In Situ Microarray Fabrication and Analysis Using a Microfluidic Flow Cell Array Integrated with Surface Plasmon Resonance Microscopy

Novel fluorescence nano-orbital biosensor for highly sensitive microRNA detection

BACKGROUND

MicroRNAs play an important role in regulating cell function and gene expression. Early prevention and clinical diagnosis of diseases have high requirements for high-sensitivity detection of microRNAs. Due to the limitations of tedious operation and large sample size, miRNA with small molecular weight and low expression abundance cannot be accurately detected in traditional miRNA detection. To improve the sensitivity and accuracy of detection, we established a novel biosensor based on nucleic acid circuit of signal amplification, which converted miRNA recognition into a fluorescence signal for amplification.

RESULTS

We designed a biosensor based on an exponential amplification reaction with cascaded HCR and DNAzyme nucleic acid circuit (named E-NOF biosensor) by amplicon sub-fragments to trigger the construction of fluorescence nano-orbitals (NOF), which could be used to detect miRNA ultrasensitively. By modifying two fluorophores (Cy3 and Cy5) on the chain of constructing nano-orbitals, when the amplicon triggered the construction of nano-orbitals, fluorescence resonance energy transfer (FRET) occurred between Cy3 and Cy5, and then two fluorescence signals with different trends could be observed. Therefore, through the ratio of the two signals, we could quantitatively and quickly detect the miRNA from 1 fM to 100 nM, and the E-NOF biosensor detection limit was as low as 0.129 fM. Furthermore, the HCR nucleic acid circuit cascaded with DNAzyme could enrich the fluorophores on the nano-orbitals and significantly enhance the fluorescence signal by accelerating the reaction rate.

SIGNIFICANCE

According to our understanding, the E-NOF biosensor is the first strategy to cascade EXPAR with HCR and DNAzyme nucleic acid circuit for miRNA-1246 detection. Accurate results can be obtained in only 120 min. Compared with the traditional HCR system, the sensitivity of the new E-NOF biosensor is increased by 1 × 109 times. Furthermore, the biosensor can also detect biomarkers in human serum samples. It has great potential in miRNA detection and identification.

Microfluidic Platforms for Real-Time In Situ Monitoring of Biomarkers for Cellular Processes

Cellular processes are mechanisms carried out at the cellular level that are aimed at guaranteeing the stability of the organism they comprise. The investigation of cellular processes is key to understanding cell fate, understanding pathogenic mechanisms, and developing new therapeutic technologies. Microfluidic platforms are thought to be the most powerful tools among all methodologies for investigating cellular processes because they can integrate almost all types of the existing intracellular and extracellular biomarker-sensing methods and observation approaches for cell behavior, combined with precisely controlled cell culture, manipulation, stimulation, and analysis. Most importantly, microfluidic platforms can realize real-time in situ detection of secreted proteins, exosomes, and other biomarkers produced during cell physiological processes, thereby providing the possibility to draw the whole picture for a cellular process. Owing to their advantages of high throughput, low sample consumption, and precise cell control, microfluidic platforms with real-time in situ monitoring characteristics are widely being used in cell analysis, disease diagnosis, pharmaceutical research, and biological production. This review focuses on the basic concepts, recent progress, and application prospects of microfluidic platforms for real-time in situ monitoring of biomarkers in cellular processes.

Detection of RNA viruses from influenza and HIV to Ebola and SARS-CoV-2: a review

