ACS Sensors

Pancreatic beta cells face exceptional protein folding demands from high insulin production requirements, placing extraordinary stress on the ER and contributing to dysfunction in diabetes pathogenesis. Monitoring ER stress dynamics in living cells remains challenging due to the destructive nature of traditional biochemical methods and the limitations of existing fluorescent sensors. Here, we present Apollo-IRE1, a genetically encoded sensor that reports on stress-induced IRE1 oligomerization and associated change in homoFRET via changes in fluorescence anisotropy. Apollo-IRE1 provides a ratiometric, intensity-independent readout, resulting in low day-to-day variability and a minimal spectral bandwidth, enabling multiplexed imaging alongside other cellular parameters. Photobleaching and enhancement curve analysis show that Apollo-IRE1 exists in apparent monomeric, dimeric, and oligomeric states corresponding to baseline, moderate, and terminal ER stress conditions. The sensor also responds rapidly to chemical and physiological ER stressors in both immortalized beta-cell lines and primary mouse islet cells. These data establish Apollo-IRE1 as a practical tool for investigating ER stress dynamics in beta cells and other contexts where longitudinal single-cell measurements are essential.

Inorganic polyphosphate (polyP), a linear polymer of orthophosphate residues, is involved in a range of cellular processes, including phosphate storage, blood clotting, chromatin remodeling, RNA processing, and mitochondrial function. Despite its significance, tools for monitoring polyP with specificity and in real time are lacking, limiting insights into its dynamics. Here, we present FRAPPe (FRET-based Ratiometric Analysis of Polyphosphate), a FRET-based sensor for polyP. FRAPPe consists of an eCFP-eYFP FRET pair flanking CHAD, a polyP-binding domain. The sensor remains unresponsive to nucleic acids and other polyanions, while polyP binding induces a significant decrease in FRET, allowing quantitative estimation of polyP. We further show that FRAPPe can qualitatively estimate polyP levels from crude cell extracts, supporting its utility in high-throughput genetic and pharmacological screens to identify regulators of polyP metabolism and signaling.

Adenosine triphosphate (ATP) is a central molecule in cellular metabolism, serving as the primary energy currency that links catabolic and anabolic pathways. Monitoring intracellular ATP in vivo is essential for understanding the dynamics of metabolic states, as well as intracellular functions and intercellular interactions in health and disease. We report the design and application of ATPLyzer, a series of genetically encoded, ratiometric biosensors for the monitoring of ATP levels in living cells. The matryoshka design consists of an ATP-binding cassette linked to a circularly permutated GFP coupled with an internal large stokes shift reference fluorophore, allowing for single-wavelength excitation and ratiometric output. This design overcomes limitations of conventional biosensors, reliance on dual excitation wavelengths, and susceptibility to photobleaching. Multi-colour ATPLyzer variants with different dissociation constants were characterized in vitro, exhibiting high specificity for ATP over ADP. Monitoring ATP in Escherichia coli confirmed in vivo utility and revealed growth-phase and carbon-supply-dependent ATP dynamics. The ATPLyzer biosensor offers a robust and tuneable tool for minimally invasive, time-resolved monitoring of intracellular ATP dynamics.

Staphylococcus aureus is the leading cause of soft tissue infections that can be treated with antibiotics. However, it can also cause significant mortality and morbidity due to systemic infections and infections of surgical implants. Implant infections typically require invasive surgery, and treatment often necessitates removal of the implant because S. aureus biofilms are extremely difficult to eradicate with antibiotic treatment alone. Therefore, there is a significant need for improved diagnostic tools for rapid, non-invasive confirmation of S. aureus infections. We recently developed an activity-based probe containing an oxadiazolone electrophile that selectively labels the S. aureus-specific serine hydrolase, FphE, by covalent binding to its active site serine residue. Here we describe a Cy5-labeled version of the probe, JJ-OX-012, and its characterization as an imaging agent for detecting biofilms both in vitro and in vivo. The probe labeled S. aureus biofilms in vitro, with virtually no background labeling of bacteria that lack FphE expression. Furthermore, we demonstrate that JJ-OX-012 can be used for non-invasive fluorescent imaging as a way to detect S. aureus biofilms in vivo. Overall, these findings support the potential for using covalent probes targeting FphE as imaging agents for rapid detection and diagnosis of staphylococcal infections in vivo.

