limit as low as 2.7 CFU/mL. Finally, this nanoplatform is successfully applied for broad-spectrum capture of bacterial species in several practical application scenarios including water, serum, and blood samples, achieving ultrasensitive detection and identification of bacteria below 10 CFU/mL. Overall, the proposed nanochannel with cell membrane nanointerface shows broad applicability in bacterial analysis, highlighting its potential in diagnosing infectious diseases.

Reversible engineering of cell membrane receptors based on host-guest recognition for on-demand regulation of cellular behavior

Cell receptors are key regulators of cellular signaling. However, on-demand reversible engineering of cell receptors to intervene in cellular behavior remains a challenge. Herein, a reversible receptor engineer strategy (SL1/NCDP/Ada) was developed. Initially, ferrocene (Fc)-modified aptamer (SL1-Fc) engaged in biorecognition with the mesenchymal epidermal transition factor (Met) receptor. Subsequently, β-cyclodextrin polymers (β-CDPs) recognized SL1-Fc through host-guest interactions, spatially engineering the Met receptor and, consequently, influencing cell proliferation and migration behavior (SL1/CDP strategy). In addition, due to the stronger host-guest recognition of adamantane (Ada) and β-CD, Ada could compete with SL1-Fc to bind CDPs, causing CDPs to be released from the cell surface, thereby eliminating the regulatory effect of SL1/CDPs and achieving reversible regulation of cell migration behavior. This approach employed cross-networked (NCDP) and linear cyclodextrin polymers (LCDP). The results showed that SL1/NCDP could induce Met receptor aggregation and activated the Met receptor due to the compact network structure of NCDP. In contrast, SL1/LCDP could not induce Met receptor aggregation due to the large spatial spacing of monomers in LCDP. However, SL1/LCDP could significantly inhibit ligand hepatocyte growth factor (HGF)-induced Met receptor activation by targeting the Met receptor and indirectly regulate cell proliferation and migration behavior. This work provides a novel strategy to reversibly engineer cell receptors in a customized manner to regulate cell proliferation and migration behavior on demand.

Innovative Progress of LSPR-Based Dark-Field Scattering Spectral Imaging in the Biomedical Assay at the Single-Particle Level

The growing demand for detection and sensing in the biomedical field is placing higher demands on technology. In clinical testing, it is expected to be able to realize both rapid large-field imaging and analysis of single particles (or single molecules or single cells), and it is expected to be able to grasp both the unique individuality of single particles in time and space during the complex reaction process, as well as the regular correlation between single particles in the same population distribution. Supported and promoted by the theory of localized surface plasmon resonance (LSPR), dark-field microscopy, as a single-particle optical imaging technique with a very high signal-to-noise ratio, provides a powerful new means to address the above clinical detection needs. This review will focus on the innovative applications of dark-field microscopy in biomedical-related assays in the past five years, introducing the basic principles and listing the impressing works. We also summarize how dark-field microscopy has been combined with other techniques, including surface-enhanced Raman scattering, fluorescence, colorimetry, electrochemistry, etc., to witness the joint progress and promotion of detection methods in the future. It also provides an outlook on the current challenges and future trends in this field.

Aggregation-induced color-coded imaging for HOCl detection in living cells with dark-field microscopy

In this work, we develop a nanoprobe for the detection of hypochlorous acid (HOCl), a key reactive oxygen species, utilizing dark-field microscopy (DFM). The nanoprobe is constructed by covalently attaching PEG-SH and an HOCl-sensitive molecule, FD, to gold nanoparticles (GNPs-FD-PEG). This probe detects HOCl by observing a color shift from green to red due to the aggregation of GNPs, which is triggered by HOCl-induced the cleavage of FD molecule. This aggregation occurs primarily due to electrostatic interactions between the differently charged particles following the cleavage. By recording the scattering signal changes of the GNPs-FD-PEG nanoprobe, we have achieved quantitative detection of HOCl, with a linear response range of 0.5-50 μM and a detection limit of 0.16 μM. By integrating the high-resolution capabilities of DFM imaging with the distinct color change due to electrostatic-induced nanoparticle aggregation, the constructed nanoprobe effectively monitors HOCl in live cells.