RNA-based viruses likely make up the highest pandemic threat among all known pathogens in about the last 100 years, since the Spanish Flu of 1918 with 50 M deaths up to COVID-19. Nowadays, an efficient and affordable testing strategy for such viruses have become the paramount target for the fields of virology and bioanalytical chemistry. The detection of the viruses (influenza, hepatitis, HIV, Zika, SARS, Ebola, SARS-CoV-2, etc.) and human antibodies to these viruses is described and tabulated in terms of the reported methods of detection, time to results, accuracy and specificity, if they are reported. The review is focused, but not limited to publications in the last decade. Finally, the limits of detection for each representative publication are tabulated by detection methods and discussed. These methods include PCR, lateral flow immunoassays, LAMP-based methods, ELISA, electrochemical methods (e.g., amperometry, voltammetry), fluorescence spectroscopy, AFM, SPR and SERS spectroscopy, silver staining and CRISPR-Cas based methods, bio-barcode detection, and resonance light scattering. The review is likely to be interesting for various scientists, and particularly helpful with information for establishing interdisciplinary research.

One-Step Ligand Immobilization and Single Sample Injection for Regeneration-Free Surface Plasmon Resonance Measurements of Biomolecular Interactions

Surface plasmon resonance (SPR) has been well established as a method of choice for label-free kinetic measurements of biomolecular interactions. The conventional approach involves multiple injections of an analyte of different concentrations into a fluidic channel covered with a fixed ligand density. Optimization of the experimental conditions and assessment of the data quality can be complicated by issues such as disruption of the ligand structure by the regeneration step and the limited availability of the sample solution. By sequentially closing fluidic channels on a five-channel SPR instrument, different densities of a ligand can be immobilized and determined in one step. With a subsequent injection of a single sample solution, SPR sensorgrams can be simultaneously collected to yield binding and dissociation rate constants (k_a and k_d) and dissociation constant (K_D) between the ligand and analyte. For biomolecular interactions that obey the Langmuir isotherm, we show that the fidelity of the kinetic data can only be reliably confirmed when there exists a strong linear correlation between the SPR signals and the ligand densities. The use of a multichannel SPR instrument also obviates the regeneration step, allowing the binding kinetics between the green fluorescent protein and its antibody to be measured. In comparison to the conventional approach, the method simplifies the experimental procedure, reduces costs associated with sensor chips and biological samples, expedites kinetic measurements, and allows affinity constants to be determined more straightforwardly.

Surface conformations of an anti-ricin aptamer and its affinity for ricin determined by atomic force microscopy and surface plasmon resonance

We used atomic force microscopy (AFM) and surface plasmon resonance (SPR) to study the surface conformations of an anti-ricin aptamer and its specific binding affinity for ricin molecules. The effect of surface modification of the Au(111) substrate on the aptamer affinity was also estimated. The AFM topography images had a resolution high enough to distinguish different aptamer conformations. The specific binding site on the aptamer molecule was clearly located by the AFM recognition images. The aptamer on a Au(111) surface modified with carboxymethylated-dextran (CD) showed both similarities to and differences from the one without CD modification. The influence of CD modification was evaluated using AFM images of various aptamer conformations on the Au(111) surface. The affinity between ricin and the anti-ricin aptamer was estimated using the off-rate values measured using AFM and SPR. The SPR measurements of the ricin sample were conducted in the range from 83.3 pM to 8.33 nM, and the limit of detection was estimated as 25 pM (1.5 ng mL(-1)). The off-rate values of the ricin-aptamer interactions were estimated using both single-molecule dynamic force spectroscopy (DFS) and SPR as (7.3 ± 0.4) × 10(-4) s(-1) and (1.82 ± 0.067) × 10(-2) s(-1), respectively. The results show that single-molecule measurements can obtain different reaction parameters from bulk solution measurements. In AFM single-molecule measurements, the various conformations of the aptamer immobilized on the gold surface determined the availability of each specific binding site to the ricin molecules. The SPR bulk solution measurements averaged the signals from specific and non-specific interactions. AFM images and DFS measurements provide more specific information on the interactions of individual aptamer and ricin molecules.