pH-sensitive fluorescent proteins (FPs) play a crucial role in investigating pH-related cellular processes, such as endocytosis and exocytosis. Existing pH-sensitive FPs generated from Aequorea victoria green fluorescent protein (GFP), such as superecliptic pHluorin (SEP) and Lime, have been widely employed to study these processes, but suffer from low photostability. Here, we report the development and characteristics of serapH, a genetically encodable pH biosensor with improved photostability compared to GFP analogues, which we generated using mStayGold as a scaffold. To aid in the development of serapH, we developed a method for screening pH-sensitive FP variants by directly evaluating both brightness and pH sensitivity in bacterial colonies on agar. This significantly increased the number of colonies that could be screened per round and reduced the time needed per round. The photostability of serapH should improve spatiotemporal resolution by increasing tolerance to higher excitation intensities and longer imaging durations, thereby expanding the range of applications of pH-sensitive FPs.

TNF- (Tumor Necrosis Factor) is a proinflammatory cytokine that amplifies inflammatory response and promotes leukocyte recruitment. TNF- is primarily produced by activated macrophages, among others, in response to infection, inflammation, or tissue damage. Given its central role in normal and abnormal immune responses, it is the target of several therapeutics, such as adalimumab and etanercept. TNF- is also a prognostic and diagnostic biomarker associated with Rheumatoid Arthritis, Alzheimers disease, Multiple Sclerosis, several kidney diseases, several cancers, Type 2 diabetes, sepsis, and others. Spatial quantification of TNF- in disease models can also be a powerful tool to understand the contributions of inflammatory processes to disease progression. Single-walled carbon nanotubes (SWCNT) are cylindrical carbon lattices that emit distinct near-infrared bandgap photoluminescence. In this work, we evaluated three aptamer-based sensor constructs, plus an additional two iterations of one aptamer sequence, and two antibody-based sensor constructs for TNF- that use SWCNT near-infrared photoluminescence signal transduction. Several, but not all, of these aptamer and antibody-based sensors sensitively and selectively detected TNF- in serum in a physiologically relevant range, and we found that their sensing was improved by both passivation and incorporating an exogenous quencher onto the aptamer sequence. Specifically, we found that modification of one aptamer sequence with a Black Hole Quencher induced selective detection in serum when passivated with poly-L-Lysine. This study highlights the importance, and challenges, of translating previously-validated molecular recognition elements to new detection conditions, in this case on the surface of SWCNT and in challenging serum conditions. It also validated a lead sensor construct that builds upon constructs that failed in serum. We anticipate that the sensors evaluated here will have utility in both the diagnosis and study of inflammation-driven chronic disease, while the sensor assessment framework will help drive the broader field of molecularly specific diagnostics.

Diagnostic sensor development and clinical translation lag, in part, due to a lack of rapid, high-throughput screening methodology. Optimization of high-throughput sensor development and deployment will likely help in expediting tools toward the clinic. To address this issue, we optimized high-throughput screening parameters using a near-infrared (NIR-II) plate reader attached to an external probe for in vivo testing. We assessed spectroscopy parameters to improve speed and precision in screening a single-walled carbon nanotube (SWCNT)-based optical sensor. To do so, we assessed the appropriate well plate specifications, including laser power, excitation wavelength, exposure time, and focal height parameters for SWCNT-based optical sensor development. We also used the plate reader to screen fluorescent SWCNT which were endocytosed by a macrophage cell line. We then performed NIR probe spectroscopy to assess SWCNT embedded within a methylcellulose hydrogel. Finally, we used the NIR probe to measure SWCNT center wavelength and intensity from live immunocompetent mice. We anticipate that this framework may be broadly applicable to the development of near infrared nanosensors with the potential for more rapid clinical diagnostic translation.

