Multiplexed detection and label-free quantitation of microRNAs using arrays of silicon photonic microring resonators

Whispering gallery mode optical resonators for biological and chemical detection: current practices, future perspectives, and challenges

Sensors are important for a wide variety of applications include medical diagnostics and environmental monitoring. Due to their long photon confinement times, whispering gallery mode (WGM) sensors are among the most sensitive sensors currently in existence. We briefly discuss what are WGM sensors, the principles of WGM sensing, and the history of the field, beginning with Mie theory. We discuss recent work in the field on using these WGM resonators as sensors, focusing particularly on biological and chemical sensing applications. We discuss how sensorgrams are acquired and fundamental measurement limits. In addition, we discuss how to interpret binding curves and extract physical parameters such as binding affinity constants. We discuss the controversy surrounding single-molecule detection and discuss hybrid WGM nanoparticle sensors. In addition, we place these sensors in context with others sensing technologies both labeled and label-free. Finally, we discuss what we believe are the most promising applications for these devices, outline remaining challenges, and provide an outlook for the future.

Whispering Gallery Mode Micro/Nanolasers for Intracellular Probing at Single Cell Resolution

Intracellular probing at single cell resolution is key to revealing the heterogeneity of cells, learning new cell subtypes and functions, understanding the pathophysiology of disease, and ensuring precise diagnosis and treatment. Despite the best efforts, an enormous challenge remains due to the very small size, extremely low content, and dynamic microenvironment of a single cell. Whispering gallery mode (WGM) micro/nanolasers (active WGM) offer unique advantages of small mode volume, high quality factors, bright and low threshold laser emission, and narrow line width, particularly suitable for integration within a single cell. In this review, we provide a focused overview of WGM micro/nanolasers for intracellular probing. We deliver information on WGM micro/nanolaser concepts, sensing mechanism, and biocompatibility, as well as recent progress in intracellular probing applications mainly covering cellular-level sensing, molecular-level detection, and feasibility for cellular imaging. At the end, challenges and prospects of WGM micro/nanolasers for intracellular applications are discussed.

Microfluidics and Nanofluidics in Strong Light-Matter Coupling Systems

The combination of micro- or nanofluidics and strong light-matter coupling has gained much interest in the past decade, which has led to the development of advanced systems and devices with numerous potential applications in different fields, such as chemistry, biosensing, and material science. Strong light-matter coupling is achieved by placing a dipole (e.g., an atom or a molecule) into a confined electromagnetic field, with molecular transitions being in resonance with the field and the coupling strength exceeding the average dissipation rate. Despite intense research and encouraging results in this field, some challenges still need to be overcome, related to the fabrication of nano- and microscale optical cavities, stability, scaling up and production, sensitivity, signal-to-noise ratio, and real-time control and monitoring. The goal of this paper is to summarize recent developments in micro- and nanofluidic systems employing strong light-matter coupling. An overview of various methods and techniques used to achieve strong light-matter coupling in micro- or nanofluidic systems is presented, preceded by a brief outline of the fundamentals of strong light-matter coupling and optofluidics operating in the strong coupling regime. The potential applications of these integrated systems in sensing, optofluidics, and quantum technologies are explored. The challenges and prospects in this rapidly developing field are discussed.

Subwavelength Grating Cascaded Microring Resonator Biochemical Sensors with Record-High Sensitivity

Photonic integrated circuit biochemical and biomedical sensors show promising applications in medical diagnosis, food security, healthcare, and environmental monitoring. Silicon-on-insulator subwavelength grating waveguides and cascaded microring resonator structures enhance photon-analyte interaction, offering superior sensing performance (higher sensitivity with lower limit of detection and larger free spectral range) compared to traditional strip and slot waveguide microring resonator structures. In this study, we design, simulate, and experimentally demonstrate a novel and compact biochemical sensor integrating subwavelength grating cascaded microring resonators and multibox subwavelength grating straight waveguides on a silicon-on-insulator platform. We achieve a record-high refractive index sensitivity of 810 nm/RIU with a limit of detection value of 2.04 × 10-5 RIU. The measured concentration sensitivity for sodium chloride solutions is 1430 pm/% with a limit of detection of 0.04%. The free spectral range is 35.8 nm, and the measured Q factor is 1.9 × 103. By combining the advantages of cascaded microring resonators with those subwavelength gratings, our sensor offers unprecedented sensitivity for biochemical sensing applications, promising significant enhancements in healthcare diagnostics and environmental monitoring systems.

Advances in the detection and diagnosis of tuberculosis using optical-based devices

Tuberculosis (TB), a bacterial infection caused by Mycobacterium tuberculosis, is highly contagious and can lead to severe health complications if left untreated. This review article discusses the importance of early detection and treatment and its global incidence and epidemiology, emphasizing its impact on vulnerable populations and its role as a major cause of death worldwide. Furthermore, it highlights the challenges faced with diagnosing TB. To overcome these challenges, point-of-care devices have emerged as promising tools for rapid and accurate TB detection. These include devices such as nucleic acid amplification tests (NAATs), lateral flow assays (LFAs), and microfluidic-based assays, which offer advantages such as rapid results, portability, and the ability to detect drug-resistant strains. Optical-based devices, such as photonic micro-ring sensors, silicon platform-based sensors, plasmonic-based platforms, microfluidics, and smartphone imaging, are some of the highlighted optical-based devices with the potential to detect TB. These devices can detect TB in sputum samples with high sensitivity and specificity. Optical-based diagnostic devices have the potential to offer the advantages of detecting low concentrations of target molecules and being adaptable to detect multiple targets simultaneously. Using these devices in a clinical setting makes them suitable for their application in improving access to diagnostic testing that enables earlier detection and treatment of TB. Furthermore, these devices would improve TB's global health issue, which requires comprehensive research, prevention, and treatment efforts.