Trends and challenges of refractometric nanoplasmonic biosensors: a review

Motivated by potential benefits such as sensor miniaturization, multiplexing opportunities and higher sensitivities, refractometric nanoplasmonic biosensing has profiled itself in a short time span as an interesting alternative to conventional Surface Plasmon Resonance (SPR) biosensors. This latter conventional sensing concept has been subjected during the last decades to strong commercialization, thereby strongly leaning on well-developed thin-film surface chemistry protocols. Not surprisingly, the examples found in literature based on this sensing concept are generally characterized by extensive analytical studies of relevant clinical and diagnostic problems. In contrast, the more novel Localized Surface Plasmon Resonance (LSPR) alternative finds itself in a much earlier, and especially, more fundamental stage of development. Driven by new fabrication methodologies to create nanostructured substrates, published work typically focuses on the novelty of the presented material, its optical properties and its use - generally limited to a proof-of-concept - as a label-free biosensing scheme. Given the different stages of development both SPR and LSPR sensors find themselves in, it becomes apparent that providing a comparative analysis of both concepts is not a trivial task. Nevertheless, in this review we make an effort to provide an overview that illustrates the progress booked in both fields during the last five years. First, we discuss the most relevant advances in SPR biosensing, including interesting analytical applications, together with different strategies that assure improvements in performance, throughput and/or integration. Subsequently, the remaining part of this work focuses on the use of nanoplasmonic sensors for real label-free biosensing applications. First, we discuss the motivation that serves as a driving force behind this research topic, together with a brief summary that comprises the main fabrication methodologies used in this field. Next, the sensing performance of LSPR sensors is examined by analyzing different parameters that can be invoked in order to quantitatively assess their overall sensing performance. Two aspects are highlighted that turn out to be especially important when trying to maximize their sensing performance, being (1) the targeted functionalization of the electromagnetic hotspots of the nanostructures, and (2) overcoming inherent negative influence that stem from the presence of a high refractive index substrate that supports the nanostructures. Next, although few in numbers, an overview is given of the most exhaustive and diagnostically relevant LSPR sensing assays that have been recently reported in literature, followed by examples that exploit inherent LSPR characteristics in order to create highly integrated and high-throughput optical biosensors. Finally, we discuss a series of considerations that, in our opinion, should be addressed in order to bring the realization of a stand-alone LSPR biosensor with competitive levels of sensitivity, robustness and integration (when compared to a conventional SPR sensor) much closer to reality.

Single-molecule fluorescence imaging of DNA at a potential-controlled interface

Many interfacial chemical phenomena are governed in part by electrostatic interactions between polyelectrolytes and charged surfaces; these phenomena can influence the performance of biosensors, adsorption of natural polyelectrolytes (humic substances) on soils, and production of polyelectrolyte multilayer films. In order to understand electrostatic interactions that govern these phenomena, we have investigated the behavior of a model polyelectrolyte, 15 kbp fluorescently labeled plasmid DNA, near a polarized indium tin oxide (ITO) electrode surface. The interfacial population of DNA was monitored in situ by imaging individual molecules through the transparent electrode using total-internal-reflection fluorescence microscopy. At applied potentials of +0.8 V versus Ag/AgCl, the DNA interfacial population near the ITO surface can be increased by 2 orders of magnitude relative to bulk solution. The DNA molecules attracted to the interface do not adsorb to ITO, but rather they remain mobile with a diffusion coefficient comparable to free solution. Ionic strength strongly influences the sensitivity of the interfacial population to applied potential, where the increase in the interfacial population over a +300 mV change in potential varies from 20% in 30 mM ionic strength to over 25-fold in 300 μM electrolyte. The DNA accumulation with applied potential was interpreted using a simple Boltzmann model to predict average ion concentrations in the electrical double layer and the fraction of interfacial detection volume that is influenced by applied potential. A Gouy-Chapman model was also applied to the data to account for the dependence of the ion population on distance from the electrode surface, which indicates that the net charge on DNA responsible for interactions with the polarized surface is low, on the order of one excess electron. The results are consistent with a small fraction of the DNA plasmid being resident in the double-layer and with counterions screening much of the DNA excess charge.