Cholesterol- and ssDNA-binding fusion protein-mediated DNA tethering on the plasma membrane

DNA modification of the plasma membrane is an excellent approach for controlling membrane-protein interactions, modulating cell-cell/cell-biomolecule interactions, and extending the biosensing field. The hydrophobic insertion of DNA conjugated with hydrophobic anchoring molecules is utilized for tethering DNA on the cell membrane. In this study, we developed an alternative approach to tether DNA on the plasma membrane based on ssDNA- and cholesterol-binding proteins. We designed a fusion protein (Rep-ALOD4) composed of domain 4 of anthrolysin O (ALOD4), which binds to cholesterol in the plasma membrane, and a replication initiator protein derived from porcine circovirus type 2 (Rep), which forms covalent bonds with single-stranded DNA (ssDNA) with a Rep recognition sequence. Rep-ALOD4 conjugates ssDNA to Rep and binds to the plasma membrane via cholesterol, thus tethering ssDNA to the cells. Quartz crystal microbalance measurements showed that membrane cholesterol binding of Rep-ALOD4 to the lipid bilayer containing cholesterol was accelerated above 20% (w/w) cholesterol in the lipid bilayer. Rep-ALOD4 was conjugated to fluorescein-labeled ssDNA (S-FITC-Rep-ALOD4) and used to treat human cervical tumor HeLa cells. The green signal assigned to S-FITC-Rep-ALOD4 was detected along HeLa cells, whereas diminished by cholesterol removal with methyl β-cyclodextrins. Moreover, ssDNA-conjugated Rep-ALOD4 tethered ssDNA-conjugated functional proteins on the HeLa cell plasma membrane via complementary base pairing. Collectively, Rep-ALOD4 has the potential as an ssDNA-tethering material via plasma membrane cholesterol to extend cell surface engineering.

Efficient Multidriven Strand Displacement Reaction for Biosensing

A key challenge for achieving high-efficient DNA strand displacement reaction (SDR) with existing technologies is the inferior kinetic performance due to the alternately cumbersome conjunction and dissociation of dsDNA. In this work, a novel multidriven SDR collaborated by toehold initiator, strand towing, and click chemistry is engineered. The invasion strand (O) endows the hybridization with a basal strand (M) in dsDNA for releasing a displacement strand (P), which can be significantly boosted by the towing of a helper strand and impetus from the click reaction. Accordingly, the hybridization rate and dissociation extent of P can be largely improved and showed a desiring displacement rate close to 6-fold compared with the traditional method, providing a newly high-efficient SDR strategy for potential application in biosensing, clinical diagnostics, and DNA nanotechnology. In view of this, a practical biosensing platform by combining the multidriven SDR (MSDR) with waste-free DNA multi-cycle amplification is constructed for the rapid and ultrasensitive electrochemical detection of cancer-related miRNA-21. The substantial output DNA as an invasion strand (O) from target-triggered waste-free DNA multicycle can high-efficiently release a signal probe (Fc)-labeled displacement strand (P) on an electrode by using the proposed MSDR, obtaining a low detection limit below 106.8 aM.

DNA-modulated dimerization and oligomerization of cell membrane receptors

DNA-based nanostructures and nanodevices have recently been employed for a broad range of applications in modulating the assemblies and interaction patterns of different cell membrane receptors. These versatile nanodevices can be rationally designed with modular structures, easily programmed and tweaked such that they may act as smart chemical biology and cell biology tools to reveal insights into complicated cellular signaling processes. Their outstanding in vitro and cellular features have also begun to be further validated for some in vivo applications and demonstrated their great biomedical potential. In this review, we will highlight some key current advances in the molecular engineering and biological applications of DNA-based functional nanodevices, with a focus on how these tools have been used to respond and modulate membrane receptor dimerizations and/or oligomerizations, as a way to control cellular signaling processes. Some current challenges and future directions to further develop and apply these DNA nanodevices will also be discussed.

