Dynamic single-cell intracellular pH sensing using a SERS-active nanopipette

Development of a 3D Hydrogel SERS Chip for Noninvasive, Real-Time pH and Glucose Monitoring in Sweat

Traditional diagnostic methods, such as blood tests, are invasive and time-consuming, while sweat biomarkers offer a rapid physiological assessment. Surface-enhanced Raman spectroscopy (SERS) has garnered significant attention in sweat analysis because of its high sensitivity, label-free nature, and nondestructive properties. However, challenges related to substrate reproducibility and interference from the biological matrix persist with SERS. This study developed a novel ratio-based 3D hydrogel SERS chip, providing a noninvasive solution for real-time monitoring of pH and glucose levels in sweat. Encapsulating the probe molecule (4-MBN) in nanoscale gaps to form gold nanoflower-like nanotags with internal standards and integrating them into an agarose hydrogel to create a 3D flexible SERS substrate significantly enhances the reproducibility and stability of sweat analysis. Gap-Au nanopetals modified with probe molecules are uniformly dispersed throughout the porous hydrogel structure, facilitating the effective detection of the pH and glucose in sweat. The 3D hydrogel SERS chip demonstrates a strong linear relationship in pH and glucose detection, with a pH response range of 5.5-8.0 and a glucose detection range of 0.01-5 mM, with R2 values of 0.9973 and 0.9923, respectively. In actual sweat samples, the maximum error in pH detection accuracy is only 1.13%, with a lower glucose detection limit of 0.25 mM. This study suggests that the ratio-based 3D hydrogel SERS chip provides convenient, reliable, and rapid detection capabilities with substantial application potential for analyzing body fluid pH and glucose.

Machine Learning-Driven SERS Nanoendoscopy and Optophysiology

A frontier of analytical sciences is centered on the continuous measurement of molecules in or near cells, tissues, or organs, within the biological context in situ, where the molecular-level information is indicative of health status, therapeutic efficacy, and fundamental biochemical function of the host. Following the completion of the Human Genome Project, current research aims to link genes to functions of an organism and investigate how the environment modulates functional properties of organisms. New analytical methods have been developed to detect chemical changes with high spatial and temporal resolution, including minimally invasive surface-enhanced Raman scattering (SERS) nanofibers using the principles of endoscopy (SERS nanoendoscopy) or optical physiology (SERS optophysiology). Given the large spectral data sets generated from these experiments, SERS nanoendoscopy and optophysiology benefit from advances in data science and machine learning to extract chemical information from complex vibrational spectra measured by SERS. This review highlights new opportunities for intracellular, extracellular, and in vivo chemical measurements arising from the combination of SERS nanosensing and machine learning.

SERS in 3D cell models: a powerful tool in cancer research

Unraveling the cellular and molecular mechanisms underlying tumoral processes is fundamental for the diagnosis and treatment of cancer. In this regard, three-dimensional (3D) cancer cell models more realistically mimic tumors compared to conventional 2D cell cultures and are more attractive for performing such studies. Nonetheless, the analysis of such architectures is challenging because most available techniques are destructive, resulting in the loss of biochemical information. On the contrary, surface-enhanced Raman spectroscopy (SERS) is a non-invasive analytical tool that can record the structural fingerprint of molecules present in complex biological environments. The implementation of SERS in 3D cancer models can be leveraged to track therapeutics, the production of cancer-related metabolites, different signaling and communication pathways, and to image the different cellular components and structural features. In this review, we highlight recent progress in the use of SERS for the evaluation of cancer diagnosis and therapy in 3D tumoral models. We outline strategies for the delivery and design of SERS tags and shed light on the possibilities this technique offers for studying different cellular processes, through either biosensing or bioimaging modalities. Finally, we address current challenges and future directions, such as overcoming the limitations of SERS and the need for the development of user-friendly and robust data analysis methods. Continued development of SERS 3D bioimaging and biosensing systems, techniques, and analytical strategies, can provide significant contributions for early disease detection, novel cancer therapies, and the realization of patient-tailored medicine.

Recent advances of nanopore technique in single cell analysis

Single cells and their dynamic behavior are closely related to biological research. Monitoring their dynamic behavior is of great significance for disease prevention. How to achieve rapid and non-destructive monitoring of single cells is a major issue that needs to be solved urgently. As an emerging technology, nanopores have been proven to enable non-destructive and label-free detection of single cells. The structural properties of nanopores enable a high degree of sensitivity and accuracy during analysis. In this article, we summarize and classify the different types of solid-state nanopores that can be used for single-cell detection and illustrate their specific applications depending on the size of the analyte. In addition, their research progress in material transport and microenvironment monitoring is also highlighted. Finally, a brief summary of existing research challenges and future trends in nanopore single-cell analysis is tentatively provided.