A localized surface plasmon resonance imaging instrument for multiplexed biosensing

Localized surface plasmon resonance (LSPR) spectroscopy has been widely used for label-free, highly sensitive measurements of interactions at a surface. LSPR imaging (LSPRi) has the full advantages of LSPR but enables high-throughput, multiplexed measurements by simultaneously probing multiple individually addressable sensors on a single sample surface. Each spatially distinct sensor can be tailored to provide data regarding different surface functionalities or reaction environments. Previously, LSPRi has focused on single-particle sensing where the size scale is very small. Here, we create defined macroscale arrays of nanoparticles that are compatible with common patterning methods such as dip-pen nanolithography and multichannel microfluidic delivery devices. With this new LSPR sensing format, we report the first demonstration of multiplexed LSPR imaging and show that the increased throughput of our instrument enables the collection of a complete Langmuir binding curve on a single sensor surface. In addition, the multiplexed LSPR sensor is highly selective, as demonstrated by the hybridization of single-stranded DNA to complementary sequences immobilized on the sensor surface. The LSPR arrays described in this work exhibit uniform sensitivity and tailorable optical properties, making them an ideal platform for high-throughput, label-free analysis of a variety of molecular binding interactions.

Microfluidic chips for immunoassays

The use of microfluidic chips for immunoassays has been extensively explored in recent years. The combination of immunoassays and microfluidics affords a promising platform for multiple, sensitive, and automatic point-of-care (POC) diagnostics. In this review, we focus on the description of recent achievements in microfluidic chips for immunoassays categorized by their detection method. Following a brief introduction to the basic principles of each detection method, we examine current microfluidic immunosensor detection systems in detail. We also highlight interesting strategies for sensitive immunosensing configurations, multiplexed analysis, and POC diagnostics in microfluidic immunosensors.

Applications of microfluidics for molecular diagnostics

Diagnostic assays implemented in microfluidic devices have developed rapidly over the past decade and are expected to become commonplace in the next few years. Hundreds of microfluidics-based approaches towards clinical diagnostics and pathogen detection have been reported with a general theme of rapid and customizable assays that are potentially cost-effective. This chapter reviews microfluidics in molecular diagnostics based on application areas with a concise review of microfluidics in general. Basic principles of microfabrication are briefly reviewed and the transition to polymer fabricated devices is discussed. Most current microfluidic diagnostic devices are designed to target a single disease, such as a given cancer or a variety of pathogens, and there will likely be a large market for these focused devices; however, the future of molecular diagnostics lies in highly multiplexed microfluidic devices that can screen for potentially hundreds of diseases simultaneously.

Surface plasmon resonance imaging for nucleic acid detection

Surface plasmon resonance imaging (SPRI) is a powerful tool for simple, fast and cheap nucleic acid detection. Great efforts have been made during the last decade with the aim of developing even more sensitive and specific SPRI-based methods to be used for the direct detection of DNA and RNA. Here, after a description of the fundamentals of SPRI, the state of the art of recent platform and assay developments is presented, with special attention given to advances in SPRI signal enhancement procedures.

Joining plasmonics with microfluidics: from convenience to inevitability

Along the advances in optofluidics, functionalities based on the surface plasmon-polariton have also been finding an increasing level of involvement within micro/nano-fluidic systems, gradually forming a new field of plasmo-fluidics. This survey of the burgeoning field reveals that judicious selection and combination of plasmonic and micro/nano-fluidic features render the plasmo-fluidic integration useful and mutually beneficial to the point of inevitability. We establish categories for the level of integration and utilize them as a framework for surveying existing work and extracting future perspectives.

