FRET Nanoflares for Intracellular mRNA Detection: Avoiding False Positive Signals and Minimizing Effects of System Fluctuations

Facile Strategy for Visible Disassembly of Spherical Nucleic Acids Programmed by Catalytic DNA Circuits

The programmable toehold-mediated DNA-strand-displacement reaction has demonstrated its extraordinary capability in driving the spherical nucleic acid assembly. Here, a facile strategy of integrating a DNA-strand-displacement-based DNA circuit with a universal spherical nucleic acid aggregate system was developed for the visible disassembly of spherical nucleic acids. This integrated system exhibited rapid colorimetric response and good sensitivity in the disassembly reaction and demonstrated its capability in the application of single nucleotide polymorphism discrimination. Moreover, an OR logic gate used for multiplex detection was constructed through combining the fixed spherical nucleic acid disassembly system with two DNA circuits. This strategy will have great potential in the fabrication of a portable low-cost DNA diagnostic kit, and it is also a very promising method to be used in other applications, such as complex DNA networks and programmable phase transformation of nanoparticle superlattices.

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.

A spherical nucleic acid-based two-photon nanoprobe for RNase H activity assay in living cells and tissues

We report here a two-photon nanoprobe for the detection of RNase H activity in living cells and ex vivo tissues by combining a two-photon dye with a spherical nucleic acid (SNA) featuring a DNA/RNA duplex corona and a gold nanoparticle core.

Three-Dimensional Molecular Transfer from DNA Nanocages to Inner Gold Nanoparticle Surfaces

It is of great interest to construct DNA-functionalized gold nanoparticles (DNA-AuNPs) with a controllable number of DNA strands and relative orientations. Herein, we describe a three-dimensional (3D) molecular transfer strategy, in which a pattern of DNA strands can be transferred from a DNA icosahedron cage (I-Cage) to the wrapped AuNP surface. The results show that DNA-AuNPs produced by this method inherit DNA pattern information encoded in the transient I-Cage template with high fidelity. Controllable numbers and positions of DNA on the surface of AuNPs can be simultaneously realized by direct "printing" of a DNA pattern from the nanoshell (I-Cage) to the nanocore (AuNP), further expanding the applications of DNA nanotechnology to nanolithography. Prospectively, the customized DNA-printed nanoparticles possess great potential for constructing programmable architectures for optoelectronic devices as well as smart biosensors for biomedical applications.

DNA-Coated Gold Nanoparticles for the Detection of mRNA in Live Hydra Vulgaris Animals

Advances in nanoparticle design have led to the development of nanoparticulate systems that can sense intracellular molecules, alter cellular processes, and release drugs to specific targets in vitro. In this work, we demonstrate that oligonucleotide-coated gold nanoparticles are suitable for the detection of mRNA in live Hydra vulgaris, a model organism, without affecting the animal's integrity. We specifically focus on the detection of Hymyc1 mRNA, which is responsible for the regulation of the balance between stem cell self-renewal and differentiation. Myc deregulation is found in more than half of human cancers, thus the ability to detect in vivo related mRNAs through innovative fluorescent systems is of outmost interest.

Real-Time in Situ Visualizing of the Sequential Activation of Caspase Cascade Using a Multicolor Gold-Selenium Bonding Fluorescent Nanoprobe

The caspase cascade is an ensemble of very important signaling molecules that plays a critical role in cell apoptosis. Real-time monitoring of the upstream and downstream activation relationships of the caspases in the signal pathway is of great significance for understanding the regulatory mechanisms of these signaling molecules in the development of various diseases. Herein, a multicolor fluorescent nanoprobe, GNP-Se-Casp, has been developed based on Au-Se bonding for real-time in situ monitoring caspase- (casp-) 3, 8, and 9 during cell apoptosis. In the real-time fluorescence imaging of apoptotic HeLa cells induced by staurosporine using GNP-Se-Casp, the fluorescence signals corresponding to casp-8 and casp-9 sequentially turn on, followed by the appearance of the fluorescence of casp-3, which visualizes the upstream and downstream relationships of casp-3, -8, and -9. Thus, GNP-Se-Casp is an effective tool for real-time in situ monitoring of caspase cascade activation in the apoptosis process of tumor cells. This design strategy is easily adaptable to in situ detection of other signal molecules, especially those with upstream and downstream activation relationships.

