Sandwich DNA Hybridization Fluorescence Resonance Energy-Transfer Strategy for miR-122 Detection by Core-Shell Upconversion Nanoparticles

Programmable Entropy-Driven Circuit-Cascaded Self-Feedback DNAzyme Network for Ultra-Sensitive Fluorescence and Photoelectrochemical Dual-Mode Biosensing

Inspired by natural DNA networks, programmable artificial DNA networks have become an attractive tool for developing high-performance biosensors. However, there is still a lot of room for expansion in terms of sensitivity, atom economy, and result self-validation for current microRNA sensors. In this protocol, miRNA-122 as a target model, an ultrasensitive fluorescence (FL) and photoelectrochemical (PEC) dual-mode biosensing platform is developed using a programmable entropy-driven circuit (EDC) cascaded self-feedback DNAzyme network. The well-designed EDC realizes full utilization of the DNA strands and improves the atomic economy of the signal amplification system. The unique and rational design of the double-CdSe quantum-dot-released EDC substrate and the cascaded self-feedback DNAzyme amplification network significantly avoids high background signals and enhances sensitivity and specificity. Also, the enzyme-free, programmable EDC cascaded DNAzyme network effectively avoids the risk of signal leakage and enhances the accuracy of the sensor. Moreover, the introduction of superparamagnetic Fe3O4@SiO2-cDNA accelerates the rapid extraction of E2-CdSe QDs and E3-CdSe QDs, which greatly improves the timeliness of sensor signal reading. In addition to the strengths of linear range (6 orders of magnitude) and stability, the biosensor design with dual signal reading makes the test results self-confirming.

Aptameric Fluorescent Biosensors for Liver Cancer Diagnosis

Liver cancer is a prevalent global health concern with a poor 5-year survival rate upon diagnosis. Current diagnostic techniques using the combination of ultrasound, CT scans, MRI, and biopsy have the limitation of detecting detectable liver cancer when the tumor has already progressed to a certain size, often leading to late-stage diagnoses and grim clinical treatment outcomes. To this end, there has been tremendous interest in developing highly sensitive and selective biosensors to analyze related cancer biomarkers in the early stage diagnosis and prescribe appropriate treatment options. Among the various approaches, aptamers are an ideal recognition element as they can specifically bind to target molecules with high affinity. Furthermore, using aptamers, in conjunction with fluorescent moieties, enables the development of highly sensitive biosensors by taking full advantage of structural and functional flexibility. This review will provide a summary and detailed discussion on recent aptamer-based fluorescence biosensors for liver cancer diagnosis. Specifically, the review focuses on two promising detection strategies: (i) Förster resonance energy transfer (FRET) and (ii) metal-enhanced fluorescence for detecting and characterizing protein and miRNA cancer biomarkers.

Understanding FRET in Upconversion Nanoparticle Nucleic Acid Biosensors

Upconversion nanoparticles (UCNPs) have been frequently applied in Förster resonance energy transfer (FRET) bioanalysis. However, the understanding of how surface coatings, bioconjugation, and dye-surface distance influence FRET biosensing performance has not significantly advanced. Here, we investigated UCNP-to-dye FRET DNA-hybridization assays in H₂O and D₂O using ∼24 nm large NaYF₄:Yb³⁺,Er³⁺ UCNPs coated with thin layers of silica (SiO₂) or poly(acrylic acid) (PAA). FRET resulted in strong distance-dependent PL intensity changes. However, the PL decay times were not significantly altered because of continuous Yb³⁺-to-Er³⁺ energy migration during Er³⁺-to-dye FRET. Direct bioconjugation of DNA to the thin PAA coating combined with the closest possible dye-surface distance resulted in optimal FRET performance with minor influence from competitive quenching by H₂O. The better comprehension of UCNP-to-dye FRET was successfully translated into a microRNA (miR-20a) FRET assay with a limit of detection of 100 fmol in a 80 μL sample volume.