Absolute Quantification of Serum Exosomes in Patients with an SERS-Lateral Flow Strip Biosensor for Noninvasive Clinical Cancer Diagnosis

Exosomes (exos) widely existing in body fluids show great potential for noninvasive cancer diagnosis. Quantitative analysis of exos is traditionally performed by targeting specific exosomal surface proteins, but it is often imprecise due to the common expression of exosomal proteins and subtle expression differences between different cancer subtypes. Herein, we report quantitative surface-enhanced Raman spectroscopy (SERS) of serum exos through a combination of a paper-based lateral flow strip (LFS) biosensor with multivariate spectral unmixing analysis rather than simply quantifying exosomal proteins. Our SERS-LFS biosensor enables absolute quantification of two different serum exos with a limit of detection down to ∼106 particles/mL for both exos. We further exemplify the application of this strategy in quantitative dual-plex detection of serum exos from breast cancer patients. We find that human epidermal growth factor receptor 2+ (HER2+) and luminal A breast cancer patients undergoing no surgery are enriched in serum exos derived from SKBR-3 cells and MCF-7 cells (denoted as SKBR and MCF exos), respectively. The surgical treatment of these breast cancer patients accompanies an obvious decrease of either SKBR or MCF exos in the serum. These results suggest the great potential of the combination of the SERS-LFS biosensor and multivariate spectral unmixing for breast cancer subtyping and therapeutic surveillance with the powerful quantitative capability of exos in clinical samples.

Rapid genetic screening with high quality factor metasurfaces

Genetic analysis methods are foundational to advancing personalized medicine, accelerating disease diagnostics, and monitoring the health of organisms and ecosystems. Current nucleic acid technologies such as polymerase chain reaction (PCR) and next-generation sequencing (NGS) rely on sample amplification and can suffer from inhibition. Here, we introduce a label-free genetic screening platform based on high quality (high-Q) factor silicon nanoantennas functionalized with nucleic acid fragments. Each high-Q nanoantenna exhibits average resonant quality factors of 2,200 in physiological buffer. We quantitatively detect two gene fragments, SARS-CoV-2 envelope (E) and open reading frame 1b (ORF1b), with high-specificity via DNA hybridization. We also demonstrate femtomolar sensitivity in buffer and nanomolar sensitivity in spiked nasopharyngeal eluates within 5 minutes. Nanoantennas are patterned at densities of 160,000 devices per cm2, enabling future work on highly-multiplexed detection. Combined with advances in complex sample processing, our work provides a foundation for rapid, compact, and amplification-free molecular assays.

Research on sensing characteristics of third-order runway series symmetric microring resonator based on hybrid plasma waveguide and metal insulator metal

In this paper, a high-sensitivity refractive index sensor based on a hybrid plasma waveguide and metal-insulator-metal waveguide combined third-order runway series mosaic microring resonator is proposed. In this structure, a GaAs waveguide ring surrounds a gold waveguide ring in the middle, and the innermost layer is a disk made of gold material. The outer groove waveguide is composed of GaAs-air-alloy, and the inner groove waveguide is made of the Gold-Air-Gold material disc. By filling different substances in the groove, the change of refractive index will affect the optical signal strength of the output spectrum. The finite element method simulates the transmission spectrum and electric field distribution of the sensor structure. The amplitude coupling coefficient and attenuation factor affecting the resonator's performance are analyzed, and the structural parameters of the slot waveguide are optimized. The numerical simulation results show that the sensor quality factor of this structure is 1.54 × 10⁴ , the sensitivity is 1.2 × 10³  nm/RIU which is about 1.5 times higher than that of the Si ring with the same structure, the detection limit can reach 8.1892 × 10^-7 RIU, and the free spectral range can reach 109 nm. Compared with the traditional microring structure, this microring has higher design freedom and free spectral range and is more suitable for producing biosensors with high sensitivity, low detection limit, and multi-parameter measurement.

Biofunctionalization of Multiplexed Silicon Photonic Biosensors

Silicon photonic (SiP) sensors offer a promising platform for robust and low-cost decentralized diagnostics due to their high scalability, low limit of detection, and ability to integrate multiple sensors for multiplexed analyte detection. Their CMOS-compatible fabrication enables chip-scale miniaturization, high scalability, and low-cost mass production. Sensitive, specific detection with silicon photonic sensors is afforded through biofunctionalization of the sensor surface; consequently, this functionalization chemistry is inextricably linked to sensor performance. In this review, we first highlight the biofunctionalization needs for SiP biosensors, including sensitivity, specificity, cost, shelf-stability, and replicability and establish a set of performance criteria. We then benchmark biofunctionalization strategies for SiP biosensors against these criteria, organizing the review around three key aspects: bioreceptor selection, immobilization strategies, and patterning techniques. First, we evaluate bioreceptors, including antibodies, aptamers, nucleic acid probes, molecularly imprinted polymers, peptides, glycans, and lectins. We then compare adsorption, bioaffinity, and covalent chemistries for immobilizing bioreceptors on SiP surfaces. Finally, we compare biopatterning techniques for spatially controlling and multiplexing the biofunctionalization of SiP sensors, including microcontact printing, pin- and pipette-based spotting, microfluidic patterning in channels, inkjet printing, and microfluidic probes.

