Oligonucleotide Sensor Based on Selective Capture of Upconversion Nanoparticles Triggered by Target-Induced DNA Interstrand Ligand Reaction

Construction of a Spatial-Confined Self-Stacking Catalytic Circuit for Rapid and Sensitive Imaging of Piwi-Interacting RNA in Living Cells

Piwi-interacting RNAs (piRNAs) are small noncoding RNAs that repress transposable elements to maintain genome integrity. The canonical catalytic hairpin assembly (CHA) circuit relies on random collisions of free-diffused reactant probes, which substantially slow down reaction efficiency and kinetics. Herein, we demonstrate the construction of a spatial-confined self-stacking catalytic circuit for rapid and sensitive imaging of piRNA in living cells based on intramolecular and intermolecular hybridization-accelerated CHA. We rationally design a 3WJ probe that not only accelerates the reaction kinetics by increasing the local concentration of reactant probes but also eliminates background signal leakage caused by cross-entanglement of preassembled probes. This strategy achieves high sensitivity and good specificity with shortened assay time. It can quantify intracellular piRNA expression at a single-cell level, discriminate piRNA expression in tissues of breast cancer patients and healthy persons, and in situ image piRNA in living cells, offering a new approach for early diagnosis and postoperative monitoring.

Impact of excitation pulse width on the upconversion luminescence lifetime of NaYF4:Yb3+,Er3+ nanoparticles

The upconversion luminescence (UCL) lifetime has a wide range of applications, serving as a critical parameter for optimizing the performance of upconversion nanoparticles (UCNPs) in various fields. It is crucial to understand that this lifetime does not directly correlate with the decay time of the emission level; rather, it represents a compilation of all the physical phenomena taking place in the upconversion process. To delve deeper into this, we analyzed the dependence of the UCL lifetime on the excitation pulse width for β-NaYF4:Yb3+,Er3+ nanoparticles. The results revealed a significant increase in the UCL lifetime with both the excitation pulse width and the excitation intensity. The laser fluence was identified as the parameter governing the UCL decay dynamics. We showcased the universality of the pulse-width-dependent UCL lifetime phenomenon by employing UCNPs of various sizes, surface coatings, host matrices, Yb3+ and Er3+ ratios, and dispersing UCNPs in different solvents. Theoretical explanations for the experimental findings were derived through a rate equation analysis. Finally, we discussed the implications of these results in UCNP-FRET (Förster resonance energy transfer)-based applications.

Multiparametric modulation of magnetic transduction for biomolecular sensing in liquids

The recent COVID19 pandemic has remarkably boosted the research on in vitro diagnosis assays to detect biomarkers in biological fluids. Specificity and sensitivity are mandatory for diagnostic kits aiming to reach clinical stages. Whilst the modulation of sensitivity can significantly improve the detection of biomarkers in liquids, this has been scarcely explored. Here, we report on the proof of concept and parametrization of a novel biosensing methodology based on the changes of AC magnetic hysteresis areas observed for magnetic nanoparticles following biomolecular recognition in liquids. Several parameters are shown to significantly modulate the transducing capacity of magnetic nanoparticles to detect analytes dispersed in saline buffer at concentrations of clinical relevance. Magnetic nanoparticles were bio-conjugated with an engineered recognition peptide as a receptor. Analytes are engineered tetratricopeptide binding domains fused to the fluorescent protein whose dimerization state allows mono- or divalent variants. Our results unveil that the number of receptors per particle, analyte valency and concentration, nanoparticle composition and concentration, and field conditions play a key role in the formation of assemblies driven by biomolecular recognition. Consequently, all these parameters modulate the nanoparticle transduction capacity. Our study provides essential insights into the potential of AC magnetometry for customizing biomarker detection in liquids.