Atomic Force Microscopy Lifetime Analysis: An Intuitive Method for Evaluating Receptor Tyrosine Kinase Dimer-Targeting Inhibitors

Overexpression of receptor tyrosine kinases (RTKs) or binding to ligands can lead to the formation of specific unliganded and liganded RTK dimers, and these two RTK dimers are potential targets for preventing tumor metastasis. Traditional RTK dimer inhibitor analysis was mostly based on end point assays, which required cumbersome cell handling and behavior monitoring. There are still challenges in developing intuitive process-based analytical methods to study RTK dimer inhibitors, especially those used to visually distinguish between unliganded and liganded RTK dimer inhibitors. Herein, taking the mesenchymal-epithelial transition factor (MET) receptor, an intuitive method for evaluating MET inhibitors has been developed based on atomic force microscopy (AFM) lifetime analysis. The time interval between the start of the force and the bond break point was regarded as the bond lifetime, which could reflect the stability of the MET dimer. The results showed that there was a significant difference in the lifetime (τ) of unliganded MET dimers (τ1 = 207.87 ± 4.69 ms) and liganded MET dimers (τ2 = 330.58 ± 15.60 ms) induced by the hepatocyte growth factor, and aptamer SL1 could decrease τ1 and τ2, suggesting that SL1 could inhibit both unliganded and liganded MET dimers. However, heparin only decreased τ2, suggesting that it could inhibit only the liganded MET dimer. AFM-based lifetime analysis methods could monitor RTK dimer status rather than provide overall average results, allowing for intuitive process-based analysis and evaluation of RTK dimers and related inhibitors at the single-molecule level. This study provides a novel complementary strategy for simple and intuitive RTK inhibitor research.

Self-Powered Engineering of Cell Membrane Receptors to On-Demand Regulate Cellular Behaviors

On-demand engineering of cell membrane receptors to nongenetically intervene in cellular behaviors is still a challenge. Herein, a membraneless enzyme biofuel cell-based self-powered biosensor (EBFC-SPB) was developed for autonomously and precisely releasing Zn2+ to initiate DNAzyme-based reprogramming of cell membrane receptors, which further mediates signal transduction to regulate cellular behaviors. The critical component of EBFC-SPB is a hydrogel film on a biocathode which is prepared using a Fe3+-cross-linked alginate hydrogel film loaded with Zn2+ ions. In the working mode in the presence of glucose/O2, the hydrogel is decomposed due to the reduction of Fe3+ to Fe2+, accompanied by rapid release of Zn2+ to specifically activate a Zn2+-responsive DNAzyme nanodevice on the cell surface, leading to the dimerization of homologous or nonhomologous receptors to promote or inhibit cell proliferation and migration. This EBFC-SPB platform provides a powerful "sensing-actuating-treating" tool for chemically regulating cellular behaviors, which holds great promise in precision biomedicine.

Dark-field imaging and fluorescence dual-mode detection of microRNA-21 in living cells by core-satellite plasmonic nanoprobes

The in situ precise quantification and simultaneous imaging of low abundance microRNAs (miRNAs) within living cells is critical for cancer diagnosis, yet it remains a significant challenge. Leveraging the excellent sensitivity and spatiotemporal resolution of dark-field microscopy (DFM) and fluorescence imaging, we have successfully devised a novel detection approach using dual-signal reporter probes (DSRPs). These probes allow for highly sensitive detection of miRNA-21 in living cells via toehold-mediated strand displacement cascades. The DSRPs were constructed by Au nanoparticles and Ag nanoclusters core-satellite nanostructures. After the recognition of miRNA-21, the strand displacement cascades were triggered, inducing the disassembly of the Au/Ag core-satellite nanostructure with apparent scattering intensity decrease and peak wavelength shifts. Additionally, the fluorescence of Ag clusters could be recovered and further enhanced when in close proximity to specific guanine-rich strands. The dual-signal response capability enables the accurate detection of miRNA-21 from 1 fM to 1 nM, with a limit of detection reached 0.75 fM. DFM and fluorescent imaging of living cells efficiently confirms the applicable detection of miRNA-21 in complex detection media. The biosensor based on DSRPs represents a promising nanoplatform for visual monitoring and imaging of biomolecules in living cells, even at the single particle level.

