Inexpensive Near-Infrared Fluorimeters: Enabling Translation of nIR-Based Assays to the Field

Resolving the Kinetics of Single-Walled Carbon Nanotube-Polyester Polyurethane Nanoparticle Conjugate Fluorescence Sensors toward Polymer Degrading Enzymes

Single-walled carbon nanotubes (SWCNTs) are fluorescent materials that have been developed as sensors for measuring the activities of enzymes. However, most sensors to date rely on end-point measurement and empirical functions to correlate enzyme concentrations with fluorescence responses. Less emphasis is put on analyzing time-dependent fluorescence responses and their connections with enzymatic kinetics. Here, improved from our previous sensor design, we use trimethylchitosan-wrapped SWCNTs to measure the enzymatic degradation rate of Impranil nanoparticles, a polyester polyurethane model substrate. Through careful analysis of the characteristic time constant and saturation fluorescence, which are resolved from time-dependent brightening responses of the sensors, linear relations are found between fluorescence change rates and both enzyme concentrations and Impranil-to-SWCNT ratios, thus showing that the reaction is first-ordered toward both enzyme and substrate concentrations. The proposed sensor design and data analysis strategy can quantitively determine the relative enzymatic activity and provide insights into the kinetics of sensors and enzymatic reactions.

High-Throughput Approaches to Engineer Fluorescent Nanosensors

Optical sensors are powerful tools to identify and image (biological) molecules. Because of their optoelectronic properties, nanomaterials are often used as building blocks. To transduce the chemical interaction with the analyte into an optical signal, the interplay between surface chemistry and nanomaterial photophysics has to be optimized. Understanding these aspects promises major opportunities for tailored sensors with optimal performance. However, this requires methods to create and explore the many chemical permutations. Indeed, many current approaches are limited in throughput. This affects the chemical design space that can be studied, the application of machine learning approaches as well as fundamental mechanistic understanding. Here, an overview of selection-limited and synthesis-limited approaches is provided to create and identify molecular nanosensors. Bottlenecks are discussed and opportunities of non-classical recognition strategies are highlighted such as corona phase molecular recognition as well as the requirements for high throughput and scalability. Fluorescent carbon nanotubes are powerful building blocks for sensors and their huge chemical design space makes them an ideal platform for high throughput approaches. Therefore, they are the focus of this article, but the insights are transferable to any nanosensor system. Overall, this perspective aims to provide a fresh perspective to overcome current challenges in the nanosensor field.

Facile Mechanochemical Functionalization of Hydrophobic Substrates for Single-Walled Carbon Nanotube Based Optical Reporters of Hydrolase Activity

Single walled carbon nanotubes (SWCNT) have recently been demonstrated as modular, near-infrared (nIR) probes for reporting hydrolase activity; however, these have been limited to naturally amphipathic substrate targets used to noncovalently functionalize the hydrophobic nanoparticles. Many relevant substrate targets are hydrophobic (such as recalcitrant biomass) and pose a challenge for modular functionalization. In this work, a facile mechanochemistry approach was used to couple insoluble substrates, such as lignin, to SWCNT using l-lysine amino acid as a linker and tip sonication as the mechanochemical energy source. The proposed coupling mechanism is ion pairing between the lysine amines and lignin carboxylic acids, as evidenced by FTIR, NMR, SEM, and elemental analyses. The limits of detection for the lignin-lysine-SWCNT (LLS) probe were established using commercial enzymes and found to be 0.25 ppm (volume basis) of the formulated product. Real-world use of the LLS probes was shown by evaluating soil hydrolase activities of soil samples gathered from different corn root proximal locations and soil types. Additionally, the probes were used to determine the effect of storage temperature on the measured enzyme response. The modularity of this mechanochemical functionalization approach is demonstrated with other substrates such as zein and 9-anthracenecarboxylic acid, which further corroborate the mechanochemical mechanism.

Monitoring Enzyme Activity Using Near-Infrared Fluorescent Single-Walled Carbon Nanotubes

Enzymes serve as pivotal biological catalysts that accelerate essential chemical reactions, thereby influencing a variety of physiological processes. Consequently, the monitoring of enzyme activity and inhibition not only yields crucial insights into health and disease conditions but also forms the basis of research in drug discovery, toxicology, and the understanding of disease mechanisms. In this context, near-infrared (NIR) fluorescent single-walled carbon nanotubes (SWCNTs) have emerged as effective tools for tracking enzyme activity and inhibition through diverse strategies. This perspective explores the physicochemical attributes of SWCNTs that render them well-suited for such monitoring. Additionally, we delve into the various strategies developed so far for successfully monitoring enzyme activity and inhibition, emphasizing the distinctive features of each principle. Furthermore, we contrast the benefits of SWCNT-based NIR probes with conventional gold standards in monitoring enzyme activity. Lastly, we highlight the current challenges faced in this field and suggest potential solutions to propel it forward. This perspective aims to contribute to the ongoing progress in biodiagnostics and seeks to engage the wider community in developing and applying enzymatic assays using SWCNTs.