Predicting the size and morphology of nanoparticle clusters driven by biomolecular recognition

Nanoparticle aggregation is a driving principle of innovative materials and biosensing methodologies, improving transduction capabilities displayed by optical, electrical or magnetic measurements. This aggregation can be driven by the biomolecular recognition between target biomolecules (analytes) and receptors bound onto nanoparticle surface. Despite theoretical advances on modelling the entropic interaction in similar systems, predictions of the fractal morphologies of the nanoclusters of bioconjugated nanoparticles are lacking. The morphology of resulting nanoclusters is sensitive to the location, size, flexibility, average number of receptors per particle f̄, and the analyte-particle concentration ratio. Here we considered bioconjugated iron oxide nanoparticles (IONPs) where bonds are mediated by a divalent protein that binds two receptors attached onto different IONPs. We developed a protocol combining analytical expressions for receptors and linker distributions, and Brownian dynamics simulations for bond formation, and validated it against experiments. As more bonds become available (e.g., by adding analytes), the aggregation deviates from the ideal Bethe's lattice scenario due to multivalence, loop formation, and steric hindrance. Generalizing Bethe's lattice theory with a (not-integer) effective functionality feff leads to analytical expressions for the cluster size distributions in excellent agreement with simulations. At high analyte concentration steric impediment imposes an accessible limit value facc to feff, which is bounded by facc < feff < f̄. A transition to gel phase, is correctly captured by the derived theory. Our findings offer new insights into quantifying analyte amounts by assessing nanocluster size, and predicting nanoassembly morphologies accurately is a first step towards understanding variations of physical properties in clusters formed after biomolecular recognition.

Phone Camera Nano-Biosensor Using Mighty Sensitive Transparent Reusable Upconversion Paper

Lycopene, a natural colorant and antioxidant with a huge growing market, is highly susceptible to photo/thermal degradation, which demands real-time sensors. Hence, here a transparent upconversion nanoparticles (UCNPs) strip having 30 mol % Yb, 0.1 mol % Tm, and β-NaYF4 UCNPs, which shows an intense emission at 475 nm, has been developed. This strip has been found to be sensitive to lycopene with a detection limit as low as 10 nM using a smartphone camera, which is due to static quenching that is confirmed by the lifetime study. In comparison to previous paper strips, here the transparent strip has minimal scattering with maximum sensitivity in spite of not using any metal quenchers. An increase in strip hydrophobicity during the fabrication process complements the strip to selectively permeate and present an extraction-free substitute analysis for chromatography. Hydrophobicity endows the strip with the capability to reuse the strip with ∼100% luminescence recovery.

Upconversion Nanoparticle@Au Core-Satellite Assemblies for In Situ Amplified Imaging of MicroRNA in Living Cells and Combined Cancer Phototherapy

Stimuli-responsive therapy of cancer with spatial and temporal control is crucial in improving the treatment efficacy and minimizing the side effects. MicroRNA (miRNA) as an important biomarker has become one of the most promising endogenous stimuli for cancer therapy. However, the therapy efficacy is often impeded by the low expression amount of miRNA. Herein, the upconversion nanoparticle@Au (UCNP@Au) core-satellite nanostructures are rationally fabricated for isothermal amplification detection and in situ imaging of microRNA-21 (miR-21) in living cells based on the toehold-mediated strand displacement (TMSD) reaction, which is further applied to miRNA-responsive combined photothermal and photodynamic therapy of breast cancer. The UCNP@Au are constructed by linking AuNPs to photosensitizers Rose Bengal (RB)-loaded UCNPs through DNA hybridization. The upconversion luminescence (UCL) is quenched by AuNPs, resulting in the attenuation of singlet oxygen generation of RB. Once UCNP@Au are internalized into MCF-7 cells, the overexpressed intracellular miR-21 trigger the cyclic disassembly of UCNP@Au through cascade TMSD reactions, which facilitate the restoration of UCL for in situ imaging of miR-21 with signal amplification. Moreover, the released AuNPs are aggregated for photothermal therapy (PTT), while the singlet oxygen generated by RB is enhanced for photodynamic therapy (PDT). Compared with single-mode therapy, the miRNA-activated combinational phototherapy has demonstrated a greatly improved therapeutic efficacy for breast cancer. Therefore, our proposed core-satellite nanostructures cannot only achieve in situ amplified imaging of endogenous miRNA but also provide an effective nanoplatform for stimuli-responsive combinational phototherapy, which hold great prospects in early diagnosis and treatment of cancers.