Polymeric membrane potentiometric sensors based on template-removal-free imprinted receptors for determination of antibiotics

Currently, Nernstian-response-based polymeric membrane potentiometric sensors using molecularly imprinted polymers (MIPs) as receptors have been successfully developed for determination of organic ionic species. However, the preparation of these MIP receptors usually involves tedious and time-consuming template-removal procedures. Herein, a template-removal-free MIP is proposed and used as a receptor for fabrication of a potentiometric sensor. The proposed methodology not only significantly shortens the preparation time of MIP-based potentiometric sensors but also improves the batch-to-batch reproducibility of these sensors. By using antibiotic vancomycin as a model, the new concept offers a linear concentration range of 1.0 × 10-7 to 1.0 × 10-4 mol L-1 with a detection limit of 2.51 × 10-8 mol L-1. It can be expected that the template-removal-free MIP-based sensing strategy could lay the foundation for simple fabrication of electrochemical sensors without the need for template removal such as potentiometric and capacitive sensors and ion-sensitive field-effect transistors.

Amplified and Specific Staining of Protein Dimerization on Cell Membrane Catalyzed by Responsively Installed DNA Nanomachines for Cancer Diagnosis

In situ staining of protein dimerization on cell membrane has an important significance in accurate diagnosis during perioperative period, yet facile integration of specific recognition function and local signal conversion/amplification abilities on membrane surface remains a great challenge. Herein, a two-stage catalytic strategy is developed by installing DNA nanomachines and employing. Specifically, dual-aptamer-assisted DNA scaffold perform a "bispecific recognition-then-computing" operation and the output signal initiate a membrane-anchored biocatalysis for self-assembly of DNA catalytic converters, that is, G-quadruplex nanowire/hemin DNAzyme. Then, localized-deposition of chromogenic polydopamine is chemically catalyzed by horseradish peroxidase-mimicking DNAzyme and guided by supramolecular interactions between conjugate rigid plane of G-tetrad and polydopamine oligomer. The catalytic products exhibit nanofiber morphology with a diameter of 80-120 nm and a length of 1-10 µm, and one-to-one localize on DNA scaffold for amplified and specific staining of protein dimers. The bispecific staining leads to a higher (≈3.4-fold) signal intensity than traditional immunohistochemistry, which is beneficial for direct visualization. Moreover, an efficient discrimination ability of the bispecific staining strategy is observed in co-culture model staining. This study provides a novel catalytic method for controlling deposition of chromogens and paves a new avenue to sensitively stain of protein-protein interactions in disease diagnosis.

Imaging GPCR Dimerization in Living Cells with Cucurbit[7]uril and Hemicyanine as a "Turn-On" Fluorescence Probe

Although multiple forms of dimers have been described for GPCR, their dynamics and function are still controversially discussed field. Fluorescence microscopy allows GPCR to be imaged within their native context; however, a key challenge is to site-specifically incorporate reporter moieties that can produce high-quality signals upon formation of GPCR dimers. To this end, we propose a supramolecular sensor approach to detect agonist-induced dimer formation of μ-opioid receptors (μORs) at the surface of intact cells. With the macrocyclic host cucurbit[7]uril and its guest hemicyanine dye tethered to aptamer strands directed against the histidine residues, the sensing module is assembled by host-guest complexation once the histidine-tagged μORs dimerize and bring the discrete supramolecular units into close proximity. With the enhanced sensitivity attributed by the "turn-on" fluorescence emission and high specificity afforded by the intermolecular recognition, in situ visualization of dynamic GPCR dimerization was realized with high precision, thereby validating the supramolecular sensing entity as a sophisticated and versatile strategy to investigate GPCR dimers, which represent an obvious therapeutic target.

Quality Control of Mass-Encoded Nanodevices by Compartmented DNA Origami Frames for Precision Information Coding and Logic Mapping

Encoded nanostructures afford an ideal platform carrying multi-channel signal components for multiplexed assay and information security. However, with the demand on exclusivity and reproducibility of coding signals, precise control on the structure and composition of nanomaterials featuring fully distinguishable signals remains challenging. By using the multiplexing capability of mass spectrometry (MS) and spatial addressability of DNA origami nanostructures, we herein propose a quality control methodology for constructing mass-encoded nanodevices (namely MNTs-TDOFs) in the scaffold of compartmented tetrahedral DNA origami frames (TDOFs), in which the arrangement and stoichiometry of four types of mass nanotags (MNTs) can be finely regulated and customized to generate characteristic MS patterns. The programmability of combinatorial MNTs and orthogonality of individual compartments allows further evolution of MNTs-TDOFs to static tagging agents and dynamic nanoprobes for labeling and sensing of multiple targets. More importantly, structure control at single TDOF level ensures the constancy of prescribed MS outputs, by which a high-capacity coding system was established for secure information encryption and decryption. In addition to the multiplexed outputs in parallel, the nanodevices could also map logic circuits with interconnected complexity and logic events of c-Met recognition and dimerization on cell surface for signaling regulation by MS interrogation.