The sensitive detection of nucleic acids is crucial for the accurate diagnosis of infections. In this context, amplification-based methods, such as the quantitative Polymerase Chain Reaction (qPCR) are the gold standard for ultrasensitive DNA or RNA detection and quantification. However, despite its widespread use in developed countries during the COVID-19 pandemic, qPCR remains a costly tool, difficult to implement into low-infrastructure locations. Efforts for the development of alternative tools have yielded high sensitivity approaches but sensitivity is typically reached at the expense of complexity. We here report the development of a simple, sensitive, amplification-, and enzyme-free nucleic acid detection technique using YVO4:Eu luminescent nanoparticles. We established an optimized interaction scheme to efficiently reveal target DNA fragments with nanoparticles. By exploiting the extremely strong absorption of the vanadate matrix in the UV to excite the nanoparticles inducing the characteristic Eu3+ emission at 617 nm via energy transfer, we achieved a highly sensitive (down to 500 particles/mm2; 17,000 particles/well) read-out in standard microplates using a home-made optical reader with light-emitting diode (LED), 275-nm excitation. We reached a 50-aM (30,000 copies/mL) sensitivity for the detection of the 72-base DNA fragment of the SARS-CoV-2 n1 gene. Our new quantitative analytical method detects nucleic acids without amplification with performances close to standard PCR (10,000 copies/mL)1, and could be the basis for a transportable alternative for the diagnosis of infectious diseases.

Proximity ligation assay (PLA), in which the ligation of two DNA probes is greatly accelerated by the associating target molecules, has emerged as a highly sensitive technique for protein detection. The detection of the ligated DNA typically relies on PCR, which requires temperature cycling. In this study, we report on a novel discontinuous (DISCO)-LAMP assay that enables the wash-free detection of PLA products via loop-mediated isothermal amplification (LAMP). Due to the exponential amplification nature of LAMP, a careful balance between efficient amplification of the ligated full-length DNA and minimal background amplification from the individual constituent probes is essential but often challenging to achieve. After extensive template/primer design and assay optimization, DISCO-LAMP assay achieved a detection limit of 1 fM for the ligated DNA probe while maintaining undetectable background amplification at 1 nM of each individual probe. DISCO-LAMP detected Shiga toxin 2 (Stx2) with a limit of detection (LoD) of 100 fM when functionalized with Stx2-binders, as well as both Wuhan-1 and Omicron spike protein when functionalized with DS16, a newly engineered DARPin targeting a conserved epitope on the SARS-CoV-2 Spike protein. We believe DISCO-LAMP represents a versatile and efficient LAMP-based PLA technology that is readily adaptable for sensing diverse targets.

Monitoring dopamine in complex biological environments is essential for understanding neurological disorders and disease diagnosis, though it presents a unique chemical challenge. In this work, we rationally designed several single-walled carbon nanotube (SWCNT)-based near-infrared fluorescent sensors for dopamine using ssDNA aptamers as selective molecular recognition elements. The performance of three dopamine-selective aptamer-SWCNT hybrids and sensitive but non-selective (GT)10-SWCNT constructs were evaluated and compared for their magnitude of response, sensitivity, and selectivity to dopamine. We performed these studies in buffer, in complex media with noradrenaline and serotonin, and in synthetic cerebrospinal fluid. We evaluated sensor constructs alone, with heat + divalent cation addition, and with four different molecular passivation agents. Ultimately, sensors passivated with bovine serum albumin (BSA) demonstrated strong selectivity for dopamine relative to noradrenaline, serotonin, and ascorbic acid, with a greater magnitude of response compared to (GT)10-SWCNT. Concentration-response curves in PBS, in a serotonin and noradrenaline solution, and artificial cerebrospinal fluid (aCSF) revealed dynamic ranges between 30 and 200 nM, and we found that the response occurs within five minutes. Together, these results demonstrate that dopamine aptamer-SWCNT sensors enable more selective and robust optical detection in complex biological environments.