Abnormal scar identification with spherical-nucleic-acid technology

The accurate diagnosis of scar type and severity relies on histopathology of biopsied tissue, which is invasive and time-consuming, causes discomfort and may exacerbate scarring. Here, we show that imaging nanoprobes for the live-cell detection of intracellular messenger RNA (mRNA) (also known as NanoFlares) enable measurements of the expression of connective tissue growth factor (CTGF) as a visual indicator of hypertrophic scars and keloids. During cell culture, NanoFlares enabled the distinction of hypertrophic and keloidal fibroblasts from normal fibroblasts, and the detection of changes in CTGF expression resulting from the regulatory effects of transforming growth factor-β (TGF-β) agonists and TGF-β antagonists. We also applied the NanoFlares topically to the skin of live mice and rabbits, and to ex vivo human skin models. Transepidermal penetration of the NanoFlares enabled the visual and spectroscopic quantification of underlying abnormal fibroblasts on the basis of CTGF mRNA expression. Our proof-of-concept studies of topically applied NanoFlare technology as a means of biopsy-free scar diagnosis may eventually inform therapeutic decisions on the basis of the mRNA-expression patterns of skin disorders.

A graphene oxide-based hairpin probe coupling duplex-specific nuclease signal amplification for detection and imaging of mRNA in living cells

In situ imaging of mRNA in living cells can help to monitor the real time mRNA expression and also useful for diagnosis and prognosis of the diseases. In this study, a new strategy was designed for simple, sensitive, and selective platform to detect the mRNA levels by combining a hairpin probe-graphene oxide (HP1/GO) and duplex-specific nuclease signal amplification (DSNSA). Initially, the DNA probe was adsorbed on the surface of GO to protect it from enzymatic digestion. Then, the target mRNA (T1) was hybridized with a partial hairpin probe which formed a duplex. Finally, under the action of DSN nuclease, the ssDNA in the DNA/RNA hybrid was selectively cleaved and produced small fragments. Then, T1 triggered the next reaction cycle, constituting a new circular exponential amplification. Here, we conclude that this assay is highly sensitive for the detection of target mRNA with the lower detection limit of 1 fM under optimal conditions. Furthermore, this strategy was successfully used for imaging of mRNA in living cells.

Biomedical applications of nanoflares: Targeted intracellular fluorescence probes

Nanoflares are intracellular probes consisting of oligonucleotides immobilized on various nanoparticles that can recognize intracellular nucleic acids or other analytes, thus releasing a fluorescent reporter dye. Single-stranded DNA (ssDNA) complementary to mRNA for a target gene is constructed containing a 3'-thiol for binding to gold nanoparticles. The ssDNA "recognition sequence" is prehybridized to a shorter DNA complement containing a fluorescent dye that is quenched. The functionalized gold nanoparticles are easily taken up into cells. When the ssDNA recognizes its complementary target, the fluorescent dye is released inside the cells. Different intracellular targets can be detected by nanoflares, such as mRNAs coding for genes over-expressed in cancer (epithelial-mesenchymal transition, oncogenes, thymidine kinase, telomerase, etc.), intracellular levels of ATP, pH values and inorganic ions can also be measured. Advantages include high transfection efficiency, enzymatic stability, good optical properties, biocompatibility, high selectivity and specificity. Multiplexed assays and FRET-based systems have been designed.

Microfluidic paper-based photoelectrochemical sensing platform with electron-transfer tunneling distance regulation strategy for thrombin detection

This work reports a microfluidic paper-based photoelectrochemical (μ-PEC) sensing platform for thrombin (TB) detection with electron-transfer tunneling distance regulation (ETTDR) and aptamer target-triggering nicking enzyme signaling amplification (NESA) dual strategies. Specifically, paper-based TiO₂ nanosheets (PTNs) were prepared with an efficient hydrothermal process, serving as the direct pathway for the charge carriers transfer. When CeO₂-labeled hairpin DNA 3 (HP3) was closely located at the PTNs, the CeO₂-PTNs heterostructure was formed, which could great facilitate the photogenerated carries separation of CeO₂. In addition, with the aid of aptamer target-triggering NESA strategy, the input TB could be transducted to numerous output target of DNA (tDNA), achieving the goal of desirable signal amplification. In the presence of TB, the output tDNA could be further hybridized with HP3 and unfold its hairpin loop, which forced the CeO₂ away from the surface of PTNs and vanished the CeO₂-PTNs heterostructure, resulting in the obviously reducing of photocurrent signal. The as-designed sensing platform exhibited a linear range from 0.02 pM to 100 pM with a detection limit of 6.7 fM. Importantly, this μ-PEC sensing platform could not only realize the highly efficient TB detection, but also pave a luciferous way for the detection of other protein in bioanalysis.

