Amplification-free Detection of Cytomegalovirus miRNA Using a Modification-free Surface Plasmon Resonance Biosensor

PCR Independent Strategy-Based Biosensors for RNA Detection

RNA is an important information and functional molecule. It can respond to the regulation of life processes and is also a key molecule in gene expression and regulation. Therefore, RNA detection technology has been widely used in many fields, especially in disease diagnosis, medical research, genetic engineering and other fields. However, the current RT-qPCR for RNA detection is complex, costly and requires the support of professional technicians, resulting in it not having great potential for rapid application in the field. PCR-free techniques are the most attractive alternative. They are a low-cost, simple operation method and do not require the support of large instruments, providing a new concept for the development of new RNA detection methods. This article reviews current PCR-free methods, overviews reported RNA biosensors based on electrochemistry, SPR, microfluidics, nanomaterials and CRISPR, and discusses their challenges and future research prospects in RNA detection.

Nanomaterials Connected to Bioreceptors to Introduce Efficient Biosensing Strategy for Diagnosis of the TORCH Infections: A Critical Review

TORCH infection is a significant risk factor for severe fetal damage, especially congenital malformations. Screening pregnant women for TORCH pathogens could reduce the incidence of adverse pregnancy outcomes and prevent birth defects. Hence, timely identification and inhibition of TORCH infections are effective ways to successfully prevent them in pregnant women. Recently, the superiority of biosensors in TORCH pathogen sensing has been emphasized due to their intrinsic benefits, such as rapid response time, portability, cost-effectiveness, much friendlier preparation and determination steps. With the introduction of advanced nanomaterials into biosensing, the diagnostic properties of biosensors have significantly improved. This study core presents and debates the current progress in biosensing systems for TORCH pathogens using various artificial and natural receptors. The incorporation of nanomaterials into various transduction systems can enhance diagnostic performance. The key performance characteristics of optical and electrochemical biosensors, such as response time, limit of detection (LOD), and linear detection range, are systematically discussed, along with the current TORCH pathogens used for constructing biosensors. Finally, the major problems that exist for converting scientific investigation into product development are also outlined.

Decoding human cytomegalovirus for the development of innovative diagnostics to detect congenital infection

Cytomegalovirus is the most common cause of congenital infectious disease and the leading nongenetic etiology of sensorineural hearing loss. Although most infected neonates are asymptomatic at birth, congenital cytomegalovirus infection is responsible for nearly 400 infant deaths annually in the United States and may lead to significant long-term neurodevelopmental impairments in survivors. The resulting financial and social burdens of congenital cytomegalovirus infection have led many medical centers to initiate targeted testing after birth, with a growing advocacy to advance universal newborn screening. While no cures or vaccines are currently available to eliminate or prevent cytomegalovirus infection, much has been learned over the last five years regarding disease pathophysiology and viral replication cycles that may enable the development of innovative diagnostics and therapeutics. This Review will detail our current understanding of congenital cytomegalovirus infection, while focusing our discussion on routine and emerging diagnostics for viral detection, quantification, and long-term prognostication. IMPACT: This review highlights our current understanding of the fetal transmission of human cytomegalovirus. It details clinical signs and physical findings of congenital cytomegalovirus infection. This submission discusses currently available cytomegalovirus diagnostics and introduces emerging platforms that promise improved sensitivity, specificity, limit of detection, viral quantification, detection of genomic antiviral resistance, and infection staging (primary, latency, reactivation, reinfection).

Aflatoxin detection technologies: recent advances and future prospects

Aflatoxins have posed serious threat to food safety and human health. Therefore, it is important to detect aflatoxins in samples rapidly and accurately. In this review, various technologies to detect aflatoxins in food are discussed, including conventional ones such as thin-layer chromatography (TLC), high performance liquid chromatography (HPLC), enzyme linked immunosorbent assay (ELISA), colloidal gold immunochromatographic assay (GICA), radioimmunoassay (RIA), fluorescence spectroscopy (FS), as well as emerging ones (e.g., biosensors, molecular imprinting technology, surface plasmon resonance). Critical challenges of these technologies include high cost, complex processing procedures and long processing time, low stability, low repeatability, low accuracy, poor portability, and so on. Critical discussion is provided on the trade-off relationship between detection speed and detection accuracy, as well as the application scenario and sustainability of different technologies. Especially, the prospect of combining different technologies is discussed. Future research is necessary to develop more convenient, more accurate, faster, and cost-effective technologies to detect aflatoxins.