Recent advances in tumor biomarker detection by lanthanide upconversion nanoparticles

Early tumor diagnosis could reliably predict the behavior of tumors and significantly reduce their mortality. Due to the response to early cancerous changes at the molecular or cellular level, tumor biomarkers, including small molecules, proteins, nucleic acids, exosomes, and circulating tumor cells, have been employed as powerful tools for early cancer diagnosis. Therefore, exploring new approaches to detect tumor biomarkers has attracted a great deal of research interest. Lanthanide upconversion nanoparticles (UCNPs) provide numerous opportunities for bioanalytical applications. When excited by low-energy near-infrared light, UCNPs exhibit several unique properties, such as large anti-Stoke shifts, sharp emission lines, long luminescence lifetimes, resistance to photobleaching, and the absence of autofluorescence. Based on these excellent properties, UCNPs have demonstrated great sensitivity and selectivity in detecting tumor biomarkers. In this review, an overview of recent advances in tumor biomarker detection using UCNPs has been presented. The key aspects of this review include detection mechanisms, applications in vitro and in vivo, challenges, and perspectives of UCNP-based tumor biomarker detection.

Activators Confined Upconversion Nanoprobe with Near-Unity Förster Resonance Energy Transfer Efficiency for Ultrasensitive Detection

Lanthanide-doped upconversion nanoparticles (UCNPs) as energy donors for Förster resonance energy transfer (FRET) are promising in biosensing, bioimaging, and therapeutic applications. However, traditional FRET-based UC nanoprobes show low efficiency and poor sensitivity because only partial activators in UCNPs possessing suitable distance with energy acceptors (<10 nm) can activate the FRET process. Herein, a novel excited-state energy distribution-modulated upconversion nanostructure is explored for highly efficient FRET. Integration of the optimal 4% Er³⁺ doped shell and 100% Yb³⁺ core achieves ∼4.5-fold UC enhancement compared with commonly used NaYF₄:20%Yb³⁺,2%Er³⁺ nanoparticles, enabling maximum donation of excitation energy to an acceptor. The spatial confinement strategy shortens significantly the energy-transfer distance (∼4.5 nm) and thus demonstrates experimentally a 91.9% FRET efficiency inside the neutral red (NR)-conjugated NaYbF₄@NaYF₄:20%Yb³⁺,4%Er³⁺ nanoprobe, which greatly outperforms the NaYbF₄@NaYF₄:20%Yb³⁺,4%Er³⁺@SiO₂@NR nanoprobe (27.7% efficiency). Theoretical FRET efficiency calculation and in situ single-nanoparticle FRET measurement further confirm the excellent energy-transfer behavior. The well-designed nanoprobe shows a much lower detection limit of 0.6 ng/mL and higher sensitivity and is superior to the reported NO₂^- probes. Our work provides a feasible strategy to exploit highly efficient FRET-based luminescence nanoprobes for ultrasensitive detection of analytes.

Engineering the Compositional Architecture of Core-Shell Upconverting Lanthanide-Doped Nanoparticles for Optimal Luminescent Donor in Resonance Energy Transfer: The Effects of Energy Migration and Storage

Förster Resonance Energy Transfer (FRET) between single molecule donor (D) and acceptor (A) is well understood from a fundamental perspective and is widely applied in biology, biotechnology, medical diagnostics, and bio-imaging. Lanthanide doped upconverting nanoparticles (UCNPs) have demonstrated their suitability as alternative donor species. Nevertheless, while they solve most disadvantageous features of organic donor molecules, such as photo-bleaching, spectral cross-excitation, and emission bleed-through, the fundamental understanding and practical realizations of bioassays with UCNP donors remain challenging. Among others, the interaction between many donor ions (in donor UCNP) and many acceptors anchored on the NP surface and the upconversion itself within UCNPs, complicate the decay-based analysis of D-A interaction. In this work, the assessment of designed virtual core-shell NP (VNP) models leads to the new designs of UCNPs, such as …@Er, Yb@Er, Yb@YbEr, which are experimentally evaluated as donor NPs and compared to the simulations. Moreover, the luminescence rise and decay kinetics in UCNP donors upon RET is discussed in newly proposed disparity measurements. The presented studies help to understand the role of energy-transfer and energy migration between lanthanide ion dopants and how the architecture of core-shell UCNPs affects their performance as FRET donors to organic acceptor dyes.

