Nanoparticle-Based Proximity Ligation Assay for Ultrasensitive, Quantitative Detection of Protein Biomarkers

Recent Updates on Diverse Nanoparticles and Nanostructures in Therapeutic and Diagnostic Applications with Special Focus on Smart Protein Nanoparticles: A Review

Nanomedicine enables advanced therapeutics, diagnostics, and predictive analysis, enhancing treatment outcomes and patient care. The choices and development of high-quality organic nanoparticles with relatively lower toxicity are important for achieving advanced medical goals. Among organic molecules, proteins have been prospected as smart candidates to revolutionize nanomedicine due to their inherent fascinating features. The advent of protein nanoarchitectures, which explore the biomolecular corona, offers new insights into their efficient tissue penetration and therapeutic potential. This review examines various animal- and plant-based protein nanoparticles, highlighting their source, activity, products, and unique biomedical applications in regenerative medicine, targeted therapies, gene and drug delivery, antimicrobial activity, bioimaging, immunological adjuvants, etc. It provides an extensive discussion on recent applications of protein nanoparticles across diverse biomedical fields as well as the evolving landscape of other nanoproducts and nanodevices for sensitive medical procedures. Furthermore, this review introduces different preparation technologies of protein nanoparticles, emphasizing how their design and construction significantly influence loading capacity, stability, and targeting effects. Additionally, we delve into the construction of different user-friendly multifunctional modular bioarchitectures by the assembly of protein nanoparticles (PNPs), marking a significant breakthrough in therapies. This review also considers the challenges of synthetic nanomaterials and the emergence of natural alternatives, which provides insights into protein nanoparticle research.

Recent advances in quantum dot-based fluorescence-linked immunosorbent assays

Fluorescence immunoassays have been given considerable attention among the quantitative detection methods in the clinical medicine and food safety testing fields. In particular, semiconductor quantum dots (QDs) have become ideal fluorescent probes for highly sensitive and multiplexed detection due to their unique photophysical properties, and the QD fluorescence-linked immunosorbent assay (FLISA) with high sensitivity, high accuracy, and high throughput has been greatly developed recently. In this manuscript, the advantages of applying QDs to FLISA platforms and some strategies for their application to in vitro diagnostics and food safety are discussed. Given the rapid development of this field, we classify these strategies based on the combination of QD types and detection targets, including traditional QDs or QD micro/nano-spheres-FLISA, and multiple FLISA platforms. In addition, some new sensors based on the QD-FLISA are introduced; this is one of the hot spots in this field. The current focus and future direction of QD-FLISA are also discussed, which provides important guidance for the further development of FLISA.

Nucleic Acid Amplification Techniques in Immunoassay: An Integrated Approach with Hybrid Performance

An immunoassay is mostly employed for the direct detection of food contaminants, and a molecular assay for targeting nucleic acids employs amplification techniques for distinguishing genes. The integration of an immunoassay with nucleic acid amplification techniques inherits the direct and rapid performance of an immunoassay and the ultrasensitive merit of a molecular assay. Enthusiastic attention has been attracted in recent years on the utilization of isothermal amplification techniques in an immunoassay, as well as the employment of a lateral flow immunoassay in a molecular assay. Thus, this Review discussed these kinds of approaches from two categories: immuno-nucleic acid amplification (I-NAA) and nucleic acid amplification-immunoassay (NAA-I). The advantages, drawbacks, and future developments were discussed for a comprehensive understanding.

Pre-coated interface proximity extension reaction assay enables trace protein detection with single-digit accuracy

Advances in trace protein detection contribute to the early diagnosis of diseases and exploration of stem cell development. The pre-coated interface proximity extension reaction (PIPER) assay enables target protein detection at trace levels and was developed based on protein biomarker recognition using sets of three specific antibodies and the extension of antibody-bound nucleic acid chains in proximity, accompanied by amplification and reading of protein signals via real-time quantitative polymerase chain reaction (qPCR). Noise generated in binding reactions and enzymatic steps was decreased by transferring the liquid-liquid reactions onto a liquid-solid interface in glutaraldehyde-treated tubes pre-coated with antibodies. Nucleic acid sequences of oligo-antibody-based probes were designed for extension and qPCR without pre-amplification when binding to a target molecule. As a proof of concept, the PIPER assay was used to profile slight variations in crucial biomarkers, high-sensitivity C-reactive protein, and cardiac troponin I. The detection sensitivity of the assay for the biomarkers was 0.05 pg/mL (1.25 fM) in 10% human serum. In phosphate-buffered saline, the PIPER assay detected fewer than 10 protein molecules per μL. The simple, widely applicable PIPER assay can detect trace protein biomarkers with single-digit accuracy, making it appropriate for the development of clinical hypersensitive protein detection and single-cell protein detection technology.