Cyclic dinucleotide (CDN) signaling molecules, such as cyclic di-GMP (c-di-GMP) and 3,3 cyclic GMP-AMP (cGAMP), are second messengers that play critical roles in phenotypic regulation, such as biofilm formation, host colonization, and bacterial virulence. Recently, hybrid promiscuous (Hypr) GGDEF proteins have been identified in certain bacteria to produce both cyclic dinucleotides. One such enzyme, Bd0367, from the predatory Bdellovibrio bacteriovorus, switches between synthesizing c-di-GMP and cGAMP to regulate the bacterial predation cycle and prey exit. However, the molecular mechanism controlling this switch remains unknown. Here, we introduce an RNA-based ratiometric, dual metabolite biosensor that enables simultaneous detection of c-di-GMP and cGAMP in live cells. This sensor integrates a Pepper-based biosensor for c-di-GMP detection and a Spinach2-based biosensor for cGAMP detection into a single transcript, producing distinct fluorescent outputs. In E. coli, the dual metabolite sensor reliably reported shifts in c-di-GMP/cGAMP production ratios from various CDN synthases, including Bd0367. Additionally, a histidine kinase was discovered as the probable regulatory partner of Bd0367. These findings demonstrate the sensors capacity to assess relative CDN levels and to uncover complex signaling pathways. Together, this ratiometric dual metabolite biosensor provides a foundation for broader applications of fluorogenic RNA biosensors in dissecting bacterial signaling networks, microbial ecology, and host-pathogen interactions.

Antibiotic treatment can fail due to insufficient drug availability at the site of infection or limited accumulation within bacterial pathogens. However, it is poorly understood how antibiotics penetrate infected tissues and complex bacterial aggregates, limiting insights into the mechanisms of treatment failure. Here, we present genetically-encoded allosteric biosensors for two antibiotic classes, trimethoprim and tetracycline, which enable real-time monitoring of antibiotic concentrations inside bacterial cells. The biosensors consist of circularly permuted EGFP linked to the sensory domains DHFR or TetR. To extend this approach to low oxygen environments, we engineered an oxygen-independent trimethoprim biosensor by fusing DHFR to a circularly permuted version of the fluorogenic protein FAST. Using these biosensors, we monitored the antibiotic exposure dynamics of intracellular Salmonella enterica during macrophage infection at the single-cell level, and antibiotic penetration into anaerobic regions of Vibrio cholerae biofilms, as well as antibiotic availability in microoxic conditions in a human bladder tissue model infected with uropathogenic Escherichia coli. These fluorescent biosensors have the potential to be broadly applied for determining antibiotic distributions at infection sites with high spatial and temporal resolution.

Digital immunoassays provide exceptional analytical sensitivity for detecting low-abundance biomarkers, but their broad adoption is limited by practical barriers. Commercial platforms are prohibitively expensive for routine use by individual laboratories, and laboratory-scale concepts typically describe specialized biosensors and sophisticated workflows. Here, we introduce a nanomembrane-based Catch-and-Display Immunoassay (CAD-IA) as an accessible digital immunoassay for common laboratory settings. In CAD-IA, fluorescent nanoparticles are "captured" by the nanoscale pores of ultrathin silicon nitride membranes through a pipette powered filtration. The captured nanoparticles serve as optically isolated hotspots for fluorescent immunocomplex formation when target antigen is present. Co-localization of the fluorescent particles and fluorescent immunocomplexes are then "displayed" and quantified by standard confocal microscopy to generate digital signals. CAD-IA is implemented using the {micro}SiM-DX (microfluidic device featuring an ultrathin silicon membrane for diagnostics) platform, which is manually assembled from mass produced, cost-effective components. Using the traumatic brain injury (TBI) biomarker S100B as a model, we demonstrate that CAD-IA provides consistent digital outputs and linear quantification with a dynamic range of at least two orders of magnitude when digital and analog analysis are combined on the same image sets. We further demonstrate that the assay maintains linearity in serum matrices and achieves suitable sensitivity (LoD = 0.02 g/mL) for clinically relevant diagnostic with the addition of tyramide signal amplification (TSA). While further optimization of CAD-IA is possible, these results constitute a proof-of-concept demonstration of a novel digital immunoassay that is accessible to most laboratory environments.