"Two-in-one" core-shell nanozyme probes with double signal amplification for high-performing surface plasmon resonance immunosensing

Herein, a "two-in-one" Ag@Au core-shell nanozyme probe inducing double-signal amplification has been developed to significantly elevate the sensitivity of SPR sensors via sandwich immunoassay. The Ag@Au core-shell nanozyme with intrinsic peroxide-like activity was demonstrated to catalyze a polymerization reaction leading to formation of polyaniline, allowing further improvement of detection performance of SPR immunosensor. The method demonstrated here offers a universal strategy for enhanced SPR detection and further expands the application of nanozymes.

Tetrahedral DNA Nanostructure-Engineered Paper-Based Sensor with an Enhanced Antifouling Ability for Photoelectrochemical Sensing

Herein, a newly designed two-in-one tetrahedral DNA (TDN) nanostructure with an antifouling surface and backbone-rigidified interfacial tracks was developed for highly sensitive and selective detection of miRNA-182-5p. The well-regulated TDN tracks were assembled onto the surface of the TiO₂/MIL-125-NH₂-functionalized paper electrode, which efficiently avoided the obstacle of DNA strand tangling and decreased the probability of suspension during the walking process, thus greatly promoting the moving efficiency of DNA walkers. More interestingly, the TDN-modified sensing interfaces demonstrated incomparable antifouling ability against protein samples and interfering miRNAs due to the strong hydrophilic capacity and special molecular conformations, which addressed the dilemma of low sensitivity from traditional antifouling coating strategies. As a proof of concept, the designed bifunctional tetrahedron-modified paper-based photoelectrochemical sensor was successfully used to quantify miRNA-182-5p with a low detection limit of 0.09 fM and high specificity and was validated for monitoring of miRNA-182-5p in real samples. This TDN-engineered biointerface could be used as a universal platform for tracking various targets by substituting the biorecognition events, providing great promise for bioanalysis and clinical diagnosis.

Microelectromechanical system-based biosensor for label-free detection of human cytomegalovirus

The human cytomegalovirus (HCMV) is an asymptomatic common virus that is typically harmless, but in some cases, it can be life threatening. Thus, there is an urgent need to develop novel diagnostic methods and strengthen the efforts to combat this virus. A microcantilever-based biosensor functionalised with the UL83-antibody of HCMV (UL83-HCMV antibody) has been developed to detect the UL83-antigen of HCMV (UL83-HCMV antigen) at different concentrations ranging from 0.3 to 300 ng/ml. The response of the biosensor to the presence of UL83-HCMV antigen was measured through the shift in resonance frequency before and after antigen-antibody binding. The system shows a low detection limit of 84 pg/ml, which is comparable to traditional sensors, and a detection time of less than 15 min was achieved. The selectivity of the sensor was demonstrated using three different proteins with and without the UL83-HCMV antigen. The biosensor shows high selectivity for the UL83-HCMV antigen. Mass loading by the UL83-HCMV antigen was roughly estimated with a sensitivity of ∼30 fg/Hz. This technique is crucial for the fabrication of portable and low-cost biosensors that can be used in real-time monitoring and enables early medical diagnosis.