Quantitative zeptomolar imaging of miRNA cancer markers with nanoparticle assemblies

Multiplexed detection of small noncoding RNAs responsible for posttranscriptional regulation of gene expression, known as miRNAs, is essential for understanding and controlling cell development. However, the lifetimes of miRNAs are short and their concentrations are low, which inhibits the development of miRNA-based methods, diagnostics, and treatment of many diseases. Here we show that DNA-bridged assemblies of gold nanorods with upconverting nanoparticles can simultaneously quantify two miRNA cancer markers, namely miR-21 and miR-200b. Energy upconversion in nanoparticles affords efficient excitation of fluorescent dyes via energy transfer in the superstructures with core-satellite geometry where gold nanorods are surrounded by upconverting nanoparticles. Spectral separation of the excitation beam and dye emission wavelengths enables drastic reduction of signal-to-noise ratio and the limit of detection to 3.2 zmol/ng_RNA (0.11 amol or 6.5 × 10⁴ copies) and 10.3 zmol/ng_RNA (0.34 amol or 2.1 × 10⁵ copies) for miR-21 and miR-200b, respectively. Zeptomolar sensitivity and analytical linearity with respect to miRNA concentration affords multiplexed detection and imaging of these markers, both in living cells and in vivo assays. These findings create a pathway for the creation of an miRNA toolbox for quantitative epigenetics and digital personalized medicine.

A gold-nanodot-decorated hollow carbon nanosphere based nanoplatform for intracellular miRNA imaging in colorectal cancer cells

We report a new biofunctionalized nanoplatform based on hyaluronic acid-coated gold-nano-dot-decorated hollow carbon nanospheres (AuHCNs-HA) for microRNA imaging in living cells.

Gold nanoparticle based fluorescent oligonucleotide probes for imaging and therapy in living systems

Gold nanoparticles (AuNPs) with unique physical and chemical properties have become an integral part of research in nanoscience.

Assembly of DNA Probes into Superstructures for Dramatically Enhancing Enzymatic Stability and Signal-to-Background Ratio

DNA fluorescent probes are versatile tools that are widely used for biological detection in tubes. Using DNA probes in living systems, however, represents a significant challenge because of the endogenous nuclease-induced DNA degradation and strong background fluorescence in complex biological environments. Here, we show that assembling DNA probes into core-satellite gold nanoparticle (AuNP) superstructures could unprecedentedly enhance enzymatic stability and reduce background interference. The embedded DNA probes are protected from interaction with nuclease, eliminating the enzymatic degradation. In the meantime, the AuNP superstructures show extremely high quenching efficiency (>98%) toward the embedded DNA probes, whose fluorescence can be instantly turned on by the target binding, resulting in high signal-to-background ratio. To demonstrate these distinct properties, we made use of the assembled nanoprobes to monitor the ATP levels under different stimuli in living cells. The assembly strategy leads to a new opportunity for accurately sensing targets in living systems.

Accessibility of Densely Localized DNA on Soft Polymer Nanoparticles

The dense localization of DNA on soluble nanoparticles can lead to effects distinct from equivalent amounts of the DNA in solution. However, the specific effect may depend on the nature of the assembly and the nanoparticle core. Here we examine the accessibility of densely packed DNA duplexes that extend from a bottle-brush polymer core. We find that unlike spherical nucleic acids, the DNA duplex bristles on the bottle-brush polymer remain accessible to sequence-specific cleavage by endonucleases. In addition, the hybridized strand of the duplex can be displaced through a toehold-mediated strand exchange even at the polymer interface. These results demonstrate that the DNA on bottle-brush polymer remains sufficiently flexible to allow enzymatic degradation or DNA hybridization.