Cortisol is a primary biomarker of stress, released in sweat at concentrations that directly correlate with physiological stress levels. Detecting cortisol non-invasively offers significant potential for real-time stress monitoring and healthcare applications. Biosensors capable of binding cortisol can thus enable the development of novel diagnostic platforms for personalised health management. In our earlier work, a 38-mer peptide fragment derived from the protein 2V95 was identified as a functional binder to cortisol. In the present study, we applied generative artificial intelligence (AI) approaches to expand the sequence space and identify superior candidate peptides with improved binding affinity. By integrating sequence-based and structure-based AI models, we generated and screened a peptide library of nearly 10,000 sequences against cortisol, leading to the identification of high-affinity candidates for further evaluation.

Early diagnosis of Parkinsons disease (PD) is critical, as clinical symptoms typically emerge only after substantial neuronal loss. While -synuclein (-Syn) oligomers in blood are promising biomarkers for early detection, their clinical utility is limited by their low abundance and the presence of inhibitory components in the plasma matrix. To address these limitations, we tailored the Nanoparticle-enhanced Quaking-Induced Conversion (Nano-QuIC) platform specifically for the ultrasensitive detection of -Syn oligomers in human plasma. We identified critical reaction determinants by investigating buffer pH, ionic strength, detergent types, and shaking conditions. Furthermore, the integration of silica nanoparticles (siNPs) proved essential in mitigating plasma matrix interference, ensuring robust and reproducible protein aggregation. Under these optimized conditions, the assay achieved a detection limit of 100 pg/mL for -Syn oligomers spiked into human plasma. These results demonstrate that our adapted Nano-QuIC platform provides a highly sensitive and minimally invasive method for detecting pathological -Syn species, offering a significant advancement toward the development of early-stage PD diagnostics.

Continuous monitoring of protein biomarkers could transform the management of acute and chronic diseases. Despite tremendous potential, wearable health monitors have remained largely limited to metabolites and small molecules. A key challenge is the limited availability of biointerfaces that reversibly track low-abundance proteins in vivo without user intervention. Here, we present the Differential Aptalyzer, a minimally invasive hydrogel microneedle platform for continuous monitoring of proteins in skin interstitial fluid. The platform combines high-affinity antibodies for selective target capture with aptamers for reversible electrochemical signal transduction. When integrated into a differential electrochemical chip and pulse-assisted sensor regeneration, this approach enables continuous monitoring of proteins in a wearable format. Using cardiac troponin I (cTnI) as a clinically-relevant model analyte, Differential Aptalyzer offers a broad dynamic range (0.003-0.640 ng/mL) and strong specificity against interfering proteins. Importantly, this platform reliably tracks both rising and falling exogenous cTnI levels injected into healthy mice, as well as endogenously elevated cTnI in a double-knockout mouse model of coronary artery disease, demonstrating its capability in continuous protein monitoring and identifying coronary artery disease cohorts.

Fluorescence microscopic methods are critical for spatial profiling of multiple biological targets in cells and tissues to study cell and tissue functions, but their multiplexity was limited to 3[~]5 targets under a conventional setup using different fluorescent channels because of spectra overlap. Here, we introduce a simple, rapid, multiplexed fluorescence imaging method in cells and tissues, termed DNA based plasmonic heating activated signal exchange reaction (PHASER). PHASER uses infrared light-induced plasmonic heating of gold bipyramid nanoparticles to sequentially activate thermodynamically calibrated DNA thermal probes in situ for rapid and multiplexed fluorescent imaging of biological targets. We showed that the signal exchange per round between biological targets in PHASER can be completed within 30 seconds, and that 5 irradiation pulses of photothermal heating can activate DNA thermal probes with 5 different signal temperatures in cells and tissues. To demonstrate its practical use, we applied PHASER to profile the subcellular spatial organization of different organelles in cultured cells and resolved different protein spatial expression profiles in mouse brain tissue with dimensions of millimeters in a single fluorophore channel. PHASER is expected to have broad biotechnical applications with multiplexed fluorescence imaging for a wide variety of biological targets across diverse samples.