Raman signal optimization based on residual network adaptive focusing

Due to its high sensitivity and specificity, Micro-Raman spectroscopy has emerged as a vital technique for molecular recognition and identification. As a weakly scattered signal, ensuring the accurate focus of the sample is essential for acquiring high quality Raman spectral signal and its analysis, especially in some complex microenvironments such as intracellular settings. Traditional autofocus methods are often time consuming or necessitate additional hardware, limiting real-time sample observation and device compatibility. Here, we propose an adaptive focusing method based on residual network to realize rapid and accurate focusing on Micro-Raman measurements. Using only a bright field image of the sample acquired on any image plane, we can predict the defocus distance with a residual network trained by Resnet50, in which the focus position is determined by combining the gradient and discrete cosine transform. Further, detailed regional division of the bright field map used for characterizing the height variation of actual sample surface is performed. As a result, a focus prediction map with 1μm accuracy is obtained from a bright field image in 120 ms. Based on this method, we successfully realize Raman signal optimization and the necessary correction of spectral information. This adaptive focusing method based on residual network is beneficial to further enhance the sensitivity and accuracy of Micro-Raman spectroscopy technology, which is of great significance in promoting the wide application of Raman spectroscopy.

Recent advances in the design of intracellular pH sensing nanoprobes based on organic and inorganic materials

In the biological system, the intracellular pH (pHi) plays an important role in regulating diverse physiological activities, including enzymatic action, ion transport, cell proliferation, metabolism, and programmed cell death. The monitoring of pH inside living cells is also crucial for studying cellular events such as phagocytosis, endocytosis, and receptor-ligand internalization. Furthermore, some organelles, viz., endosomes and lysosomes, have intracompartmental pH, which is critical for maintaining the stability of protein structure and function. The dysfunction and abnormal pH regulation can result in terminal diseases such as cancer, Alzheimer, and so forth. Therefore, the accuracy of intracellular pH measurement is always the top priority and demands cutting-edge research and analysis. Such techniques, such as Raman spectroscopy and fluorescence imaging, preferably use nanotechnology due to their remarkable advantages, such as a non-invasive approach and providing accuracy, repeatability, and reproducibility. In the past decades, there have been numerous attempts to design and construct non-invasive organic and inorganic materials-based nanoprobes for pHi sensing. For Raman-based techniques, metal nanostructures such as Au/Ag/Cu nanoparticles are utilized to enhance the signal intensity. As for the fluorescence-based studies, the organic-based small molecules, such as dyes, show higher sensitivity toward pH. However, they possess several drawbacks, including high photobleaching rate, and autofluorescence background signals. To this end, there are alternative nanomaterials proposed, including semiconductor quantum dots (QDs), carbon QDs, upconversion nanoparticles, and so forth. Moreover, the fluorescence technique allows for ratiometric measurement of pHi, which as a result, offers a reliable calibration curve. This timely review will critically examine the current progression in the existing nanoprobes. In addition, based on our knowledge and available research findings, we provide a brief future outlook that may advance the state-of-the-art methodologies for pHi sensing.

Single-Cell Analysis with Silver-Coated Pipette by Combined SERS and SICM

The study of individual cell processes that occur both on their surface and inside is highly interesting for the development of new medical drugs, cytology and cell technologies. This work presents an original technique for fabricating the silver-coated pipette and its use for the cell analysis by combination with surface-enhanced Raman spectroscopy (SERS) and scanning ion-conducting microscopy (SICM). Unlike the majority of other designs, the pipette opening in our case remains uncovered, which is important for SICM. SERS-active Ag nanoparticles on the pipette surface are formed by vacuum-thermal evaporation followed by annealing. An array of nanoparticles had a diameter on the order of 36 nm and spacing of 12 nm. A two-particle model based on Laplace equations is used to calculate a theoretical enhancement factor (EF). The surface morphology of the samples is investigated by scanning electron microscopy while SICM is used to reveal the surface topography, to evaluate Young's modulus of living cells and to control an injection of the SERS-active pipettes into them. A Raman microscope-spectrometer was used to collect characteristic SERS spectra of cells and cell components. Local Raman spectra were obtained from the cytoplasm and nucleus of the same HEK-293 cancer cell. The EF of the SERS-active pipette was 7 × 105. As a result, we demonstrate utilizing the silver-coated pipette for both the SICM study and the molecular composition analysis of cytoplasm and the nucleus of living cells by SERS. The probe localization in cells is successfully achieved.