Multifunction fluorescence open source in vivo/in vitro imaging system (openIVIS)

The widespread availability and diversity of open-source microcontrollers paired with off-the-shelf electronics and 3D printed technology has led to the creation of a wide range of low-cost scientific instruments, including microscopes, spectrometers, sensors, data loggers, and other tools that can be used for research, education, and experimentation. These devices can be used to explore a wide range of scientific topics, from biology and chemistry to physics and engineering. In this study, we designed and built a multifunction fluorescent open source in vivo/in vitro imaging system (openIVIS) system that integrates a Raspberry Pi with commercial cameras and LEDs with 3D printed structures combined with an acrylic housing. Our openIVIS provides three excitation wavelengths of 460 nm, 520 nm, and 630 nm integrated with Python control software to enable fluorescent measurements across the full visible light spectrum. To demonstrate the potential applications of our system, we tested its performance against a diverse set of experiments including laboratory assays (measuring fluorescent dyes, using optical nanosensors, and DNA gel electrophoresis) to potentially fieldable applications (plant and mineral imaging). We also tested the potential use for a high school biology environment by imaging small animals and tracking their development over the course of ten days. Our system demonstrated its ability to measure a wide dynamic range fluorescent response from millimolar to picomolar concentrations in the same sample while measuring responses across visible wavelengths. These results demonstrate the power and flexibility of open-source hardware and software and how it can be integrated with customizable manufacturing to create low-cost scientific instruments with a wide range of applications. Our study provides a promising model for the development of low-cost instruments that can be used in both research and education.

Lipid-Functionalized Single-Walled Carbon Nanotubes as Probes for Screening Cell Wall Disruptors

Membrane-active molecules are of great importance to drug delivery and antimicrobials applications. While the ability to prototype new membrane-active molecules has improved greatly with the advent of automated chemistries and rapid biomolecule expression techniques, testing methods are still limited by throughput, cost, and modularity. Existing methods suffer from feasibility constraints of working with pathogenic living cells and by intrinsic limitations of model systems. Herein, we demonstrate an abiotic sensor that uses semiconducting single-walled carbon nanotubes (SWCNTs) as near-infrared fluorescent transducers to report membrane interactions. This sensor is composed of SWCNTs aqueously suspended in lipid, creating a cylindrical, bilayer corona; these SWCNT probes are very sensitive to solvent access (changes in permittivity) and thus report morphological changes to the lipid corona by modulation of fluorescent signals, where binding and disruption are reported as brightening and attenuation, respectively. This mechanism is first demonstrated with chemical and physical membrane-disruptive agents, including ethanol and sodium dodecyl sulfate, and application of electrical pulses. Known cell-penetrating and antimicrobial peptides are then used to demonstrate how the dynamic response of these sensors can be deconvoluted to evaluate different parallel mechanisms of interaction. Last, SWCNTs functionalized in several different bacterial lipopolysaccharides (Pseudomonas aeruginosa, Klebsiella pneumoniae, and Escherichia coli) are used to evaluate a panel of known membrane-disrupting antimicrobials to demonstrate that drug selectivity can be assessed by suspension of SWCNTs with different membrane materials.

Screening Enzymatic Degradation of Polyester Polyurethane with Fluorescent Single-walled Carbon Nanotube and Polymer Nanoparticle Conjugates

Enzymatic biodegradation is a promising method to reclaim plastic materials. However, to date, a high-throughput method for screening potential enzyme candidates for biodegradation is still lacking. Here, we propose a single-walled carbon nanotube (SWCNT) fluorescence sensor for screening the enzymatic degradation of polyester polyurethane nanoparticles. Through wrapping the SWCNT with cationic chitosan, an electrostatic bond is formed between the SWCNT and Impranil, a widely applied model substrate of polyester polyurethane. As Impranil is being degraded by the enzymes, a characteristic quenching at a short reaction time followed by a brightening at a longer reaction time in the fluorescence signal is observed. The time-dependent fluorescence response is compared with turbidity measurement, and we conclude that the brightening in fluorescence results from the binding of the degradation product with the SWCNT. The proposed SWCNT sensor design has the potential to screen enzyme candidates for selective degradation of other plastic particles.