Towards Multiplexed and Multimodal Biosensor Platforms in Real-Time Monitoring of Metabolic Disorders

Metabolic syndrome (MS) is a cluster of conditions that increases the probability of heart disease, stroke, and diabetes, and is very common worldwide. While the exact cause of MS has yet to be understood, there is evidence indicating the relationship between MS and the dysregulation of the immune system. The resultant biomarkers that are expressed in the process are gaining relevance in the early detection of related MS. However, sensing only a single analyte has its limitations because one analyte can be involved with various conditions. Thus, for MS, which generally results from the co-existence of multiple complications, a multi-analyte sensing platform is necessary for precise diagnosis. In this review, we summarize various types of biomarkers related to MS and the non-invasively accessible biofluids that are available for sensing. Then two types of widely used sensing platform, the electrochemical and optical, are discussed in terms of multimodal biosensing, figure-of-merit (FOM), sensitivity, and specificity for early diagnosis of MS. This provides a thorough insight into the current status of the available platforms and how the electrochemical and optical modalities can complement each other for a more reliable sensing platform for MS.

Rapid detection of an Ebola biomarker with optical microring resonators

Ebola virus (EBOV) is a highly infectious pathogen, with a case mortality rate as high as 89%. Rapid therapeutic treatments and supportive measures can drastically improve patient outcome; however, the symptoms of EBOV disease (EVD) lack specificity from other endemic diseases. Given the high mortality and significant symptom overlap, there is a critical need for sensitive, rapid diagnostics for EVD. Facile diagnosis of EVD remains a challenge. Here, we describe a rapid and sensitive diagnostic for EVD through microring resonator sensors in conjunction with a unique biomarker of EBOV infection, soluble glycoprotein (sGP). Microring resonator sensors detected sGP in under 40 min with a limit of detection (LOD) as low as 1.00 ng/mL in serum. Furthermore, we validated our assay with the detection of sGP in serum from EBOV-infected non-human primates. Our results demonstrate the utility of a high-sensitivity diagnostic platform for detection of sGP for diagnosis of EVD.

Surface Plasmon Resonance (SPR) Spectroscopy and Photonic Integrated Circuit (PIC) Biosensors: A Comparative Review

Label-free direct-optical biosensors such as surface-plasmon resonance (SPR) spectroscopy has become a gold standard in biochemical analytics in centralized laboratories. Biosensors based on photonic integrated circuits (PIC) are based on the same physical sensing mechanism: evanescent field sensing. PIC-based biosensors can play an important role in healthcare, especially for point-of-care diagnostics, if challenges for a transfer from research laboratory to industrial applications can be overcome. Research is at this threshold, which presents a great opportunity for innovative on-site analyses in the health and environmental sectors. A deeper understanding of the innovative PIC technology is possible by comparing it with the well-established SPR spectroscopy. In this work, we shortly introduce both technologies and reveal similarities and differences. Further, we review some latest advances and compare both technologies in terms of surface functionalization and sensor performance.

Rapid colorimetric analysis of multiple microRNAs using encoded hydrogel microparticles

microRNAs (miRNAs) have attracted much attention as potential biomarkers for the diagnosis of various fatal diseases. With increasing interest in miRNA detection at practical sites, colorimetric bead-based assays have garnered much attention, because these allow for simple analysis with cheap and portable devices. Among them, the encoded hydrogel microparticle-based colorimetric miRNA assay is considered as one of the promising techniques, due to its strengths, such as large multiplex capacity, acceptable sensitivity, and simple analysis. However, it still imposes a limitation in terms of the assay time, particularly the colorimetric reaction time, which is too long, making the practical application of the assay difficult and undermining its detection accuracy. In this work, we present a rapid colorimetric assay based on encoded hydrogel microparticles, which exhibits a significant decrease in the colorimetric reaction time due to two factors: (1) an increase in the number of enzymes bound to hydrogel microparticles via a post-synthesis functionalization method, and (2) an elevation in the enzyme reaction temperature during colorimetric labeling. We obtained a comparable sensitivity of the colorimetric assay with three different miRNA targets, even with a shortened colorimetric reaction time. Furthermore, we validated that our colorimetric detection method is suitable for multiplex miRNA detection, owing to its low cross-reactivity.

Functional Micro-/Nanomaterials for Multiplexed Biodetection

When analyzing biological phenomena and processes, multiplexed biodetection has many advantages over single-factor biodetection and is highly relevant to both human health issues and advancements in the life sciences. However, many key problems with current multiplexed biodetection strategies remain unresolved. Herein, the main issues are analyzed and summarized: 1) generating sufficient signal to label targets, 2) improving the signal-to-noise ratio to ensure total detection sensitivity, and 3) simplifying the detection process to reduce the time and labor costs of multiple target detection. Then, available solutions made possible by designing and controlling the properties of micro- and nanomaterials are introduced. The aim is to emphasize the role that micro-/nanomaterials can play in the improvement of multiplexed biodetection strategies. Through analyzing existing problems, introducing state-of-the-art developments regarding relevant materials, and discussing future directions of the field, it is hopeful to help promote necessary developments in multiplexed biodetection and associated scientific research.