Peptide-Based Photocathodic Biosensors: Integrating a Recognition Peptide with an Antifouling Peptide

Accurate and sensitive detection of targets in practical biological matrixes such as blood, plasma, serum, or tissue fluid is a frontier issue for most biosensors since the coexistence of both potential reducing agents and protein molecules has the possibility of causing signal interference. Herein, aiming at detection in a complex environment, an advanced and robust peptide-based photocathodic biosensor, which integrated a recognition peptide with an antifouling peptide in one probe electrode, was first proposed. Selecting human chorionic gonadotropin (hCG) as a model target, the recognition peptide with the sequence PPLRINRHILTR was first anchored on the CuBi₂O₄/Au (CBO/Au) photocathode and then the antifouling peptide with the sequence EKEKEKEPPPPC was further anchored to generate an antifouling biointerface. The peptide-based photocathodic biosensor demonstrated excellent anti-interference to both nonspecific proteins and reducing agents because of the capability of the antifouling peptide. It also exhibited good sensitivity owing to the utilization of the recognition peptide rather than an antibody probe. This peptide-integrated method offers a new perspective for practical applications of photocathodic biosensors.

Proximity hybridization-triggered DNA assembly for label-free surface-enhanced Raman spectroscopic bioanalysis

We have developed a versatile label-free surface-enhanced Raman spectroscopic platform for detecting various biotargets via proximity hybridization-triggered DNA assembly based on the 736 cm^-1 Raman peak of adenine breathing mode. We initially immobilized the first probe to AuNPs and modified the second with poly adenine. Presence of target DNA or protein molecules assembled a sandwich complex that brought the poly adenine close to the AuNPs surface, generating Raman signals, that were proportional to target molecule concentration. These approach exhibits high sensitivity, with a detection limit of 5.4 pM, 47 fM, and 0.51 pg/mL for target DNA, thrombin and CEA, respectively. Owing to a one step proximity dependent complex formation, this technique is simple and can be completed within 40 min, making it a promising candidate for point-of-care testing applications.

Neutral DNA-avidin nanoparticles as ultrasensitive reporters in immuno-PCR

We have developed an immuno-PCR based diagnostic platform which couples detection antibodies to self-assembled, ultra-detectable DNA-avidin nanoparticles stabilized with poly(ethylene glycol) to link DNA amplification to target protein concentration. Electrostatic neutralization and cloaking of the PCR-amplifiable DNA labels by avidin and PEG coating reduces non-specific "stickiness" and enhances assay sensitivity. We further optimized the detectability of the nanoparticles by incorporating four repeats of a unique synthetic DNA PCR target into each nanoparticle. Using human chorionic gonadotropin hormone (hCG) as a model analyte, this platform was able to quantitate the target hCG protein in femtomolar concentrations using only standard laboratory equipment.

Peroxidase activities of gold nanowires synthesized by TMV as template and their application in detection of cancer cells

A sensing methodology that combines Au, tobacco mosaic virus (TMV), and folic acid for selective, sensitive, and colorimetric detection of tumor cells based on the peroxidase-like activity was reported in this study. Gold nanowires with a high aspect ratio were synthesized using TMV as a template. Au@TMV nanowire (AT) complex was obtained with diameter of 4 nm and length between 200 and 300 nm. In addition, since TMV was biocompatible and had many amino and carboxyl groups on its surface, AT was conjugated by folate to form a folic acid (FA)-conjugated AT composite (ATF) and tested by FTIR measurements. Furthermore, the peroxidase-like properties were studied and the optimal conditions for mimic enzyme activity were optimized. Finally, HeLa and other tumor cells expressed excessive receptors of folate on the surface, which can specifically bind to folic acid. As the specific binding of ATF with HeLa cells, the peroxidase properties of ATF were used for detection of cancer cells (Scheme 1). The cancer cells were detected not only qualitatively but also quantitatively. In this study, as low as 2000 cancer cells/mL could be detected using the current method.