Lanthanide-Doped Upconversion Luminescent Nanoparticles-Evolving Role in Bioimaging, Biosensing, and Drug Delivery

Upconverting luminescent nanoparticles (UCNPs) are "new generation fluorophores" with an evolving landscape of applications in diverse industries, especially life sciences and healthcare. The anti-Stokes emission accompanied by long luminescence lifetimes, multiple absorptions, emission bands, and good photostability, enables background-free and multiplexed detection in deep tissues for enhanced imaging contrast. Their properties such as high color purity, high resistance to photobleaching, less photodamage to biological samples, attractive physical and chemical stability, and low toxicity are affected by the chemical composition; nanoparticle crystal structure, size, shape and the route; reagents; and procedure used in their synthesis. A wide range of hosts and lanthanide ion (Ln³⁺) types have been used to control the luminescent properties of nanosystems. By modification of these properties, the performance of UCNPs can be designed for anticipated end-use applications such as photodynamic therapy (PDT), high-resolution displays, bioimaging, biosensors, and drug delivery. The application landscape of inorganic nanomaterials in biological environments can be expanded by bridging the gap between nanoparticles and biomolecules via surface modifications and appropriate functionalization. This review highlights the synthesis, surface modification, and biomedical applications of UCNPs, such as bioimaging and drug delivery, and presents the scope and future perspective on Ln-doped UCNPs in biomedical applications.

Highly Sensitive Detection of Elevated Exosomal miR-122 Levels in Radiation Injury and Hepatic Inflammation Using an Aptamer-Functionalized SERS-Sandwich Assay

Radiation-induced organ injury is one of the major fallouts noticed during radiotherapy treatment of malignancies and other detrimental radiation exposures. MicroRNA (miRNA), which is involved in multiple critical cellular processes, is released from the cells of damaged organs in cellular vesicles, commonly known as exosomes. Specifically, exosomal miR-122 is reported to be actively involved in radiation-actuated rectal and hepatic injuries or inflammation. In this work, we developed a surface-enhanced Raman spectroscopy (SERS) assay for the quantitative and targeted detection of exosomal miR-122 in mice after drug/radiation treatments. In particular, an aptamer-functionalized magnetic capturing element and Au shell nanoparticle (NP)-based SERS tags were utilized, which upon recognition of the target miRNA constituted a "sandwich" formation, with which an 8 fM limit of detection (LOD) could be achieved. Using this SERS assay, we further found that radiation injury led to the elevated expression of exosomal miR-122 in mice at 4 h postirradiation, confirmed by the quantitative real-time PCR method. It was demonstrated that the drug-induced hepatic inflammation could also be assessed via detecting miR-122 using this SERS method. As such, this work has demonstrated the achievement of a highly selective and sensitive probe of exosomal miRNA, which may thus open a gateway for promising usage in drug/radiation-induced inflammation.

Dual-Modal FexCuySe and Upconversion Nanoparticle Assemblies for Intracellular MicroRNA-21 Detection

In situ quantification and imaging of low-level intracellular microRNAs (miRs) are important areas in biosensor research. Herein, DNA-driven Fe_xCu_ySe@upconversion nanoparticle (UCNP) core@satellite nanostructures were developed to probe microRNA-21 (miR-21). Fe_xCu_ySe@UCNP probes displayed dual signals: upconversion luminescence (UCL) and magnetic resonance imaging (MRI). In the presence of miR-21, the luminescence signal was restored and the T₂ value was significantly increased because of dissociation of UCNPs from the assemblies. There was a good linear relationship between the dual signals and the expression levels of miR-21 in the range of 0.035-31.824 amol/ng_RNA. The limit of detection (LOD) was 0.0058 amol/ng_RNA for the luminescence intensity and 0.0182 amol/ng_RNA for the MRI signal. This method opens a new avenue for intracellular miR-21 detection with high sensitivity and specificity.