Nanoporous Anodic Alumina-Based Sensor for miR-99a-5p Detection as an Effective Early Breast Cancer Diagnostic Tool

Circulating microRNAs have emerged as potential diagnostic biomarkers. The deregulation of the microRNA miR-99a-5p has been previously described as an effective biomarker of early breast cancer. Herein, we present a new nanoporous anodic alumina (NAA)-based biosensor that can detect plasma miR-99a-5p with high sensitivity and selectivity. NAA pores are loaded with rhodamine B and capped with a specific oligonucleotide that is able to block cargo release until the target is present. In the presence of miR-99a-5p, the capping oligonucleotide recognizes the miR-99a-5p sequence and displaces it allowing the release of the encapsulated dye. This method is able to successfully distinguish healthy controls from breast cancer patients, even at early stages with high efficiency, showing the presented system as a promising tool for breast cancer detection.

Label-Free Homogeneous microRNA Detection in Cell Culture Medium Based on Graphene Oxide and Specific Fluorescence Quenching

Label-free homogeneous optical detection of low concentration of oligonucleotides using graphene oxide in complex solutions containing proteins remains difficult. We used a colloidal graphene oxide (GO) as a fluorescent probe quencher to detect microRNA-21 spiked-in cell culture medium, overcoming previously reported problematic aspects of protein interference with graphene oxide. We used a "turn off" assay for specific quenching-based detection of oligo DNA-microRNA hybridization in solution. A fluorescein conjugated 30-mer single-stranded DNA (ssDNA) probe was combined with a complementary synthetic microRNA (18 nucleotides) target. The probe-target hybridization was detected by specific quenching due to photoinduced electron transfer (PET). On the next step, GO captures and quenches the unhybridized probe by fluorescence resonance energy transfer (FRET) in the presence of cell culture medium supplemented with platelet lysate, 0.1% sodium dodecyl sulfate (SDS), 0.1% Triton X-100 and 50% formamide. This resulted in sensitive measurement of the specific probe-target complexes remaining in solution. The detection is linear in the range of 1 nM and 8 nM in a single 100 μL total volume assay sample containing 25% cell culture medium supplemented with platelet lysate. We highlight a general approach that may be adopted for microRNA target detection within complex physiological media.

Optical Biosensors for the Detection of Rheumatoid Arthritis (RA) Biomarkers: A Comprehensive Review

A comprehensive review of optical biosensors for the detection of biomarkers associated with rheumatoid arthritis (RA) is presented here, including microRNAs (miRNAs), C-reactive protein (CRP), rheumatoid factor (RF), anti-citrullinated protein antibodies (ACPA), interleukin-6 (IL-6) and histidine, which are biomarkers that enable RA detection and/or monitoring. An overview of the different optical biosensors (based on fluorescence, plasmon resonances, interferometry, surface-enhanced Raman spectroscopy (SERS) among other optical techniques) used to detect these biomarkers is given, describing their performance and main characteristics (limit of detection (LOD) and dynamic range), as well as the connection between the respective biomarker and rheumatoid arthritis. It has been observed that the relationship between the corresponding biomarker and rheumatoid arthritis tends to be obviated most of the time when explaining the mechanism of the optical biosensor, which forces the researcher to look for further information about the biomarker. This review work attempts to establish a clear association between optical sensors and rheumatoid arthritis biomarkers as well as to be an easy-to-use tool for the researchers working in this field.

Necessity and Challenges of Sample Preconcentration in Analysis of Multiple MicroRNAs by Capillary Electrophoresis

Thousands of putative microRNA (miRNA)-based cancer biomarkers have been reported, but none has been validated for approval by the Food and Drug Administration. One of the reasons for this alarming discrepancy is the lack of a method that is sufficiently robust for carrying out validation studies, which may require analysis of samples from hundreds of patients across multiple institutions and pooling the results together. The capillary electrophoresis (CE)-based hybridization assay proved to be more robust than reversed transcription polymerase chain reaction (the current standard), but its limit of quantification (LOQ) exceeds 10 pM while miRNA concentrations in cell lysates are below 1 pM. Thus, CE-based separation must be preceded by on-column sample preconcentration. Here, we explain the challenges of sample preconcentration for CE-based miRNA analyses and introduce a preconcentration method that can suit CE-based miRNA analysis utilizing peptide nucleic acid (PNA) hybridization probes. The method combines field-amplified sample stacking (FASS) with isotachophoresis (ITP). We proved that FASS-ITP could retain and concentrate both near-neutral PNA with highly negatively charged PNA-miRNA hybrids. We demonstrated that preconcentration by FASS-ITP could be combined with the CE-based separation of the unreacted PNA probes from the PNA-miRNA hybrids and facilitate improvement in LOQ by a factor of 140, down to 0.1 pM. Finally, we applied FASS-ITP-CE for the simultaneous detection of two miRNAs in crude cell lysates and proved that the method was robust when used in complex biological matrices. The 140-fold improvement in LOQ and the robustness to biological matrices will significantly expand the applicability of CE-based miRNA analysis, bringing it closer to becoming a practical tool for validation of miRNA biomarkers.

A novel liquid biopsy-based approach for highly specific cancer diagnostics: mitigating false responses in assaying patient plasma-derived circulating microRNAs through combined SERS and plasmon-enhanced fluorescence analyses

Studies have shown that microRNAs, which are small noncoding RNAs, hold tremendous promise as next-generation circulating biomarkers for early cancer detection via liquid biopsies. A novel, solid-state nanoplasmonic sensor capable of assaying circulating microRNAs through a combined surface-enhanced Raman scattering (SERS) and plasmon-enhanced fluorescence (PEF) approach has been developed. Here, the unique localized surface plasmon resonance properties of chemically-synthesized gold triangular nanoprisms (Au TNPs) are utilized to create large SERS and PEF enhancements. With careful modification to the surface of Au TNPs, this sensing approach is capable of quantifying circulating microRNAs at femtogram/microliter concentrations. Uniquely, the multimodal analytical methods mitigate both false positive and false negative responses and demonstrate the high stability of our sensors within bodily fluids. As a proof of concept, microRNA-10b and microRNA-96 were directly assayed from the plasma of six bladder cancer patients. Results show potential for a highly specific liquid biopsy method that could be used in point-of-care clinical diagnostics to increase early cancer detection or any other diseases including SARS-CoV-2 in which RNAs can be used as biomarkers.