In Situ SiRNA Assembly in Living Cells for Gene Therapy with MicroRNA Triggered Cascade Reactions Templated by Nucleic Acids

The in situ generation of siRNAs in living cells can greatly enhance the specificity and efficiency of gene therapy. Inspired by the natural molecular machines that organize different compartments sequentially in a limited space to facilitate cellular process, this work constructs a DNA nanomachine (DNM) by alternately hybridizing two pairs of DNA/RNA hybrids to a DNA scaffold generated by rolling circle amplification for highly efficient in situ siRNA assembly in living cells. After target cell-specific delivery of DNM, intracellular specific microRNA can work as a trigger to operate the DNM by initiating DNA cascade displacement reaction between DNA/RNA hybrids along the scaffold for continuous generation of siRNAs. Using miR-21 as a model, efficient siRNAs generation is achieved via DNA templated cascade reaction, which demonstrated impressive suppressions to VEGF mRNA and protein expressions in cells and in vivo tumor growth and indicated promising application of the designed strategy in gene therapy.

Functional Imaging with Nucleic-Acid-Based Sensors: Technology, Application and Future Healthcare Prospects

Timely monitoring and assessment of human health plays a crucial role in maintaining the wellbeing of our advancing society. In addition to medical tools and devices, suitable probe agents are crucial to assist such monitoring, either in passive or active ways (i.e., sensors) through inducible signals. In this review we highlight recent developments in activatable optical sensors based on nucleic acids. Sensing mechanisms and bio-applications of these nucleic acid sensors in ex vivo assays, intracellular or in vivo settings are described. In addition, we discuss the limitations of these sensors and how nanotechnology can complement/enhance sensor properties to promote translation into clinical applications.

Multiplexed determination of intracellular messenger RNA by using a graphene oxide nanoprobe modified with target-recognizing fluorescent oligonucleotides

A multiplexed graphene oxide (GO) fluorescent nanoprobe is described for quantification and imaging of messenger RNAs (mRNAs) in living cells. The recognizing oligonucleotides (with sequences complementary to those of target mRNAs) were labeled with different fluorescent dyes. If adsorbed on GO, the fluorescence of the recognizing oligonucleotides is quenched. After having penetrated living cells, the oligonucleotides bind to target mRNAs and dissociate from GO. This leads to the recovery of fluorescence. Using different fluorescent dyes, various intracellular mRNAs can be simultaneously imaged and quantified by a high content analysis within a short period of time. Actin mRNA acts as the internal control. This GO-based nanoprobe allows mRNA mimics to be determined within an analytical range from 1 to 400 nM and a detection limit as low as 0.26 nM. Up to 3 intracellular mRNAs (C-myc, TK1, and actin) can be detected simultaneously in a single living cell. Hence, this nanoprobe enables specific distinction of intracellular mRNA expression levels in cancerous and normal cells. It can be potentially applied as a tool for detection of cancer progression and diagnosis. Graphical abstract A multiplexed graphene oxide (GO)-based fluorescent nanoprobe is described for quantification and imaging of intracellular messenger RNAs. After penetrating living cells, the recovered fluorescence of the dissociated recognizing oligonucleotides can be analyzed , and this allows for simultaneous detection of up to 3 intracellular messenger RNAs.

Low Background Cascade Signal Amplification Electrochemical Sensing Platform for Tumor-Related mRNA Quantification by Target-Activated Hybridization Chain Reaction and Electroactive Cargo Release

Herein a low background cascade signal amplification electrochemical sensing platform has been proposed for the ultrasensitive detection of mRNA (mRNA) by coupling the target-activated hybridization chain reaction and electroactive cargo release from mesoporous silica nanocontainers (MSNs). In this sensing platform, the 5'-phosphate-terminated DNA (5'-PO₄ cDNA) complement to target mRNA is hybridized with the trigger DNA and anchor DNA on the surface of the MSNs, aiming at forming a double-stranded DNA gate molecule and sealing the methylene blue (MB) in the inner pores of the MSNs. In the presence of target mRNA, the 5'-PO₄ cDNA is displaced from the MSNs and competitively hybridizes with mRNA, which led to the liberation of the trigger DNA and the opening of the MSNs pore. The liberated trigger DNA can be then immobilized onto the electrode surface through hybridization with the capture DNA, triggering HCR on the electrode surface. At the same time, the MB released from the MSNs will selectively intercalate into the HCR long dsDNA polymers, giving rise to significant electrochemical response. In addition, due to the λ-exonuclease (λ-Exo) cleavage reaction-assisted target recycling, more amounts of trigger DNA will be liberated and trigger HCR, and numerous MB are uncapped and intercalate into the HCR products. As proof of concept, thymidine kinase 1 (TK1) mRNA was used as a model target. Featured with amplification efficiency, label-free capability, and low background signal, the strategy could quantitatively detect TK1 mRNA down to 2.0 aM with a linear calibration range from 0.1 fM to 1 pM. We have also demonstrated the practical application of our proposed sensing platform for detecting TK1 mRNA in real samples, opening up new avenues for highly sensitive quantification of biomarkers in bioanalysis and clinical diagnosis.