CASCADE: Naked eye-detection of SARS-CoV-2 using Cas13a and gold nanoparticles

The COVID-19 pandemic has brought to light the need for fast and sensitive detection methods to prevent the spread of pathogens. The scientific community is making a great effort to design new molecular detection methods suitable for fast point-of-care applications. In this regard, a variety of approaches have been developed or optimized, including isothermal amplification of viral nucleic acids, CRISPR-mediated target recognition, and read-out systems based on nanomaterials.

Herein, we present CASCADE (CRISPR/CAS-based Colorimetric nucleic Acid DEtection), a sensing system for fast and specific naked-eye detection of SARS-CoV-2 RNA. In this approach, viral RNA is recognized by the LwaCas13a CRISPR protein, which activates its collateral RNase activity. Upon target recognition, Cas13a cleaves ssRNA oligonucleotides conjugated to gold nanoparticles (AuNPs), thus inducing their colloidal aggregation, which can be easily visualized. After an exhaustive optimization of functionalized AuNPs, CASCADE can detect picomolar concentrations of SARS-CoV-2 RNA. This sensitivity is further increased to low femtomolar (3 fM) and even attomolar (40 aM) ranges when CASCADE is coupled to RPA or NASBA isothermal nucleic acid amplification, respectively. We finally demonstrate that CASCADE succeeds in detecting SARS-CoV-2 in clinical samples from nasopharyngeal swabs.

In conclusion, CASCADE is a fast and versatile RNA biosensor that can be coupled to different isothermal nucleic acid amplification methods for naked-eye diagnosis of infectious diseases.

Effect of Excess Ligand on the Reverse Microemulsion Silica Coating of NaLnF4 Nanoparticles

Silica coating of inorganic nanoparticles (NPs) is widely employed as a means of providing colloidal stability in aqueous media and surface functionality for a variety of applications, particularly in biology. When the NPs are synthesized with a surface coating of an organic surfactant like oleic acid, silica coating is performed by using the reverse microemulsion method. There are many reports in the literature of the successful application of this method to NaYF₄ upconversion NPs (doped with Yb and Er), and we have used this method to coat NaHoF₄ NPs designed as a mass cytometry reagent. This method failed when we attempted to apply it to other NaLnF₄ NPs (Ln = Sm, Eu, Tb). In this report we describe an investigation of the problem and show how it can be overcome. To control size in the synthesis of NaLnF₄ NPs and at the same time maintain size uniformity, it is necessary to adjust the Na/F and F/Ln ratios. Problems with silica coating are associated with substoichiometric F/Ln ratios (F/Ln < 4) that leave Ln oleate salts as a byproduct, often as a phase-separated oily layer that could not be purified from the NPs by precipitation with ethanol and redispersion in hexanes. The nature of the oily byproduct was inferred from a combination of TGA, NMR, and FTIR measurements. We explored five different additional purification procedures, and by adopting the appropriate purification method, NaLnF₄ NPs with a variety of compositions and synthesized using different reaction conditions could be coated with a thin shell of silica.

Advances in fluorescence sensing enabled by lanthanide-doped upconversion nanophosphors

Lanthanide-doped upconversion nanoparticles (UCNPs), characterized by converting low-energy excitation to high-energy emission, have attracted considerable interest due to their inherent advantages of large anti-Stokes shifts, sharp and narrow multicolor emissions, negligible autofluorescence background interference, and excellent chemical- and photo-stability. These features make them promising luminophores for sensing applications. In this review, we give a comprehensive overview of lanthanide-doped upconversion nanophosphors including the fundamental principle for the construction of UCNPs with efficient upconversion luminescence (UCL), followed by state-of-the-art strategies for the synthesis and surface modification of UCNPs, and finally describing current advances in the sensing application of upconversion-based probes for the quantitative analysis of various analytes including pH, ions, molecules, bacteria, reactive species, temperature, and pressure. In addition, emerging sensing applications like photodetection, velocimetry, electromagnetic field, and voltage sensing are highlighted.