Micro-engineering and nano-engineering approaches to investigate tumour ecosystems

The interactions among tumour cells, the tumour microenvironment (TME) and non-tumour tissues are of interest to many cancer researchers. Micro-engineering approaches and nanotechnologies are under extensive exploration for modelling these interactions and measuring them in situ and in vivo to investigate therapeutic vulnerabilities in cancer and extend a systemic view of tumour ecosystems. Here we highlight the greatest opportunities for improving the understanding of tumour ecosystems using microfluidic devices, bioprinting or organ-on-a-chip approaches. We also discuss the potential of nanosensors that can transmit information from within the TME or elsewhere in the body to address scientific and clinical questions about changes in chemical gradients, enzymatic activities, metabolic and immune profiles of the TME and circulating analytes. This Review aims to connect the cancer biology and engineering communities, presenting biomedical technologies that may expand the methodologies of the former, while inspiring the latter to develop approaches for interrogating cancer ecosystems.

The Modification and Applications of Nanopipettes in Electrochemical Analysis

Nanopipette, which is fabricated by glasses and possesses a nanoscale pore in the tip, has been proven to be immensely useful in electrochemical analysis. Numerous nanopipette-based sensors have emerged with improved sensitivity, selectivity, ease of use, and miniaturization. In this minireview, we provide an overview of the recent developments of nanopipette-based electrochemical sensors based on different types of nanopipettes, including single-nanopipettes, self-referenced nanopipettes, dual-nanopipettes, and double-barrel nanopipettes. Several important modification materials for nanopipette functionalization are highlighted, such as conductive materials, macromolecular materials, and functional molecules. These materials can improve the sensing performance and targeting specificities of nanopipettes. We also discuss examples of related applications and the future development of nanopipette-based strategies.

Photoluminescent gold nanoclusters as two-photon excited ratiometric pH sensor and photoactivated peroxidase

A two-photon excited ratiometric fluorescent pH sensor is reported by combining L-cysteine-protected AuNCs (Cys@AuNCs) with fluorescein isothiocyanate (FITC). Cys@AuNCs were synthesized through a one-step self-reduction route and showed pH-responsive photoluminescence at 650 nm. Benefiting from the opposite pH response of Cys@AuNCs and FITC, the fluorescence ratio (F_{515 nm}/F_{650 nm}) of FITC&Cys@AuNCs provided a large dynamic range of 200-fold for pH measurement in the response interval of pH 5.0-8.0. Based on the excellent two-photon absorption coefficient of Cys@AuNCs, the sensor was expected to achieve sensitive quantitation of pH in living cells under two-photon excitation. In addition, colorimetric biosensing based on enzyme-like metal nanoclusters has attracted wide attention due to their low-cost, simplicity, and practicality. It is crucial to develop high catalytic activity nanozyme from the viewpoint of practical application. The synthesized Cys@AuNCs exhibited excellent photoactivated peroxidase-like activity with high substrate affinity and catalytic reaction rate, promising for rapid colorimetric biosensing of field analysis and the control of catalytic reactions by photostimulation.

Design and Detection of Cyanide Raman Tag pH-Responsive SERS Probes

As one of the most important parameters of biochemical analysis and detection, the pH value plays a very important role in cell function, food preservation and production, soil and water sources, and other applications. This makes it increasingly important to explore pH detection methods in depth. In this paper, a pH-responsive SERS probe based on the cyano Raman Tag was designed to realize pH sensing detection through the influence of the pH value of analytes on the displacement of the cyano Raman peak in the SERS probe. This cyano Raman tag exhibited not only excellent sensitivity in the liner range of pH 3.0-9.0 with a limit of detection (LOD) of pH 0.33, but also the anti-interference performance and stability (the relative standard deviation (RSD) was calculated to be 6.68%, n = 5). These results indicated that this pH SERS probe with the Raman cyano tag can provide new research ideas for future biological detection, bioimaging, and environmental detection.

Live Streaming of a Single Cell's Life over a Local pH-Monitoring Nanowire Waveguide

Spatiotemporal pH monitoring of single living cells across rigid cell and organelle membranes has been challenging, despite its significance in understanding cellular heterogeneity. Here, we developed a mechanically robust yet tolerably thin nanowire waveguide that enables in situ monitoring of pH dynamics at desired cellular compartments via direct optical communication. By chemically labeling fluorescein at one end of a poly(vinylbenzyl azide) nanowire, we continuously monitored pH variations of different compartments inside a living cell, successfully observing organelle-exclusive pH homeostasis and stimuli-selective pH regulations. Importantly, it was demonstrated for the first time that, during the mammalian cell cycle, the nucleus displays pH homeostasis in interphase but a tidal pH curve in the mitotic phase, implying the existence of independent pH-regulating activities by the nuclear envelope. The rapid and accurate local pH-reporting capability of our nanowire waveguide would be highly valuable for investigating cellular behaviors under diverse biological situations in living cells.