Compliant metamaterials for resonantly enhanced infrared absorption spectroscopy and refractive index sensing

Metamaterials can be designed to operate at frequencies from the visible to the mid-IR, making these structures useful for both refractive index sensing and surface-enhanced infrared absorption spectroscopy. Here we investigate how the mechanical deformation of compliant metamaterials can be used to create new types of tunable sensing surfaces. For split ring resonator based metamaterials on polydimethylsiloxane we demonstrate refractive index sensing with figures of merit of up to 10.1. Given the tunability of the resonance of these structures through the infrared after fabrication, they are well suited for detection of the absorption signal of many typical vibrational modes. The results highlight the promise of postfabrication tunable sensors and the potential for integration.

Thiolene-based microfluidic flow cells for surface plasmon resonance imaging

Thiolene-based microfluidic devices have been coupled with surface plasmon resonance imaging (SPRI) to provide an integrated platform to study interfacial interactions in both aqueous and organic solutions. In this work, we develop a photolithographic method that interfaces commercially available thiolene resin to gold and glass substrates to generate microfluidic channels with excellent adhesion that leave the underlying sensor surface free from contamination and readily available for surface modification through self-assembly. These devices can sustain high flow rates and have excellent solvent compatibility even with several organic solvents. To demonstrate the versatility of these devices, we have conducted nanomolar detection of streptavidin-biotin interactions using in situ SPRI.

Interface design and multiplexed analysis with surface plasmon resonance (SPR) spectroscopy and SPR imaging

Ever since the advent of surface plasmon resonance (SPR) and SPR imaging (SPRi) in the early 1990s, their use in biomolecular interaction analysis (BIA) has expanded phenomenally. An important research area in SPR sensor development is the design of novel and effective interfaces that allow for the probing of a variety of chemical and biological interactions in a highly selective and sensitive manner. A well-designed and robust interface is a necessity to obtain both accurate and pertinent biological information. This review covers the recent research efforts in this area with a specific focus towards biointerfaces, new materials for SPR biosensing, and novel array designs for SPR imaging. Perspectives on the challenges ahead and next steps for SPR technology are discussed.

New trends in instrumental design for surface plasmon resonance-based biosensors

Surface plasmon resonance (SPR)-based biosensing is one of the most advanced label free, real time detection technologies. Numerous research groups with divergent scientific backgrounds have investigated the application of SPR biosensors and studied the fundamental aspects of surface plasmon polaritons that led to new, related instrumentation. As a result, this field continues to be at the forefront of evolving sensing technology. This review emphasizes the new developments in the field of SPR-related instrumentation including optical platforms, chips design, nanoscale approach and new materials. The current tendencies in SPR-based biosensing are identified and the future direction of SPR biosensor technology is broadly discussed.

Parallel microfluidic surface plasmon resonance imaging arrays

Surface plasmon resonance imaging (SPRi) is a label-free technique used for the quantitation of binding affinities and concentrations for a wide variety of target molecules. Although SPRi is capable of determining binding constants for multiple ligands in parallel, current commercial instruments are limited to a single analyte stream on multiple ligand spots. Measurement of binding kinetics requires the serial introduction of different analyte concentrations; such repeated experiments are conducted manually and are therefore time-intensive. To address these challenges, we have developed an integrated microfluidic array using soft lithography techniques for high-throughput SPRi-based detection and determination of binding affinities of antibodies against protein targets. The device consists of 264 element-addressable chambers isolated by microvalves. The resulting 700 pL chamber volumes, combined with a serial dilution network for simultaneous interrogation of up to six different analyte concentrations, allow for further speeding detection times. To test for device performance, human alpha-thrombin was immobilized on the sensor surface and anti-human alpha-thrombin IgG was injected across the surface at different concentrations. The equilibrium dissociation constant was determined to be 5.0 +/- 1.9 nM, which agrees well with values reported in the literature. The interrogation of multiple ligands to multiple analytes in a single device was also investigated and samples were recovered with no cross-contamination. Since each chamber can be addressed independently, this array is capable of interrogating binding events from up to 264 different immobilized ligands against multiple analytes in a single experiment. The development of high-throughput protein analytic measurements is a critical technology for systems approaches to biology and medicine.