Rapid quantification of miRNAs using dynamic FRET-FISH

MicroRNAs (miRNAs) are short regulatory RNAs that control gene expression at the post-transcriptional level. Various miRNAs playing important roles in cancer development are emerging as promising diagnostic biomarkers for early cancer detection. Accurate miRNA detection, however, remains challenging because they are small and highly homologous. Recently developed miRNA detection techniques based on single-molecule imaging enabled highly specific miRNA quantification without amplification, but the time required for these techniques to detect a single miRNA was larger than 10 minutes, making rapid profiling of numerous miRNAs impractical. Here we report a rapid miRNA detection technique, dynamic FRET-FISH, in which single-molecule imaging at high probe concentrations and thus high-speed miRNA detection is possible. Dynamic FRET-FISH can detect miRNAs in 10 s at 1.2 μM probe concentration while maintaining the high-specificity of single-nucleotide discrimination. We expect dynamic FRET-FISH will be utilized for early detection of cancers by profiling hundreds of cancer biomarkers in an hour.

Boosting the detection performance of severe acute respiratory syndrome coronavirus 2 test through a sensitive optical biosensor with new superior antibody

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus emerged in late 2019 leading to the COVID-19 disease pandemic that triggered socioeconomic turmoil worldwide. A precise, prompt, and affordable diagnostic assay is essential for the detection of SARS-CoV-2 as well as its variants. Antibody against SARS-CoV-2 spike (S) protein was reported as a suitable strategy for therapy and diagnosis of COVID-19. We, therefore, developed a quick and precise phase-sensitive surface plasmon resonance (PS-SPR) biosensor integrated with a novel generated anti-S monoclonal antibody (S-mAb). Our results indicated that the newly generated S-mAb could detect the original SARS-CoV-2 strain along with its variants. In addition, a SARS-CoV-2 pseudovirus, which could be processed in BSL-2 facility was generated for evaluation of sensitivity and specificity of the assays including PS-SPR, homemade target-captured ELISA, spike rapid antigen test (SRAT), and quantitative reverse transcription polymerase chain reaction (qRT-PCR). Experimentally, PS-SPR exerted high sensitivity to detect SARS-CoV-2 pseudovirus at 589 copies/ml, with 7-fold and 70-fold increase in sensitivity when compared with the two conventional immunoassays, including homemade target-captured ELISA (4 × 103 copies/ml) and SRAT (4 × 104 copies/ml), using the identical antibody. Moreover, the PS-SPR was applied in the measurement of mimic clinical samples containing the SARS-CoV-2 pseudovirus mixed with nasal mucosa. The detection limit of PS-SPR is calculated to be 1725 copies/ml, which has higher accuracy than homemade target-captured ELISA (4 × 104 copies/ml) and SRAT (4 × 105 copies/ml) and is comparable with qRT-PCR (1250 copies/ml). Finally, the ability of PS-SPR to detect SARS-CoV-2 in real clinical specimens was further demonstrated, and the assay time was less than 10 min. Taken together, our results indicate that this novel S-mAb integrated into PS-SPR biosensor demonstrates high sensitivity and is time-saving in SARS-CoV-2 virus detection. This study suggests that incorporation of a high specific recognizer in SPR biosensor is an alternative strategy that could be applied in developing other emerging or re-emerging pathogenic detection platforms.

Surface Plasmon Resonance Biosensors with Magnetic Sandwich Hybrids for Signal Amplification

The conventional signal amplification strategies for surface plasmon resonance (SPR) biosensors involve the immobilization of receptors, the capture of target analytes and their recognition by signal reporters. Such strategies work at the expense of simplicity, rapidity and real-time measurement of SPR biosensors. Herein, we proposed a one-step, real-time method for the design of SPR biosensors by integrating magnetic preconcentration and separation. The target analytes were captured by the receptor-modified magnetic nanoparticles (MNPs), and then the biotinylated recognition elements were attached to the analyte-bound MNPs to form a sandwich structure. The sandwich hybrids were directly delivered to the neutravidin-modified SPR fluidic channel. The MNPs hybrids were captured by the chip through the neutravidin-biotin interaction, resulting in an enhanced SPR signal. Two SPR biosensors have been constructed for the detection of target DNA and beta-amyloid peptides with high sensitivity and selectivity. This work, integrating the advantages of one-step, real-time detection, multiple signal amplification and magnetic preconcentration, should be valuable for the detection of small molecules and ultra-low concentrations of analytes.