Surface-enhanced Raman scattering: An emerging tool for sensing cellular function

Continuous long-term intracellular imaging and multiplexed monitoring of biomolecular changes associated with key cellular processes remains a challenge for the scientific community. Recently, surface-enhanced Raman scattering (SERS) has been demonstrated as a powerful spectroscopic tool in the field of biology owing to its significant advantages. Some of these include the ability to provide molecule-specific information with exquisite sensitivity, working with small volumes of precious samples, real-time monitoring, and optimal optical contrast. More importantly, the availability of a large number of novel Raman reporters with narrower full width at half maximum (FWHM) of spectral peaks/vibrational modes than conventional fluorophores has created a versatile palette of SERS-based probes that allow targeted multiplex sensing surpassing the detection sensitivity of even fluorescent probes. Due to its nondestructive nature, its applicability has been recognized for biological sensing, molecular imaging, and dynamic monitoring of complex intracellular processes. We critically discuss recent developments in this area with a focus on different applications where SERS has been used for obtaining information that remains elusive for conventional imaging methods. Current reports indicate that SERS has made significant inroads in the field of biology and has the potential to be used for in vivo human applications. This article is categorized under: Diagnostic Tools > In Vitro Nanoparticle-Based Sensing Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Diagnostic Tools > Biosensing Diagnostic Tools > In Vivo Nanodiagnostics and Imaging.

Plasmonic Au@Ag@mSiO2 Nanorattles for In Situ Imaging of Bacterial Metabolism by Surface-Enhanced Raman Scattering Spectroscopy

It is well known that microbial populations and their interactions are largely influenced by their secreted metabolites. Noninvasive and spatiotemporal monitoring and imaging of such extracellular metabolic byproducts can be correlated with biological phenotypes of interest and provide new insights into the structure and development of microbial communities. Herein, we report a surface-enhanced Raman scattering (SERS) hybrid substrate consisting of plasmonic Au@Ag@mSiO₂ nanorattles for optophysiological monitoring of extracellular metabolism in microbial populations. A key element of the SERS substrate is the mesoporous silica shell encapsulating single plasmonic nanoparticles, which furnishes colloidal stability and molecular sieving capabilities to the engineered nanostructures, thereby realizing robust, sensitive, and reliable measurements. The reported SERS-based approach may be used as a powerful tool for deciphering the role of extracellular metabolites and physicochemical factors in microbial community dynamics and interactions.

Development of multifunctional nanopipettes for controlled intracellular delivery and single-entity detection

The intracellular delivery of biomolecules and nanoscale materials to individual cells has gained remarkable attention in recent years owing to its wide applications in drug delivery, clinical diagnostics, bio-imaging and single-cell analysis. It remains a challenge to control and measure the delivered amount in one cell. In this work, we developed a multifunctional nanopipette - containing both a nanopore and nanoelectrode (pyrolytic carbon) at the apex - as a facile, minimally invasive and effective platform for both controllable single-cell intracellular delivery and single-entity counting. While controlled by a micromanipulator, the baseline changes of the nanopore ionic current (I) and nanoelectrode open circuit potential (V) help to guide the nanopipette tip insertion and positioning processes. The delivery from the nanopore barrel can be facilely controlled by the applied nanopore bias. To optimize the intracellular single-entity detection during delivery, we studied the effects of the nanopipette tip geometry and solution salt concentration in controlled experiments. We have successfully delivered gold nanoparticles and biomolecules into the cell, as confirmed by the increased scattering and fluorescence signals, respectively. The delivered entities have also been detected at the single-entity level using either one or both transient I and V signals. We found that the sensitivity of the single-entity electrochemical measurement was greatly affected by the local environment of the cell and varied between cell lines.