Click and Bioorthogonal Chemistry: The Future of Active Targeting of Nanoparticles for Nanomedicines?

Over the years, click and bioorthogonal reactions have been the subject of considerable research efforts. These high-performance chemical reactions have been developed to meet requirements not often provided by the chemical reactions commonly used today in the biological environment, such as selectivity, rapid reaction rate, and biocompatibility. Click and bioorthogonal reactions have been attracting increasing attention in the biomedical field for the engineering of nanomedicines. In this review, we study a compilation of articles from 2014 to the present, using the terms "click chemistry and nanoparticles (NPs)" to highlight the application of this type of chemistry for applications involving NPs intended for biomedical applications. This study identifies the main strategies offered by click and bioorthogonal chemistry, with respect to passive and active targeting, for NP functionalization with specific and multiple properties for imaging and cancer therapy. In the final part, a novel and promising approach for "two step" targeting of NPs, called pretargeting (PT), is also discussed; the principle of this strategy as well as all the studies listed from 2014 to the present are presented in more detail.

Inner structure- and surface-controlled hollow MnO nanocubes for high sensitive MR imaging contrast effect

Manganese oxide (MnO) nanocubes were fabricated and their surface were modified by ligand encapsulation or ligand exchange, to render them water-soluble. And then, MnO formed the hollow structure by etching using acidic solution (phthalate buffer, pH 4.0). Depending on the ligand of the MnO surface, it increases the interaction between MnO and water molecules. Also, the hollow structure of MnO, as well as the ligand, can greatly enhance the accessibility of water molecules to metal ions by surface area-to-volume ratio. These factors provide high R1 relaxation, leading to strong T1 MRI signal. We have confirmed T1-weighted MR contrast effect using 4-kinds of MnO nanocubes (MnOEn, MnOEnHo, MnOEx and MnOExHo). They showed enough a MR contrast effect and biocompatibility. Especially, among them, MnOExHo exhibited high T1 relaxivity (r1) (6.02 mM^-1 s^-1), even about 1.5 times higher sensitivity than commercial T1 MR contrast agents. In vitro/in vivo studies have shown that MnOExHo provides highly sensitive T1-weighted MR imaging, thereby improving diagnostic visibility at the disease site.

Contribution of resonance energy transfer to the luminescence quenching of upconversion nanoparticles with graphene oxide

Upconversion nanoparticles (UCNP) are increasingly used due to their advantages over conventional fluorophores, and their use as resonance energy transfer (RET) donors has permitted their application as biosensors when they are combined with appropriate RET acceptors such as graphene oxide (GO). However, there is a lack of knowledge about the design and influence that GO composition produces over the quenching of these nanoparticles that in turn will define their performance as sensors. In this work, we have analysed the total quenching efficiency, as well as the actual values corresponding to the RET process between UCNPs and GO sheets with three different chemical compositions. Our findings indicate that excitation and emission absorption by GO sheets are the major contributor to the observed luminescence quenching in these systems. This challenges the general assumption that UCNPs luminescence deactivation by GO is caused by RET. Furthermore, RET efficiency has been theoretically calculated by means of a semiclassical model considering the different nonradiative energy transfer rates from each Er³⁺ ion to the GO thin film. These theoretical results highlight the relevance of the relative positions of the Er³⁺ ions inside the UCNP with respect to the GO sheet in order to explain the RET-induced efficiency measurements.