Colorimetric loop-mediated isothermal amplification (LAMP) on microfluidic paper-based analytical devices (PADs) offers a low-cost, disposable, and equipment-free alternative to liquid LAMP assays. However, amplification on PADs is consistently slower, by 5-46%, than reactions in tubes. To identify the origin of this delay, we evaluated heat transfer, diffusion in porous cellulose, and nonspecific adsorption of LAMP components across both high- and low-copy input regimes. Our results show that once thermal equilibrium is reached, reduced effective diffusion is the dominant contributor to the kinetic lag at low copy numbers, whereas nonspecific adsorption becomes the primary barrier at higher template concentrations. Pre-coating the paper with bovine serum albumin (BSA) mitigates adsorption. It narrows the tube-to-paper gap, thereby accelerating amplification of the SARS-CoV-2 ORF7ab synthetic gene by an average of 6 minutes, from 1E3 to 1E5 copies per reaction. These findings provide a mechanistic basis for the copy-number-dependent behavior of PAD LAMP and offer simple, low-cost strategies to improve the speed and reliability of PAD nucleic acid assays.

Neurotransmitters in the gut play a vital role in human health and neuroscience, and their real-time monitoring is essential for understanding underlying physiological mechanisms. However, bioelectronic systems capable of measuring neurotransmitters in vivo at the anatomical site of interest remain underdeveloped and largely depend on bulky, off-the-shelf electronic components, thereby constraining the development of systems that are both practical and minimally invasive. Here, we report a miniature ingestible pill that is capable of real-time in vivo sensing of two key neurotransmitters: serotonin (5-HT) and dopamine (DA). The system incorporates a fully printed three-electrode-based electrochemical sensor for neurotransmitter sensing and a custom application-specific integrated circuit (ASIC) that integrates all major functional blocks on a single chip, enabling a platform for fully wireless monitoring of gut neurotransmitters. The pill, measuring 5.8 mm in diameter and 19 mm in length, supports multiple electrochemical sensing techniques, including amperometry and voltammetry, with only 42 A of average current consumption. We demonstrate the ingestible platform through in vivo studies in rat animal models, enabling real-time monitoring of gut neurotransmitters.

KRAS mutations are among the most prevalent oncogenic alterations in colorectal, lung, and pancreatic cancer, yet their detection remains analytically challenging in the presence of an overwhelming wild-type (WT) background. Here, we report a photoelectrochemical (PEC) genotyping platform that integrates clamp-inhibited loop-mediated isothermal amplification (C-LAMP) with enzyme-free singlet oxygen (1O2)-driven PEC transduction for mutation-selective KRAS detection. Locked nucleic acid (LNA) clamp probes selectively suppress WT amplification during isothermal amplification, enriching mutant alleles and enabling single-nucleotide variant (SNV) discrimination with high selectivity. Amplified products are magnetically captured and transduced into photocurrent via visible-light-induced 1O2 redox cycling, eliminating enzymatic reporters and reducing background interference. The C-LAMP/PEC platform achieves a limit of detection of 35 copies {micro}L-1 (58 aM) and a minimum detectable variant allele frequency (VAF) of 4.8% in heterogeneous mutant/WT genomic DNA mixtures. Analytical performance was validated in cancer cell lines and in patient-derived fresh frozen tissues, showing complete concordance with Nanopore sequencing and droplet digital PCR (ddPCR) within the evaluated cohort (n = 16). This work introduces a robust and modular PEC biosensing strategy that combines molecular WT suppession with enzyme-free photoelectrochemistry, offering an economically competitive and instrumentation-simplified approach for clinically relevant KRAS mutation analysis toward decentralized testing.