Transformable DNA Nanorobots Reversibly Regulating Cell Membrane Receptors for Modulation of Cellular Migrations

Oligomerization of cellular membrane receptors plays crucial roles in activating intracellular downstream signaling cascades for controlling cellular behaviors in physiological and pathological processes. However, the reversible and controllable regulation of receptors in a user-defined manner remains challenging. Herein, we developed a versatile DNA nanorobot (nR) with installed aptamers and hairpin structures to reversibly and controllably regulate cell migration. This was achieved by dimerization and de-dimerization of mesenchymal-epithelial transition (Met) receptors through DNA strand displacement reactions. The functionalized DNA nR not only plays similar roles as hepatocyte growth factor (HGF) in inducing cell migration but also allows a downgrade to the original state of cell migration. The advanced DNA nanomachines can be flexibly designed to target other receptors for manipulating cellular behaviors and thus represent a powerful tool for the future of biological and medical engineering.

Enzymatic DNA repairing amplification-powered construction of an Au nanoparticle-based nanosensor for single-molecule monitoring of cytosine deaminase activity in cancer cells

APOBEC3A (A3A) is a cytidine deaminase with critical roles in molecular diagnostics. Herein, we demonstrate the enzymatic DNA repairing amplification-powered construction of an Au nanoparticle-based nanosensor for single-molecule monitoring of A3A activity in cancer cells. Target A3A can convert cytosine (C) in substrate probe to uracil (U), and then the template binds with substrate probe to form a dsDNA containing U/A base pairs. Uracil DNA glycosylase (UDG) excises the U base to produce an apurinic/apyrimidinic (AP) site that can be cleaved by apurinic/apyrimidic endonuclease 1 (APE1) to obtain the substrate fragment with 3'-OH end. Subsequently, the substrate fragment initiates cyclic enzymatic repairing amplification (ERA), releasing trigger-1 and trigger-2. The resultant trigger-1 can act as the primer to induce multiple cycles of cyclic ERA, producing numerous trigger-1 and trigger-2. The hybridization of trigger-2 with signal probe forms the dsDNA duplexes with an AP site, inducing the cyclic cleavage of signal probes by APE1 to release abundant Cy5 molecules from the AuNPs. Released Cy5 molecules can be easily quantified by single-molecule imaging. This nanosensor allows for specific and sensitive detection of A3A activity with a detection limit of 0.855 aM, and it can further measure kinetic parameters, screen inhibitors, and quantify endogenous A3A activity at the single-cell level, with prospect application in disease diagnostics and therapy.

Ultrasensitive Multiplex Imaging of Cell Surface Proteins via Core-Shell Surface-Enhanced Raman Scattering Nanoprobes

Cell surface proteins, as important components of biological membranes, cover a wide range of important markers of diseases and even cancers. In this regard, precise detection of their expression levels is of crucial importance for both cancer diagnosis and the development of responsive therapeutic strategies. Herein, a size-controlled core-shell Au@ Copper(II) benzene-1,3,5-tricarboxylate (Au@Cu-BTC) nanomaterial was synthesized for specific and simultaneous imaging of multiple protein expression levels on cell membranes. The porous shell of Cu-BTC constructed on Au nanoparticles enabled effective loading of Raman reporter molecules, followed by further modification of the targeting moieties, which equipped the nanoprobe with good specificity and stability. Additionally, given the flexibility of the types of Raman reporter molecules available for loading, the nanoprobes were also demonstrated with good multichannel imaging capabilities. Ultimately, the present strategy of electromagnetic and chemical dual Raman scattering enhancement was successfully applied for the simultaneous detection of varied proteins on cell surfaces with high sensitivity and accuracy. The proposed nanomaterial holds promising applications in biosensing and therapeutic fields, which could not only provide a general strategy for the synthesis of metal-organic framework-based core-shell surface-enhanced Raman scattering nanoprobes but also enable further utilization in multitarget and multichannel cell imaging.