Paper-based point-of-care test with xeno nucleic acid probes

Bridging the unmet need of efficient point-of-care testing (POCT) in biomedical engineering research and practice with the emerging development in artificial synthetic xeno nucleic acids (XNAs), this review summarized the recent development in paper-based POCT using XNAs as sensing probes. Alongside the signal transducing mode and immobilization methods of XNA probes, a detailed evaluation of probe performance was disclosed. With these new aspects, both researchers in synthetic chemistry / biomedical engineering and physicians in clinical practice could gain new insights in designing, manufacturing and choosing suitable reagents and techniques for POCT.

Simultaneous Sensing of Seven Pathogenic Bacteria by Guanidine-Functionalized Upconversion Fluorescent Nanoparticles

The method capable of simultaneously detecting multiple target bacterial pathogens is necessary and of great interest. In this research, we demonstrated our initial effort to simultaneously detect seven common foodborne bacteria by developing a straightforward upconversion fluorescence sensing approach. The fluorescent nanosensor was constructed from a designed guanidine-functionalized upconversion fluorescent nanoparticles (UCNPs@GDN), tannic acid, and hydrogen peroxide (HP) and could quantify pathogenic bacteria in a nonspecific manner because the luminescence of the upconversion fluorescent nanoparticle was effectively strengthened in the presence of bacteria. When the developed nanosensor was applied to quantify multiple bacteria including Escherichia coli, Salmonella, Cronobacter sakazakii, Shigella flexneri, Vibrio parahaemolyticus, Staphylococcus aureus, and Listeria monocytogenes, a linear range of 10³ to 10⁸ cfu mL^-1 and a detection limit of 1.30 × 10² cfu mL^-1 have been obtained for the seven model mixture bacteria. In addition, the similar linear range and detection limit were also obtained for the detection of single bacteria. The present approach also exhibited acceptable recovery values ranging from 70.0 to 118.2% for bacteria in real samples (water, milk, and beef). All these results suggested that the guanidine-functionalized upconversion fluorescent nanosensor could be considered as a promising candidate for the rapid detection and surveillance of microbial pollutants in food and water.

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.

Surface Functionalisation of Upconversion Nanoparticles with Different Moieties for Biomedical Applications

Lanthanide ion-doped upconversion nanoparticles (UCNPs) that can convert low-energy infrared photons into high-energy visible and ultraviolet photons, are becoming highly sought-after for advanced biomedical and biophotonics applications. Their unique luminescent properties enable UCNPs to be applied for diagnosis, including biolabeling, biosensing, bioimaging, and multiple imaging modality, as well as therapeutic treatments including photothermal and photodynamic therapy, bio-reductive chemotherapy and drug delivery. For the employment of the inorganic nanomaterials into biological environments, it is critical to bridge the gap in between nanoparticles and biomolecules via surface modifications and subsequent functionalisation. This work reviews the various ways to surface modify and functionalise UCNPs so as to impart different functional molecular groups to the UCNPs surfaces for a broad range of applications in biomedical areas. We discussed commonly used base functionalities, including carboxyl, amino and thiol moieties that are typically imparted to UCNP surfaces so as to provide further functional capacity.

Photochemical Ligation to Ultrasensitive DNA Detection with Upconverting Nanoparticles

In this work, we explore a photochemical ligation reaction to covalently modify oligonucleotide-conjugated upconverting nanoparticles (UCNPs) in the presence of a specific target DNA sequence. The target sequence acts as a hybridization template, bringing together a biotinylated photoactivatable oligonucleotide probe and the oligonucleotide probe that is attached to UCNPs. The illumination of the UCNPs by NIR light to generate UV emission internally or illuminating the photoactivatable probe directly by an external UV light promotes the photochemical ligation reaction, yielding covalently biotin functionalized UCNPs that can be selectively captured in streptavidin-coated microwells. Following this strategy, we developed a DNA sensor with a limit of detection of 1 × 10^-18 mol per well (20 fM). In addition, we demonstrate the possibility to create UCNP patterns on the surface of solid supports upon NIR illumination that are selectively formed under the presence of the target oligonucleotide.