Tag-Free Methodology for Ultrasensitive Biosensing of miRNA Based on Intrinsic Isotope Detection

MicroRNA (miRNA), of which the abnormal intracellular expression highly associates with numerous pathological diseases, is considered as an important biomarker for early diagnosis and state monitoring of cancer. To avoid the tedious and vunerable labeling process, a series of novel label-free quantification methods for miRNA have been proposed. However, current label-free miRNA assays still require the presynthesis of a sensing unit as tags. Herein, we propose a "tag-free" methodology for miRNA quantification to realize the removal of sensing labels. Combining a concatenated-HCR (C-HCR) strategy and high-resolution inductive couple plasma mass spectrometry (HR-ICPMS) detection, we utilize phosphorus as a characteristic element to quantify the concentration of nucleotides. Benefiting from the excellent amplification performance of C-HCR and element analysis capacity of HR-ICPMS, a 13 fM limit of detection (LOD) was obtained. Ulteriorly, we verify the anti-interference performance of the proposed tag-free miRNA assay with a phosphate substrate-contained cell culture medium or nontarget miRNA. Furthermore, two cell lines of human cancer were chosen to evaluate the real biological sample analysis capacity. The good correlation data indicate promising prospects of the proposed tag-free methodology for the quantification of miRNA in tumor cells and further clinical applications.

Progress of infrared guided-wave nanophotonic sensors and devices

Nanophotonics, manipulating light-matter interactions at the nanoscale, is an appealing technology for diversified biochemical and physical sensing applications. Guided-wave nanophotonics paves the way to miniaturize the sensors and realize on-chip integration of various photonic components, so as to realize chip-scale sensing systems for the future realization of the Internet of Things which requires the deployment of numerous sensor nodes. Starting from the popular CMOS-compatible silicon nanophotonics in the infrared, many infrared guided-wave nanophotonic sensors have been developed, showing the advantages of high sensitivity, low limit of detection, low crosstalk, strong detection multiplexing capability, immunity to electromagnetic interference, small footprint and low cost. In this review, we provide an overview of the recent progress of research on infrared guided-wave nanophotonic sensors. The sensor configurations, sensing mechanisms, sensing performances, performance improvement strategies, and system integrations are described. Future development directions are also proposed to overcome current technological obstacles toward industrialization.

Logic-signal-based multiplex detection of MiRNAs with high tension hybridization and multiple signal amplification

A multiplex miRNA detection scheme with simultaneous multiple signal output by single excitation has been reported.

Label-Free MicroRNA Optical Biosensors

MicroRNAs (miRNAs) play crucial roles in regulating gene expression. Many studies show that miRNAs have been linked to almost all kinds of disease. In addition, miRNAs are well preserved in a variety of specimens, thereby making them ideal biomarkers for biosensing applications when compared to traditional protein biomarkers. Conventional biosensors for miRNA require fluorescent labeling, which is complicated, time-consuming, laborious, costly, and exhibits low sensitivity. The detection of miRNA remains a big challenge due to their intrinsic properties such as small sizes, low abundance, and high sequence similarity. A label-free biosensor can simplify the assay and enable the direct detection of miRNA. The optical approach for a label-free miRNA sensor is very promising and many assays have demonstrated ultra-sensitivity (aM) with a fast response time. Here, we review the most relevant label-free microRNA optical biosensors and the nanomaterials used to enhance the performance of the optical biosensors.

Recent advances in environmental and clinical analysis using microring resonator-based sensors

Progress in the development of biosensors has dramatically improved analytical techniques. Biosensors have advantages over more conventional analytical techniques arising from attributes such as straightforward analyses, higher throughput, miniaturization, smaller sample input, and lower cost. Microring optical resonators have emerged in the area of optical sensors as an exceptional choice due to their sensitivity, ease of fabrication, multiplexity capability and label-free detection. In this paper, the sensing principle of these sensors is described. In addition, we summarize and highlight their most recent and relevant applications in environmental and clinical detection analysis.

Direct measurement and analytical description of the mode alignment in inversely tapered silicon nano-resonators

Inversely tapered silicon photonic resonators on silicon substrates were shown to host multiple high–Q whispering gallery modes and constitute versatile building blocks for CMOS compatible solid state lighting, optical sensing and modulator devices. So far, numerical analyses by the finite difference time domain method have been used to predict the height distribution of whispering gallery modes in such resonators. In this study, we provide an experimental evidence of this mode distribution along the resonator height by selectively exciting whispering gallery modes using cathodoluminescence spectroscopy. Further we derive analytical functions that permit to relate the height distribution of modes with a defined polarization, symmetry and effective refractive index to the geometrical shape of the inversely tapered resonators.