Portable Near-Infrared Fluorometer for a Liposomal Blood Lactate Assay

In sepsis, plasma lactate is a key biomarker of disease severity, prognosis, and treatment success. However, the median time to result for clinical lactate tests is 3 h. We recently reported a near-infrared fluorescent (NIRF) blood lactate assay that relies on a two-step enzymatic reaction in a liposomal reaction compartment. This assay was optimized in human blood and was capable of quantifying lactate in fresh capillary blood from human volunteers at clinically relevant concentrations in 2 min. However, these studies were performed with a tabletop fluorescence plate reader. For translation to the point of care, the liposomal lactate assay needs to be combined with a small portable NIR fluorometer. Portable NIR fluorometers were successfully used for the analysis of skin and soil samples, but reports for blood metabolite assays are scarce. We aimed at testing the performance of the liposomal lactate assay in combination with a commercial small portable NIR fluorometer. First, we tested the fluorophore of the liposomal lactate assay using the NIR dye sulfo-cyanine 7; we observed strong fluorescence signals and high linearity. Second, we performed the liposomal lactate assay in lactate-spiked human arterial blood using the portable fluorometer as the detector and observed strong and highly linear lactate sensing at clinically relevant lactate concentrations after 2 min. Finally, spiking fresh mouse blood with three clinically relevant lactate concentrations led to a significantly different response to all three concentrations after 5 min. These results highlight the usefulness of the tested portable NIR fluorometer for the liposomal lactate assay and motivate a clinical evaluation of this rapid and easy-to-use lactate assay.

Covalently Functionalized Egyptian Blue Nanosheets for Near-Infrared Bioimaging

Fluorophores emitting in the near-infrared (NIR) wavelength region present optimal characteristics for photonics and especially bioimaging. Unfortunately, only few NIR fluorescent materials are known, and even fewer are biocompatible. For this reason, the scientific interest in designing NIR fluorophores is very high. Egyptian Blue (CaCuSi₄O₁₀, EB) is an NIR fluorescent layered silicate that can be exfoliated into fluorescent nanosheets (EB-NS). So far, its surface chemistry has not been tailored, but this is crucial for colloidal stability and biological targeting. Here, we demonstrate covalent surface functionalization of EB nanosheets (EBfunc) via Si-H activation using hydrosilanes with variable functionalities. In the first part of this work, EB-NS are grafted with the visible fluorescent pyrene (Pyr) moieties to demonstrate conjugation by colocalization of the Vis/NIR fluorescence on the (single) EB-NS level. Next, the same grafting procedure was repeated and validated with carboxyl group (COOH)-containing hydrosilanes. These groups serve as a generic handle for further (bio)functionalization of the EB-NS surface. In this way, folic acid (FA) could be conjugated to EB-NS, allowing the targeting of folic acid receptor-expressing cancer cells. These results highlight the potential of this surface chemistry approach to modify EB-NS, enabling targeted NIR imaging for biomedical applications.

Non-destructive preservation state estimation of waterlogged archaeological wooden artifacts

Non-destructive preservation state estimation is an essential prerequisite for the preservation and conservation of waterlogged archaeological wooden artifacts. Herein, Near Infrared (NIR) spectroscopy coupled with orthogonal partial least squares discriminant analysis (OPLS-DA) were applied to assess sixty-four waterlogged archaeological woods collected from seven excavation sites in the period range of 2900 BCE-1912 CE, aiming at developing a non-destructive, accurate and rapid preservation state estimation methodology. The role of non-decayed recent wood of relevant species on preservation state estimation was studied in prior, showing the use of non-decayed recent wood could not improve the predictive ability. Besides, the high variability in terms of chemical structure between archaeological softwoods and archaeological hardwoods did affect the preservation state estimation. Thus, a simple OPLS-DA model of non-destructively distinguishing archaeological hardwoods from softwoods, R²X_cum of 0.659, R²Y_cum of 0.836 and Q²_cum of 0.763, was established to avoid and overcome destructive approach for wood identification. Then, the well-defined three grouped separations of slightly-decayed, moderately-decayed and severely-decayed waterlogged archaeological woods were revealed in OPLS-DA models, providing R²X_cum of 0.793, R²Y_cum of 0.738, Q²_cum of 0.680, and R²X_cum of 0.780, R²Y_cum of 0.901, Q²_cum of 0.870, for waterlogged archaeological hardwoods and waterlogged archaeological softwoods respectively. Potential predictive wood spectral bands were screened and tentatively identified as hydroxyls of crystalline cellulose, acetyl groups of hemicelluloses, C-H bands of lignin, which guaranteed the elimination of non-structural compounds, such as water and inorganic components interference. Furthermore, the developed NIR methodology was validated by an extensively used destructive method consisting of anatomical characteristics, maximum water content and basic density analyses. The results indicated that NIR coupled to chemometrics could non-destructively and accurately predict the preservation states of waterlogged archaeological wooden artifacts and avoid the interference of water and inorganic deposits.