Lighting Up MicroRNA in Living Cells by the Disassembly of Lock-Like DNA-Programmed UCNPs-AuNPs through the Target Cycling Amplification Strategy

Intracellular microRNAs imaging based on upconversion nanoprobes has great potential in cancer diagnostics and treatments. However, the relatively low detection sensitivity limits their application. Herein, a lock-like DNA (LLD) generated by a hairpin DNA (H1) hybridizing with a bolt DNA (bDNA) sequence is designed, which is used to program upconversion nanoparticles (UCNPs, NaYF₄ @NaYF₄ :Yb, Er@NaYF₄ ) and gold nanoparticles (AuNPs). The upconversion emission is quenched through luminescence resonance energy transfer (LRET). The multiple LLD can be repeatedly opened by one copy of target microRNA under the aid of fuel hairpin DNA strands (H2) to trigger disassembly of AuNPs from the UCNP, resulting in the lighting up of UCNPs with a high detection signal gain. This strategy is verified using microRNA-21 as model. The expression level of microRNA-21 in various cells lines can be sensitively measured in vitro, meanwhile cancer cells and normal cells can be easily and accurately distinguished by intracellular microRNA-21 imaging via the nanoprobes. The detection limit is about 1000 times lower than that of the previously reported upconversion nanoprobes without signal amplification. This is the first time a nonenzymatic signal amplification method has been combined with UCNPs for imaging intracellular microRNAs, which has great potential for cancer diagnosis.

A Universal Upconversion Sensing Platform for the Sensitive Detection of Tumour-Related ncRNA through an Exo III-Assisted Cycling Amplification Strategy

Here, a sensitive and universal noncoding RNA (ncRNA) upconversion sensing nanoplatform is developed. Gold nanoparticles bearing one hairpin DNA (Hp) molecule are conjugated to the linker DNA modified NaYF₄ :Yb, Er@NaYF₄ upconversion nanoparticles by DNA hybridization, leading to quenching of the upconversion emission through fluorescence resonance energy transfer. A signal DNA (SDNA) sequence is designed to open Hp, recovering the upconversion emission. To achieve universality and high sensitivity of the nanoprobe, an exonuclease III (Exo III)-assisted cycling amplification strategy is introduced. A multifunctional hairpin DNA (mHp) containing ncRNA recognition sequence and SDNA sequence is designed to recognize ncRNA and trigger Exo III as a biocatalyst to stepwise disintegrate itself, releasing both ncRNA and SDNA. The released ncRNA can be reused to release more SDNA, which greatly improves the sensing sensitivity. By changing the recognition portion of mHp, various ncRNA can be detected. The sensitive detection of both homeobox (HOX) transcript antisense RNA segment and miR-21 is achieved with this novel strategy, even in human serum, indicating the universality and sensitivity of the proposed strategy. Additionally, the expression level of miR-21 in human breast cancer cell (MCF-7) lysate is successfully measured, suggesting its potential in clinical diagnosis.

Sensors and bioassays powered by upconverting materials

In recent years, considerable efforts have been done to better understand the peculiar emission properties of upconverting materials due to their widespread applications in different and important technological fields such as upconversion-based photoactivated cancer therapies, photoactivated drug-delivery, magnetic resonance imaging contrast agents, bioimaging. However, one of the most promising applications of upconverting materials concerns the field of sensing, due to their unique emission properties. In fact, the minimal autofluorescence, blinking, photo-bleaching, and high photostability makes them an excellent alternative to organic dyes or quantum dots. This article reviews the state-of-the-art, design, and sensing strategies of upconversion-based sensing platforms, with special attention to upconverting nanoparticles, as well as how the incorporation of these materials into pre-existing diagnostic tests and bioassays have improved their capabilities for the detection of different kinds of analytes.

Bimodal counterpropagating-responsive sensing material for the detection of histamine

A dual-mode system for simultaneous fluorescence and SERS sensing of histamine.

How to make nanobiosensors: surface modification and characterisation of nanomaterials for biosensing applications

This report aims to provide the audience with a guideline for construction and characterisation of nanobiosensors that are based on widely used affinity probes including antibodies and aptamers.