Advanced methods for microRNA biosensing: a problem-solving perspective

MicroRNAs (miRNAs) present several features that make them more difficult to analyze than DNA and RNA. For this reason, efforts have been made in recent years to develop innovative platforms for the efficient detection of microRNAs. The aim of this review is to provide an overview of the sensing strategies able to deal with drawbacks and pitfalls related to microRNA detection. With a critical perspective of the field, we identify the main challenges to be overcome in microRNA sensing, and describe the areas where several innovative approaches are likely to come for managing those issues that put limits on improvement to the performances of the current methods. Then, in the following sections, we critically discuss the contribution of the most promising approaches based on the peculiar properties of nanomaterials or nanostructures and other hybrid strategies which are envisaged to support the adoption of these new methods useful for the detection of miRNA as biomarkers of practical clinical utility. Graphical abstract ᅟ.

Direct Quantitative Analysis of Multiple microRNAs (DQAMmiR) with Peptide Nucleic Acid Hybridization Probes

Direct quantitative analysis of multiple miRNAs (DQAMmiR) is a hybridization-based assay, in which the excess of the DNA hybridization probes is separated from the miRNA-probe hybrids, and the hybrids are separated from each other in gel-free capillary electrophoresis (CE) using two types of mobility shifters: single-strand DNA binding protein (SSB) added to the CE running buffer and peptide drag tags conjugated with the probes. Here we introduce the second-generation DQAMmiR, which utilizes peptide nucleic acid (PNA) rather than DNA hybridization probes and requires no SSB in the CE running buffer. PNA probes are electrically neutral, while PNA-miRNA hybrids are negatively charged, and this difference in charge can be a basis for separation of the hybrids from the probes. In this proof-of-principle work, we first experimentally confirmed that the PNA-RNA hybrid was separable from the excess of the PNA probe without SSB in the running buffer, resulting in a near 10 min time window, which would allow, theoretically, separation of up to 30 hybrids. Then, we adapted to PNA-RNA hybrids our previously developed theoretical model for predicting hybrid mobilities. The calculation performed with the modified theoretical model indicated that PNA-RNA hybrids of slightly different lengths could be separated from each other without drag tags. Accordingly, we designed a simple experimental model capable of confirming: (i) separation of tag-free hybrids of different lengths and (ii) separation of same-length hybrids due to a drag tag on the PNA probe. The experimental model included three miRNAs: 20-nt miR-147a, 20-nt miR-378g, and 22-nt miR-21. The three complementary PNA probes had lengths matching those of the corresponding target miRNAs. The probe for miR-147a had a short five-amino-acid drag tag; the other two had no drag tags. We were able to achieve baseline separation of the three hybrids from each other. The LOQ of 14 pM along with the high accuracy (recovery >90%) and precision (RSD ≈ 10%) of the assay at picomolar target concentrations suggest that PNA-facilitated DQAMmiR could potentially support practical miRNA analysis of clinical samples.

Silicon Photonic Biosensors Using Label-Free Detection

Thanks to advanced semiconductor microfabrication technology, chip-scale integration and miniaturization of lab-on-a-chip components, silicon-based optical biosensors have made significant progress for the purpose of point-of-care diagnosis. In this review, we provide an overview of the state-of-the-art in evanescent field biosensing technologies including interferometer, microcavity, photonic crystal, and Bragg grating waveguide-based sensors. Their sensing mechanisms and sensor performances, as well as real biomarkers for label-free detection, are exhibited and compared. We also review the development of chip-level integration for lab-on-a-chip photonic sensing platforms, which consist of the optical sensing device, flow delivery system, optical input and readout equipment. At last, some advanced system-level complementary metal-oxide semiconductor (CMOS) chip packaging examples are presented, indicating the commercialization potential for the low cost, high yield, portable biosensing platform leveraging CMOS processes.

Fiber Light-Coupled Optofluidic Waveguide (FLOW) Immunosensor for Highly Sensitive Detection of p53 Protein

Highly sensitive detection of molecular tumor markers is essential for biomarker-based cancer diagnostics. In this work, we showcase the implementation of fiber light-coupled optofluidic waveguide (FLOW) immunosensor for the detection of p53 protein, a typical tumor marker. The FLOW consists of a liquid-core capillary and an accompanying optical fiber, which allows evanescent interaction between light and microfluidic sample. Molecular binding at internal surface of the capillary induces a response in wavelength shift of the transmission spectrum in the optical fiber. To enable highly sensitive molecular detection, the evanescent-wave interaction has been strengthened by enlarging shape factor R via fine geometry control. The proposed FLOW immunosensor works with flowing microfluid, which increases the surface molecular coverage and improves the detection limit. As a result, the FLOW immunosensor presents a log-linear response to the tumor protein at concentrations ranging from 10 fg/mL up to 10 ng/mL. In addition, the nonspecifically adsorbed molecules can be effectively removed by the fluid at an optimal flow rate, which benefits the accuracy of the measurement. Tested in serum samples, the FLOW successfully maintains its sensitivity and specificity on p53 protein, making it suitable for diagnostics applications.

Optical bio-chemical sensors based on whispering gallery mode resonators

Whispering gallery mode (WGM) resonators have attracted extensive attention and their unique characteristics have led to some remarkable achievements. In particular, when combined with optical sensing technology, the WGM reonator-based sensor offers the advantages of small size, high sensitivity and a real-time dynamic response. At present, this type of sensor is widely applied in the bio-chemical sensing field. In this paper, we briefly review the sensing principle, the structures and the sensing applications of optical bio-chemical sensors based on the WGM resonator, with particular focuses on their sensing properties and their advantages and disadvantages. In addition, the existing problems and future development trends of WGM resonator-based optical bio-chemical sensors are discussed.