Quantitation of Femtomolar-Level Protein Biomarkers Using a Simple Microbubbling Digital Assay and Bright-Field Smartphone Imaging

Quantitating ultra-low concentrations of protein biomarkers is critical for early disease diagnosis and treatment. However, most current point-of-care (POC) assays are limited in sensitivity. Herein, we introduce an ultra-sensitive and facile microbubbling assay for the quantification of protein biomarkers with a digital-readout method that requires only a smartphone camera. We used machine learning to develop a smartphone application for automated image analysis to facilitate accurate and robust counting. Using this method, post-prostatectomy surveillance of prostate specific antigen (PSA) can be achieved with a detection limit (LOD) of 2.1 fm (0.060 pg mL-1 ), and early pregnancy detection using βhCG can be achieved with a of 0.034 mIU mL-1 (2.84 pg mL-1 ). This work provides the proof-of-principle of the microbubbling assay with a digital readout as an ultra-sensitive technology with minimal requirement for power and accessories, facilitating future POC applications.

Point of care testing for infectious diseases

Infectious diseases are caused by pathogenic microorganisms and can be transmitted between individuals and populations thus threatening the general public health and potentially the economy. Efficient diagnostic tools are needed to provide accurate and timely guidance for case identification, transmission disruption and appropriate treatment administration. Point of care (POC) tests provide actionable results near the patient and thereby serve as a personal "radar". In this review, we review clinical needs for POC testing for several major pathogens, including malaria parasites, human immunodeficiency virus (HIV), human papillomavirus (HPV), dengue, Ebola and Zika viruses and Mycobacterium tuberculosis (TB). We compare different molecular approaches, including pathogen nucleic acid and protein, circulating microRNA and antibodies, used in the POC tests. Finally, we review recent advances in novel POC technologies focusing on microfluidic and plasmonic-based approaches.

Integrating a Microwave Resonator and a Microchannel with an Immunochromatographic Strip for Stable and Quantitative Biodetection

An immunochromatographic strip is an effective diagnostic tool in various fields because of its simplicity, rapidity, and cost-effectiveness. However, typical strips for preliminary screening provide only qualitative or semiquantitative results, and common solutions for quantitative detection by incorporating different kinds of nanoparticles as biomarkers still do not solve this problem thoroughly. Here, we try to tackle this challenge by integrating low-cost membrane-compatible square split-ring resonators and structure-design-flexible microchannels with flexible strips. We experimentally demonstrate that the limit of detection (LOD) and sensitivity of the strip for quantitative detection of Staphylococcus aureus reach 0.784 ng/mL and 10.214 MHz/(ng/mL), respectively. The LOD level is about 63 times higher than that of the color-based strip determined by the naked eye, and the stability is about 18 times higher than that of the fluorescent strip. This work could not only provide a powerful diagnosis tool for the quantitative detection of S. aureus or other molecules but also deliver new avenues for achieving electric field detection of biomolecules, system-level integration of biosensors, and the development of portable diagnostic devices.

Versatile and Ultrasensitive Electrochemiluminescence Biosensor for Biomarker Detection Based on Nonenzymatic Amplification and Aptamer-Triggered Emitter Release

Electrochemiluminescence (ECL), as a sensitive and controllable assay, offers a considerable opportunity for multiple types of biomarkers detection. However, constructing such a biosensor remains a significant challenge. Herein, an ultrasensitive and versatile ECL biosensor was constructed to detect multiple types of biomarkers from breast cancer by taking the strategies of nonenzymatic catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR) amplification, as well as aptamer-triggered emitter release. Concretely, with the appearance of target 1 microRNA-21 (miRNA-21), abundant double-stranded DNA (dsDNA) polymers were generated on this biosensing surface via amplification circuits of CHA and HCR, which could be intercalated into substantial ([Ru(bpy)₂dppz]Cl₂) as ECL indicators to obtain an obvious enhancement of ECL signal for target 1 detection with a detection limit (0.1 fM). Furthermore, in the presence of target 2 human mucin 1 (MUC1) protein, the ECL signal had a distinct decrease, because aptamer recognition induced the release of [Ru(bpy)₂dppz]Cl₂ from the sensing surface, thus, achieving a sensitive detection for MUC1 with a detection limit (2.4 fg·mL^-1). Simultaneously, this sensing platform was applied to monitor the biomarkers from MDA-MB-231 breast cancer cells, suggesting that this method was applicable to detect real samples. Therefore, this platform is an applicable and versatile implement for the determination of multiple types of biomarkers to improve diagnostic accuracy and efficiency.