Recent advances in plasmonic Prussian blue-based SERS nanotags for biological application

The reliability and reproducibility of surface-enhanced Raman scattering (SERS) technology is still a great challenge in bio-related analysis. Prussian blue (PB)-based SERS tags have attracted increasing interest for improving these deficiencies due to its unique Raman band (near 2156 cm-1) in the Raman-silent region, providing zero-background bio-Raman labels without interference from endogenous biomolecules. Moreover, the stable PB shell consisting of multiple layers of CN- reporters ensure a stable and strong Raman signal output, avoiding the desorption of the Raman reporter from the plasmonic region by the competitive adsorption of the analyte. More importantly, they possess outstanding multiplexing potential in biological analysis owing to the adjustable Raman shift with unique narrow spectral widths. Despite more attention having been attracted to the structure and preparation of PB-based SERS tags for their better biological applications over the past five years, there is still a great challenge for SERS suitable for applications in the actual environment. The biological applications of PB-based SERS tags are comprehensively recounted in this minireview, mainly focusing on quantification analysis, multiple-spectral analysis and cell-imaging joint phototherapy. The prospects of PB-based SERS tags in clinical diagnosis and treatment are also discussed. This review aims to draw attention to the importance of SERS tags and provide a reference for the design and application of PB-based SERS tags in future bio-applications.

Recent Progress of SERS Nanoprobe for pH Detecting and Its Application in Biological Imaging

As pH value almost affects the function of cells and organisms in all aspects, in biology, biochemical and many other research fields, it is necessary to apply simple, intuitive, sensitive, stable detection of pH and base characteristics inside and outside the cell. Therefore, many research groups have explored the design and application of pH probes based on surface enhanced Raman scattering (SERS). In this review article, we discussed the basic theoretical background of explaining the working mechanism of pH SERS sensors, and also briefly described the significance of cell pH measurement, and simply classified and summarized the factors that affected the performance of pH SERS probes. Some applications of pH probes based on surface enhanced Raman scattering in intracellular and extracellular pH imaging and the combination of other analytical detection techniques are described. Finally, the development prospect of this field is presented.

Intracellular pH - Advantages and pitfalls of surface-enhanced Raman scattering and fluorescence microscopy - A review

The value of pH in various parts of protoplasm can affect nearly all aspects of cell functions. Therefore, the determination of intracellular acid-base features is required in many areas of biological and biochemical studies. Because of a significant scientific importance of in vivo intracellular pH measurements, various groups carried out such experiments. In this review article we describe intracellular pH measurements using two the most sensitive optical spectroscopies: surface-enhanced Raman scattering (SERS) and fluorescence. It is reasonable to present these two techniques in one review article because the experimental approach in Raman and fluorescence experiments is relatively similar. The basic theoretical background explaining the mechanism of operation of fluorescence and SERS sensors are discussed and the motivations to carry out intracellular pH measurements are briefly described. Future perspectives in this field are also discussed.

Highly sensitive detection of DNA damage in living cells by SERS and electrochemical measurements using a flexible gold nanoelectrode

Guanine (G) oxidation products, such as 8-hydroxy-2'-deoxyguanosine (8-OHdG) and 8-oxo-guanine (8-OXOG), have been widely studied as promising biomarkers for DNA oxidative damage. In this work, we develop a new method to detect G oxidative products released from live cells after chromium (vi) ion or hydrogen peroxide treatments by using a glass nanopipette-based flexible gold nanoelectrode (fGNE). Specific response to G oxidative products with high sensitivity can be detected from the fGNE tip through integrated electrochemical measurements and surface-enhanced Raman spectroscopy. The fGNE apex can be positioned very close to the cell membrane noninvasively because of its high flexibility and nanoscale tip size. With the assistance of the electrophoretic force, the fGNEs can effectively collect and detect the G-derived DNA damage products released from individual cells in the cell culture medium with high sensitivity.

Target-Triggered Assembly in a Nanopipette for Electrochemical Single-Cell Analysis

Engineered nanopipette tools have recently emerged as a powerful approach for electrochemical nanosensing, which has major implications in both fundamental biological research and biomedical applications. Herein, we describe a generic method of target-triggered assembly of aptamers in a nanopipette for nanosensing, which is exemplified by sensitive and rapid electrochemical single-cell analysis of adenosine triphosphate (ATP), a ubiquitous energy source in life and important signaling molecules in many physiological processes. Specifically, a layer of thiolated aptamers is immobilized onto a Au-coated interior wall of a nanopipette tip. With backfilled pairing aptamers, the engineered nanopipette is then used for probing intracellular ATP via the ATP-dependent linkage of the split aptamers. Due to the higher surface charge density from the aptamer assembly, the nanosensor would exhibit an enhanced rectification signal. Besides, this ATP-responsive nanopipette tool possesses excellent selectivity and stability as well as high recyclability. This work provides a practical single-cell nanosensor capable of intracellular ATP analysis. More generally, integrated with other split recognition elements, the proposed mechanism could serve as a viable basis for addressing many other important biological species.