Multiplexed microRNA Expression Profiling by Combined Asymmetric PCR and Label-Free Detection using Silicon Photonic Sensor Arrays

Analysis methods based upon the quantitative, real-time polymerase chain reaction are extremely powerful; however, they face intrinsic limitations in terms of target multiplexing. In contrast, silicon photonic microring resonators represent a modularly multiplexable sensor array technology that is well-suited to the analysis of targeted biomarker panels. In this manuscript we employ an asymmetric polymerase chain reaction approach to selectively amplify copies of cDNAs generated from targeted miRNAs before multiplexed, label-free quantitation through hybridization to microring resonator arrays pre-functionalized with capture sequences. This method, which shows applicability to low input amounts and a large dynamic range, was demonstrated for the simultaneous detection of eight microRNA targets from twenty primary brain tumor samples with expression profiles in good agreement with literature precedent.

High sensitivity and label-free oligonucleotides detection using photonic bandgap sensing structures biofunctionalized with molecular beacon probes

A label-free sensor, based on the combination of silicon photonic bandgap (PBG) structures with immobilized molecular beacon (MB) probes, is experimentally developed. Complementary target oligonucleotides are specifically recognized through hybridization with the MB probes on the surface of the sensing structure. This combination of PBG sensing structures and MB probes demonstrates an extremely high sensitivity without the need for complex PCR-based amplification or labelling methods.

Combining asymmetric PCR-based enzymatic amplification with silicon photonic microring resonators for the detection of lncRNAs from low input human RNA samples

A method for quantifying biologically relevant long-non-coding RNAs by combining nucleic acid amplification via asymmetric polymerase chain reaction (PCR) with label-free PCR product detection using silicon photonic microring resonator arrays is described. This approach eliminates the need for fluorophores, which presents a limit for spectral multiplexing in conventional qPCR methods, and rather offers potential for much higher levels of plexity by spatially arraying capture probes. Here, we demonstrate the potential of this technique to detect two differentially expressed lncRNA transcripts and an internal control mRNA transcript in different commercial human tissue specimens, as well as in a glioblastoma cell line using only nanogram input amounts of total RNA. The obtained results were validated using single-plex RT-qPCR and found to be in good agreement, demonstrating the potential of this technique for lncRNA quantification applications.

Label-Free Optical Biodetection of Pathogen Virulence Factors in Complex Media Using Microtoroids with Multifunctional Surface Functionality

Early detection of pathogens or their virulence factors in complex media has a key role in early diagnosis and treatment of many diseases. Nanomolar and selective detection of Exotoxin A, which is a virulence factor secreted from Pseudomonas aeruginosa in the sputum of Cystic Fibrosis (CF) patients, can pave the way for early diagnosis of P. aeruginosa infections. In this study, we conducted a preliminary study to demonstrate the feasibility of optical biodetection of P. aeruginosa Exotoxin A in a diluted artificial sputum mimicking the CF respiratory environment. Our surface engineering approach provides an effective biointerface enabling highly selective detection of the Exotoxin A molecules in the complex media using monoclonal anti-Exotoxin A functionalized microtoroids. The highly resilient microtoroid surface toward other constituents of the sputum provides Exotoxin A detection ability in the complex media by reproducible measurements. In this study, the limit-of-detection of Exotoxin A in the complex media is calculated as 2.45 nM.

Micro-optics for microfluidic analytical applications

This critical review summarizes the developments in the integration of micro-optical elements with microfluidic platforms for facilitating detection and automation of bio-analytical applications.

A highly sensitive SPRi biosensing strategy for simultaneous detection of multiplex miRNAs based on strand displacement amplification and AuNP signal enhancement

Herein, a dual channel SPRi biosensor has been developed for the simultaneous and highly sensitive detection of multiplex miRNAs based on SDA and DNA-functionalized AuNP signal enhancement.

Tip‐mould microcontact printing for functionalisation of optical microring resonator

We present an approach to functionalise optical microring resonators as hybridisation platforms, using tip‐mould reactive microcontact printing process. Derived from reactive microcontact printing using an ad hoc mould of polydimethylsiloxane (PDMS), the method functionalises single microring resonator with a target‐specific capture agent. The authors report the functionalisation of silicon nitride (SiN) 200 μ m diameter microring resonator with single‐strand DNA and the hybridisation detection of 100 nM target analyte, while concurrently monitoring not‐functionalised microring as a control sensor. Results show that the functionalisation approach permits to address single microring resonators with mutual distance lower than 100 μ m with high precision, enabling a better integration of multiple spotting zones on the chip concerning traditional functionalisation procedures.

Measuring Ultra-low Levels of Nucleotide Biomarkers Using Quartz Crystal Microbalance and SPR Microarray Imaging Methods: A Comparative Analysis

Circulating serum nucleotide biomarkers are useful indicators for early diagnosis of cancer, respiratory illnesses, and other deadly diseases. In this work, we compared detection performances of a quartz crystal microbalance (QCM), which is a mass sensor, with that of a surface plasmon resonance (SPR) microarray for an oligonucleotide mimic of a microRNA-21 biomarker. A surface immobilized capture oligonucleotide probe was used to hybridize with the target oligonucleotide (i.e., the microRNA-21 mimic) to facilitate selective detection. To obtain ultra-low femtomolar (fM) detection sensitivity, gold nanoparticles (50 nm) were conjugated with the target oligonucleotide. We achieved detection limits of 28and 47 fM for the target oligonucleotide by the QCM and SPRi microarray, respectively. We also conducted sample recovery studies and performed matrix effect analysis. Although the QCM had a lower detection limit, the microarray approach offered better throughput for analysis of up to 16 samples. We confirmed that the designed assay was selective for the target oligonucleotide and did not show signals for the control oligonucleotide with five mismatch sites relative to the target sequence. Combination of the QCM and microarray methods that utilize the same assay chemistry on gold are useful for overcoming clinical sample matrix effects and achieving ultra-low detection of small nucleotide biomarkers with quantitative insights.