Preparation, properties and applications of near-infrared fluorescent silicate nanosheets

The layered silicates Egyptian Blue (CaCuSi₄O₁₀, EB), Han Blue (BaCuSi₄O₁₀, HB) and Han Purple (BaCuSi₂O₆, HP) are known as historic pigments, but they also possess novel optoelectronic properties with great potential for fundamental research and technology. They fluoresce in the near-infrared (NIR) range and can be exfoliated into two-dimensional (2D) nanomaterials (i.e. nanosheets, NS) which retain the photophysical properties of the bulk materials. These and other characteristics fuel the growing excitement of the scientific community about these materials. EB-, HB- and HP-NS have been used in various applications ranging from smart inks, energy storage, bioimaging, to phototherapy and more. In this review article, we report the fundamental properties of these low-dimensional silicate nanomaterials, discuss applications and outline perspectives for the future.

Prospects of Fluorescent Single-Chirality Carbon Nanotube-Based Biosensors

Semiconducting single-wall carbon nanotubes (SWCNTs) fluoresce in the near-infrared (NIR), and the emission wavelength depends on their structure (chirality). Interactions with other molecules affect their fluorescence, which has successfully been used for SWCNT-based molecular sensors. So far, most such sensors are assembled from crude mixtures of different SWCNT chiralities, which causes polydisperse sensor responses as well as spectral congestion and limits their performance. The advent of chirality-pure SWCNTs is about to overcome this limitation and paves the way for the next generation of biosensors. Here, we discuss the first examples of chirality-pure SWCNT-based fluorescent biosensors. We introduce routes to such sensors via aqueous two-phase extraction-assisted purification of SWCNTs and highlight the critical interplay between purification and surface modification procedures. Applications include the NIR detection and imaging of neurotransmitters, reactive oxygen species, lipids, bacterial motives, and plant metabolites. Most importantly, we outline a path toward how such monodisperse (chirality-pure) sensors will enable advanced multiplexed sensing with enhanced bioanalytical performance.

Biosensing with Fluorescent Carbon Nanotubes

Biosensors are powerful tools for modern basic research and biomedical diagnostics. Their development requires substantial input from the chemical sciences. Sensors or probes with an optical readout, such as fluorescence, offer rapid, minimally invasive sensing of analytes with high spatial and temporal resolution. The near-infrared (NIR) region is beneficial because of the reduced background and scattering of biological samples (tissue transparency window) in this range. In this context, single-walled carbon nanotubes (SWCNTs) have emerged as versatile NIR fluorescent building blocks for biosensors. Here, we provide an overview of advances in SWCNT-based NIR fluorescent molecular sensors. We focus on chemical design strategies for diverse analytes and summarize insights into the photophysics and molecular recognition. Furthermore, different application areas are discussed-from chemical imaging of cellular systems and diagnostics to in vivo applications and perspectives for the future.

Single-Walled Carbon Nanotube Probes for the Characterization of Biofilm-Degrading Enzymes Demonstrated against Pseudomonas aeruginosa Extracellular Matrices

Hydrolase co-therapies that degrade biofilm extracellular polymeric substances (EPS) allow for a better diffusion of antibiotics and more effective treatment; current methods for quantitatively measuring the enzymatic degradation of EPS are not amendable to high-throughput screening. Herein, we present biofilm EPS-functionalized single-walled carbon nanotube (SWCNT) probes for rapid screening of hydrolytic enzyme selectivity and activity on EPS. The extent of biofilm EPS degradation is quantified by monitoring the quenching of the SWCNT fluorescence. We used this platform to screen 16 hydrolases with varying bond breaking selectivity against a panel of wild-type Pseudomonas aeruginosa and mutants deficient or altered in one or more EPS. Next, we performed concentration-dependent studies of six enzymes on two common strains found in cystic fibrosis (CF) environments and, for each enzyme, extracted three first-order rate constants and their relative contributions by fitting a parallel, multi-site degradation model, with a good model fit (R² from 0.65 to 0.97). Reaction rates (turnover rates) are dependent on the enzyme concentration and range from 6.67 × 10^-11 to 2.80 × 10^-3 *s^-1 per mg/mL of enzymes. Lastly, we confirmed findings from this new assay using an established crystal-violet staining assay for a subset of hydrolase panels. In summary, our work shows that this modular sensor is amendable to the high-throughput screening of EPS degradation, thereby improving the rate of discovery and development of novel hydrolases.