Aptamer-modified sensitive nanobiosensors for the specific detection of antibiotics

The overuse or abuse of quinolone antibiotics such as enrofloxacin (ENR) in veterinary medicine results in the presence of their residues in food and environment. Thus, a sensitive method is needed to detect them. Herein, we demonstrate a fluorescence resonance energy transfer (FRET) based aptasensor for ENR detection, using core-shell upconversion nanoparticles (CSUNPs) as an energy donor and graphene oxide (GO) as an energy acceptor. The core-shell structure and Gd3+ doping significantly increased the fluorescence intensity of CSUNPs and the FRET efficiency. The ENR aptamer was conjugated to CSUNPs through ligand exchange, and the π-π stacking between the aptamer and GO brought the aptamer-modified CSUNPs to the surface of the GO sheets, resulting in the formation of a CSUNP-GO complex and the subsequent quenching of CSUNP fluorescence. As a result, an aptasensor was established with the fluorescence of CSUNPs correlated with the ENR concentration within the range of 0.976 ng mL-1 to 62.5 ng mL-1, allowing ENR to be detected at a limit of 0.47 ng mL-1. This method reduced the detection limit by approximately 13-fold in 2 h compared to the commercial enzyme-linked immunosorbent assay (ELISA) kit. The aptasensor could also be applied to detect ENR from commercial milk powder samples with a detection limit of 1.59 ng mL-1, which was far below the regulated maximum residue limit of ENR in milk. The aptasensor could not detect other antibiotics, suggesting its good specificity towards ENR. Our work demonstrates a highly selective, sensitive and cost-effective method for detecting antibiotic residues in veterinary medicine. Since the aptamer can be switched to one recognizing another antibiotic, the aptasensors are used as a plug-and-play platform that can detect a variety of antibiotics.

Recent advances in visual detection for cancer biomarkers and infectious pathogens

It is an urgency to detect infectious pathogens or cancer biomarkers using rapid, simple, convenient and cost-effective methods in complex biological samples. Many existing approaches (traditional virus culture, ELISA or PCR) for the pathogen and biomarker assays face several challenges in the clinical applications that require lengthy time, sophisticated sample pre-treatment and expensive instruments. Due to the simple and rapid detection manner as well as no requirement of expensive equipment, many visual detection methods have been considered to resolve the aforementioned problems. Meanwhile, various new materials and colorimetric/fluorescent methods have been tried to construct new biosensors for infectious pathogens and biomarkers. However, the recent progress of these aspects is rarely reviewed, especially in terms of integration of new materials, microdevice and detection mechanism into the visual detection systems. Herein, we provide a broad field of view to discuss the recent progress in the visual detection of infectious pathogens and cancer biomarkers along with the detection mechanism, new materials, novel detection methods, special targets as well as multi-functional microdevices and systems. The novel visual approaches for the infectious pathogens and biomarkers, such as bioluminescence resonance energy transfer (BRET), metal-induced metallization and clustered regularly interspaced short palindromic repeats (CRISPR)-based biosensors, are discussed. Additionally, recent advancements in visual assays utilizing various new materials for proteins, nucleic acids, viruses, exosomes and small molecules are comprehensively reviewed. Future perspectives on the visual sensing systems for infectious pathogens and cancers are also proposed.

Nucleic Acids Analysis

Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysis, food safety and forensic analysis. During the past decades, the field of nucleic acids analysis has been rapidly advancing with many technological breakthroughs. In this review, we focus on the methods developed for analyzing nucleic acids, nucleic acids-based analysis, device for nucleic acids analysis, and applications of nucleic acids analysis. The representative strategies for the development of new nucleic acids analysis in this field are summarized, and key advantages and possible limitations are discussed. Finally, a brief perspective on existing challenges and further research development is provided.