A Guide to Quantitative Biomarker Assay Development using Whispering Gallery Mode Biosensors

Whispering gallery mode (WGM) sensors are a class of powerful analytical techniques defined by the measurement of changes in the local refractive index at or near the sensor surface. When functionalized with target-specific capture agents, analyte binding can be measured with very low limits of detection. There are many geometric manifestations of WGM sensors, with chip-integrated silicon photonic devices first commercialized because of the robust, wafer-scale device fabrication, facile optical interrogation, and amenability to the creation of multiplexed sensor arrays. Using these arrays, a number of biomolecular targets have been detected in both label-free and label-enhanced assay formats. For example, sub-picomolar detection limits for multiple cytokines were achieved using an enzymatically enhanced sandwich immunoassay that showed high analyte specificity suitable for detection in complex, clinical matrices. This protocol describes a generalizable approach for the development of quantitative, multiplexed immunoassays using silicon photonic microrings as an example WGM platform. © 2017 by John Wiley & Sons, Inc.

Free-Energy-Driven Lock/Open Assembly-Based Optical DNA Sensor for Cancer-Related microRNA Detection with a Shortened Time-to-Result

Quantification of cancer biomarker microRNAs (miRs) by exquisitely designed biosensors with a short time-to-result is of great clinical significance. With immobilized capture probes (CPs) and fluorescent-labeled signal probes (SPs), surface-involved sandwich-type (SST) biosensors serve as powerful tools for rapid, highly sensitive, and selective detection of miR in complex matrices as opposed to the conventional techniques. One key challenge for such SST biosensors is the existence of false-negative signals when the amount of miRs exceeds SPs in solution phase for a surface with a limited number of CP. To meet this challenge, a dynamic lock/open DNA assembly was designed to rationally program the pathway for miR/SP hybrids. Based on secondary structure analysis and free-energy assessment, a "locker" strand that partially hybridizes with target miR by two separated short arms was designed to stabilize target miR, preventing possible false-negative signals. The strategy was demonstrated on a fiber-based fluorescent DNA-sensing platform. CP/miR/SP sandwiches formed on the fiber surface would generate fluorescent signals for quantitative analysis. The developed SST biosensor was able to detect miR Hsa let-7a with a detection limit of 24 pM. The applicability of this free-energy-driven lock/open assembly-based optical DNA sensor was further confirmed with spiked human urine and serum samples.

Highly Sensitive, Label-Free Detection of 2,4-Dichlorophenoxyacetic Acid Using an Optofluidic Chip

A highly sensitive approach for rapid and label-free detection of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) using an optofluidic chip is demonstrated. The optofluidic chip is prepared by covalent immobilization of 2,4-D-bovine serum albumin (2,4-D-BSA) conjugate to an integrated microring resonator. Subsequent detection of 2,4-D carried out in a competitive immunoreaction format enables selective detection of 2,4-D in different types of water samples, including bottled, tap, and lake water, at a limit of detection (LOD) of 4.5 pg/mL and in a quantitative range of 15-10⁵ pg/mL. The microring resonator-based optofluidic chip is reusable with ultrahigh sensitivity that offers real-time and on-site detection of low-molecular-weight targets for potential applications in food safety and environmental monitoring.

Use of Dimethyl Pimelimidate with Microfluidic System for Nucleic Acids Extraction without Electricity

The isolation of nucleic acids in the lab on a chip is crucial to achieve the maximal effectiveness of point-of-care testing for detection in clinical applications. Here, we report on the use of a simple and versatile single-channel microfluidic platform that combines dimethyl pimelimidate (DMP) for nucleic acids (both RNA and DNA) extraction without electricity using a thin-film system. The system is based on the adaption of DMP into nonchaotropic-based nucleic acids and the capture of reagents into a low-cost thin-film platform for use as a microfluidic total analysis system, which can be utilized for sample processing in clinical diagnostics. Moreover, we assessed the use of the DMP system for the extraction of nucleic acids from various samples, including mammalian cells, bacterial cells, and viruses from human disease, and we also confirmed that the quality and quantity of the nucleic acids extracted were sufficient to allow for the robust detection of biomarkers and/or pathogens in downstream analysis. Furthermore, this DMP system does not require any instruments and electricity, and has improved time efficiency, portability, and affordability. Thus, we believe that the DMP system may change the paradigm of sample processing in clinical diagnostics.

Towards next-generation label-free biosensors: recent advances in whispering gallery mode sensors

Whispering gallery mode biosensors have been widely exploited over the past decade to study molecular interactions by virtue of their high sensitivity and applicability in real-time kinetic analysis without the requirement to label. There have been immense research efforts made for advancing the instrumentation as well as the design of detection assays, with the common goal of progressing towards real-world sensing applications. We therefore review a set of recent developments made in this field and discuss the requirements that whispering gallery mode label-free sensors need to fulfill for making a real world impact outside of the laboratory. These requirements are directly related to the challenges that these sensors face, and the methods proposed to overcome them are discussed. Moving forward, we provide the future prospects and the potential impact of this technology.