Easy and Rapid Approach to Obtaining the Binding Affinity of Biomolecular Interactions Based on the Deep Learning Boost

Recently, the deep learning (DL) dimension of artificial intelligence has received much attention from biochemical researchers and thus has gradually become the key approach adopted in the area of biosensing applications. Studies have shown that the use of DL techniques for sensing can not only shorten the time of data analysis but also significantly increase the accuracy of data analysis and prediction, resulting in the performance improvement of biosensing systems in comparison to conventional methods. However, obtaining reliable equilibrium and rate constants of biomolecular interactions during the detection process remains difficult and time-consuming to date. In this study, we propose a transformed model based on the deep transfer learning and sequence-to-sequence autoencoder that can successfully transfer the SPR sensorgram to the protein-binding constants, that is, the association rate constant (k_a) and dissociation rate constant (k_d), which provide crucial information to understand the mechanisms of drug action and the functional structures of biomolecules. Experimentally, we first trained and tested the pre-trained model using the Langmuir model which generated ideal SPR sensorgrams and then we fine-tuned the pre-trained model through the augmented SPR sensorgrams which were synthesized by using the synthesized minority oversampling technique (SMOTE) through the moderate-scale experiment. Next, the fine-tuned model was inputted with a short experimental SPR sensorgram that only needs 110 s, and the sensorgram was directly transformed into a reconstructed ideal sensorgram. Finally, the binding kinetic constants, that is, k_a and k_d, as outputs, were obtained through fitting the reconstructed ideal sensorgram. The results showed that the prediction errors of k_a and k_d obtained by our model were less than 12 and 24%, respectively. Based on the convenience, accuracy, and reliability of the proposed DL approach, we believe our strategy significantly boosts the feasibility to monitor the binding affinity of antibodies online during production.

Highly sensitive and selective surface plasmon resonance biosensor for the detection of SARS-CoV-2 spike S1 protein

The reality that the coronavirus disease 2019 (COVID-19) is still raging around the world and making a comeback with a strong presence has highlighted the need for rapid and sensitive quantitative detection methods of viral RNA, antibody and antigen for widespread tracking and screening applications. Surface plasmon resonance (SPR) detection technology has achieved rapid development and become a standard measurement method in the fields of biosensing, biomedicine, biochemistry and biopharmaceuticals due to its advantages of high sensitivity, fast response and no need for labelling. Here, we report a sandwiched structure-based SPR biosensor for detecting a specific viral antigen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike S1 protein. The sensor combines a Ti₃C₂-MXene nanosheet modified sensing platform and polydopamine (PDA)-Ag nanoparticle (AgNP)/anti-SARS-CoV-2 spike S1 protein nanoconjugate signal enhancers, exhibiting a wide linear range of 0.0001 to 1000 ng mL^-1 with a low detection limit of 12 fg mL^-1 (S/N = 3). In the analysis of artificial saliva and human serum samples, the proposed SPR biosensor exhibits good reproducibility and high specificity, which indicates its potential for application in complex bodily fluids. The exploitation of the MXene-based SPR biochip for recognizing the SARS-CoV-2 antigen provides an accessible and rapid way for COVID-19 diagnosis, and promotes the application of 2D nanomaterial-based sensing chips in clinical diagnosis and disease screening. Significantly, the proposed method possesses general applicability that can be reprogrammed to detect any protein antigen if a corresponding specific nanobody is available.