Sensors/nanosensors based on upconversion materials for the determination of pharmaceuticals and biomolecules: An overview

Upconversion materials have been the focus of a large body of research in analytical and clinical fields in the last two decades owing to their ability to convert light between various spectral regions and their particular photophysical features. They emit efficient and sharp ultraviolet (UV) or visible luminescence after excitation with near-infrared (NIR) light. These features overcome some of the disadvantages reported for conventional fluorescent materials and provide opportunities for high sensitivity chemo-and bio-sensing. Here, we review studies that used upconversion materials as sensors for the determination of pharmaceuticals and biomolecules in the last two decades. The articles included in this review were retrieved from the SCOPUS database using the search phrases: "upconversion nanoparticles for determination of pharmaceutical compounds", and "upconversion nanoparticles for determination of biomolecules". Details of each developed upconversion nanoparticles based sensor along with their relevant analytical parameters are reported and carefully explained.

Covalent Attachment of Active Enzymes to Upconversion Phosphors Allows Ratiometric Detection of Substrates

Upconverting phosphors (UCPs) convert multiple low energy photons into higher energy emission via the process of photon upconversion and offer an attractive alternative to organic fluorophores for use as luminescent probes. Here, UCPs were capped with functionalized silica in order to provide a surface to covalently conjugate proteins with surface-accessible cysteines. Variants of green fluorescent protein (GFP) and the flavoenzyme pentaerythritol tetranitrate reductase (PETNR) were then attached via maleimide-thiol coupling in order to allow energy transfer from the UCP to the GFP or flavin cofactor of PETNR, respectively. PETNR retains its activity when coupled to the UCPs, which allows reversible detection of enzyme substrates via ratiometric sensing of the enzyme redox state.

A photo zipper locked DNA nanomachine with an internal standard for precise miRNA imaging in living cells

DNA nanomachines are capable of converting tiny triggers into autonomous accelerated cascade hybridization reactions and they have been used as a signal amplification strategy for intracellular imaging. However, the "always active" property of most DNA nanomachines with an "absolute intensity-dependent" signal acquisition mode results in "false positive signal amplification" by extracellular analytes and impairs detection accuracy. Here we design a photo zipper locked miRNA responsive DNA nanomachine (PZ-DNA nanomachine) based on upconversion nanoparticles (UCNPs) with a photo-cleavable DNA strand to block the miRNA recognition region, which provided sufficient protection to the DNA nanomachine against nonspecific extracellular activation and allowed satisfactory signal amplification for sensitive miRNA imaging after intracellular photoactivation. Multiple emissions from the UCNPs were also utilized as an internal standard to self-calibrate the intracellular miRNA responsive fluorescence signal. The presented PZ-DNA nanomachine demonstrated the sensitive imaging of intracellular miRNA from different cell lines, which resulted in good accordance with qRT-PCR measurements, providing a universal platform for precise imaging in living cells with high spatial-temporal specificity.

Self-Validated Homogeneous Immunoassay by Single Nanoparticle in-Depth Scrutinization

The most convenient method for the clinical routine analysis of disease biomarkers is homogeneous immunoassay, which minimizes the requirements for automation and time-/lab-consumption. Despite great success, because sample constituents are not removed by a separation or washing step, a major challenge in conducting homogeneous immunoassays for the practical application is the matrix effect-related inaccuracy. Herein, to guarantee an accurate quantification, a self-validated homogeneous immunoassay was proposed, by simultaneously scrutinizing both frequency and intensity of single gold nanoparticles. The two analytical modes of single particle inductively coupled plasma mass spectrometry (ICPMS) correlated well with each other, resulting in a self-validation mechanism for the accurate immunoassay. Both two modes of the proposed method provided linear ranges of 2 orders of magnitude and LODs of pM level. Thanks to the self-validated strategy and the high tolerance of the matrix effect of ICPMS, the proposed homogeneous immunoassay was successfully demonstrated in a series of human serum samples, with results in good accordance with clinical routine methods.

Synergistic Photodynamic and Photothermal Antibacterial Nanocomposite Membrane Triggered by Single NIR Light Source

Herein, we developed a nanocomposite membrane with synergistic photodynamic therapy and photothermal therapy antibacterial effects, triggered by a single near-infrared (NIR) light illumination. First, upconversion nanoparticles (UCNPs) with a hierarchical structure (UCNPs@TiO₂) were synthesized, which use NaYF₄:Yb,Tm nanorods as the core and TiO₂ nanoparticles as the outer shell. Then, nanosized graphene oxide (GO), as a photothermal agent, was doped into UCNPs@TiO₂ core-shell nanoparticles to obtain UCNPs@TiO₂@GO. Afterward, the mixture of UCNPs@TiO₂@GO in poly(vinylidene) fluoride (PVDF) was applied for electrospinning to generate the nanocomposite membrane (UTG-PVDF). Generation of reactive oxygen species (ROS) and changes of temperature triggered by NIR action were both investigated to evaluate the photodynamic and photothermal properties. Upon a single NIR light (980 nm) irradiation for 5 min, the nanocomposite membrane could simultaneously generate ROS and moderate temperature rise, triggering synergistic antibacterial effects against both Gram-positive and -negative bacteria, which are hard to be achieved by an individual photodynamic or photothermal nanocomposite membrane. Additionally, the as-prepared membrane can effectively restrain the inflammatory reaction and accelerate wound healing, thus exhibiting great potentials in treating infectious complications in wound healing progress.

In Vivo Biosensing Using Resonance Energy Transfer

Solution-phase and intracellular biosensing has substantially enhanced our understanding of molecular processes foundational to biology and pathology. Optical methods are favored because of the low cost of probes and instrumentation. While chromatographic methods are helpful, fluorescent biosensing further increases sensitivity and can be more effective in complex media. Resonance energy transfer (RET)-based sensors have been developed to use fluorescence, bioluminescence, or chemiluminescence (FRET, BRET, or CRET, respectively) as an energy donor, yielding changes in emission spectra, lifetime, or intensity in response to a molecular or environmental change. These methods hold great promise for expanding our understanding of molecular processes not just in solution and in vitro studies, but also in vivo, generating information about complex activities in a natural, organismal setting. In this review, we focus on dyes, fluorescent proteins, and nanoparticles used as energy transfer-based optical transducers in vivo in mice; there are examples of optical sensing using FRET, BRET, and in this mammalian model system. After a description of the energy transfer mechanisms and their contribution to in vivo imaging, we give a short perspective of RET-based in vivo sensors and the importance of imaging in the infrared for reduced tissue autofluorescence and improved sensitivity.

Advances in DNA/RNA detection using nanotechnology

Specific nucleic acid detection in vitro or in vivo has become increasingly important in the discovery of genetic diseases, diagnosing pathogen infection and monitoring disease treatment. One challenge, however, is that the amount of target nucleic acid in specimens is limited. Furthermore, direct sensing methods are also unable to provide sufficient sensitivity and specificity. Fortunately, due to advances in nanotechnology and nanomaterials, nanotechnology-based bioassays have emerged as powerful and promising approaches providing ultra-high sensitivity and specificity in nucleic acid detection. This chapter presents an overview of strategies used in the development and integration of nanotechnology for nucleic acid detection, including optical and electrical detection methods, and nucleic acid assistant recycling amplification strategies. Recent 5 years representative examples are reviewed to demonstrate the proof-of-concept with promising applications for DNA/RNA detection and the underlying mechanism for detection of DNA/RNA with the higher sensitivity and selectivity. Furthermore, a brief discussion of common unresolved issues and future trends in this field is provided both from fundamental and practical point of view.

Enhancing intracellular microRNA imaging: a new strategy combining double-channel exciting single colour fluorescence with the target cycling amplification reaction

Enhancing microRNA imaging in living cells using double-channel exciting single colour fluorescence coupled with the target cycling amplification reaction.