RNA interference (RNAi)-based plasmonic nanomaterials for cancer diagnosis and therapy

RNA interference (RNAi) is being extensively investigated as a potential therapeutic strategy for cancer treatment. However, RNAi-based therapeutics have not yet been used to treat cancer because of their instability and the difficulty of microRNA (miRNA) delivery. Plasmonic nanoparticle-based RNAi nanotherapeutics have been developed for accurate and sensitive diagnosis and a strong therapeutic effect on cancers by leveraging their ease-of-use and specific properties such as photothermal conversion. In this review, recent strategies and advances in plasmonic nanoparticle-based miRNA delivery are briefly presented to facilitate the detection and treatment of several cancers. The challenges and potential opportunities afforded by the RNAi-based theragnosis field are discussed. We expect that the RNAi-integrated plasmonic nanotherapeutics discussed in this review can provide insights for the early diagnosis and effective treatment of cancer.

Development of a single quantum dot-mediated FRET biosensor for amplification-free detection of ten-eleven translocation 2

Ten-eleven translocation (TET) family proteins play key roles in multiple cellular processes by mediating the oxidation of 5-methylcytosine to directly participate in DNA demethylation, and often aberrantly expressed in various diseases. In this research, we develop a single-quantum-dot (QD)-mediated fluorescence resonance energy transfer (FRET) biosensor for amplification-free measurement of ten-eleven translocation 2 (TET2). When TET2 is present, it catalyzes the oxidation of 5-vinylcytosine in dsDNA to 5-formylmethylcytosine, and the subsequent labeling of dsDNA with Cy5 generates a biotinylated Cy5-dsDNA complex. Biotinylated Cy5-dsDNA complexes are conjugated to the streptavidin-coated 605QDs to obtain a Cy5-dsDNA-605QD nanostructures, inducing FRET from 605QD to Cy5. FRET signal can be simply measured by single-molecule counting. This biosensor enables homogeneous detection of TET2 with a limit of detection (LOD) of 0.042 ng/μL, and it can accurately measure cellular TET2 down to 1 cell. Moreover, this biosensor can be used to screen TET2 inhibitors, offering a new platform for TET2-related medical research and clinical diagnostics.

A Simple Phase-Sensitive Surface Plasmon Resonance Sensor Based on Simultaneous Polarization Measurement Strategy

The SPR phenomenon results in an abrupt change in the optical phase such that one can measure the phase shift of the reflected light as a sensing parameter. Moreover, many studies have demonstrated that the phase changes more acutely than the intensity, leading to a higher sensitivity to the refractive index change. However, currently, the optical phase cannot be measured directly because of its high frequency; therefore, investigators usually have to use complicated techniques for the extraction of phase information. In this study, we propose a simple and effective strategy for measuring the SPR phase shift based on phase-shift interferometry. In this system, the polarization-dependent interference signals are recorded simultaneously by a pixelated polarization camera in a single snapshot. Subsequently, the phase information can be effortlessly acquired by a phase extraction algorithm. Experimentally, the proposed phase-sensitive SPR sensor was successfully applied for the detection of small molecules of glyphosate, which is the most frequently used herbicide worldwide. Additionally, the sensor exhibited a detection limit of 15 ng/mL (0.015 ppm). Regarding its simplicity and effectiveness, we believe that our phase-sensitive SPR system presents a prospective method for acquiring phase signals.

Nanomaterial-Based Fluorescence Resonance Energy Transfer (FRET) and Metal-Enhanced Fluorescence (MEF) to Detect Nucleic Acid in Cancer Diagnosis

Nucleic acids, including DNA and RNA, have received prodigious attention as potential biomarkers for precise and early diagnosis of cancers. However, due to their small quantity and instability in body fluids, precise and sensitive detection is highly important. Taking advantage of the ease-to-functionality and plasmonic effect of nanomaterials, fluorescence resonance energy transfer (FRET) and metal-enhanced fluorescence (MEF)-based biosensors have been developed for accurate and sensitive quantitation of cancer-related nucleic acids. This review summarizes the recent strategies and advances in recently developed nanomaterial-based FRET and MEF for biosensors for the detection of nucleic acids in cancer diagnosis. Challenges and opportunities in this field are also discussed. We anticipate that the FRET and MEF-based biosensors discussed in this review will provide valuable information for the sensitive detection of nucleic acids and early diagnosis of cancers.