Photoactivated Specific mRNA Detection in Single Living Cells by Coupling "Signal-on" Fluorescence and "Signal-off" Electrochemical Signals

The spatiotemporal detection of a target mRNA in a single living cell is a major challenge in nanoscience and nanomedicine. We introduce a versatile method to detect mRNA at a single living cell level that uses photocleavable hairpin probes as functional units for the optical (fluorescent) and electrochemical (voltammetric) detection of MnSOD mRNA in single MCF-7 cancer cells. The fluorescent probe is composed of an ortho-nitrophenylphosphate ester functionalized hairpin that includes the FAM fluorophore in a caged configuration quenched by Dabcyl. The fluorescent probe is further modified with the AS1411 aptamer to facilitate the targeting and internalization of the probe into the MCF-7 cells. Under UV irradiation, the hairpin is cleaved, leading to the intracellular mRNA toehold-stimulated displacement of the FAM-functionalized strand resulting in a switched-on fluorescence signal upon the detection of the mRNA in a single cell. In addition, a nanoelectrode functionalized with a methylene blue (MB) redox-active photocleavable hairpin is inserted into the cytoplasm of a single MCF-7 cell. Photocleavage of the hairpin leads to the mRNA-mediated toehold displacement of the redox-active strand associated with the probe, leading to the depletion of the voltammetric response of the probe. The parallel optical and electrochemical detection of the mRNA at a single cell level is demonstrated.

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

An upconversion nanoparticle (UCNP)-based fluorescence resonance energy-transfer (FRET) strategy is normally restricted by the complicated preparations, low energy-transfer efficiency, and the challenge on improving specificity. Herein, simple DNA-functionalized UCNPs were designed as energy donors for constructing a FRET-based probe to detect the liver-specific microRNA 122 (miR-122). To improve FRET efficiency, UCNPs were constructed with confined core-shell structures, in which emitting ions were precisely located in the thin shell to make them close enough to external energy acceptors. Subsequently, capture DNA was simply functionalized on the outer surface of UCNPs based on ligand exchange that contributed to shortening the energy-transfer distance without extra modification. To gain high specificity, the donor-to-acceptor distance of FRET was controlled by a sandwich DNA hybridization structure using two shorter DNAs with designed complementary sequences (capture DNA and dye-labeled report DNA) to capture the longer target of miR-122. Therefore, the sensitive detection of miR-122 was achieved based on the decreased signals of UCNPs and the increased signals of the dye labeled on reported DNA. With good biocompatibility, this method has been further applied to cancer cell imaging and in vivo imaging, which opened up a new avenue to the sensitive detection and imaging of microRNA in biological systems.

More Than a Light Switch: Engineering Unconventional Fluorescent Configurations for Biological Sensing

Fluorescence is a powerful and sensitive tool in biological detection, used widely for cellular imaging and in vitro molecular diagnostics. Over time, three prominent conventions have emerged in the design of fluorescent biosensors: a sensor is ideally specific for its target, only one fluorescence signal turns on or off in response to the target, and each target requires its own sensor and signal combination. These are conventions but not requirements, and sensors that break with one or more of these conventions can offer new capabilities and advantages. Here, we review "unconventional" fluorescent sensor configurations based on fluorescent dyes, proteins, and nanomaterials such as quantum dots and metal nanoclusters. These configurations include multifluorophore Förster resonance energy transfer (FRET) networks, temporal multiplexing, photonic logic, and cross-reactive arrays or "noses". The more complex but carefully engineered biorecognition and fluorescence signaling modalities in unconventional designs are richer in information, afford greater multiplexing capacity, and are potentially better suited to the analysis of complex biological samples, interactions, processes, and diseases. We conclude with a short perspective on the future of unconventional fluorescent sensors and encourage researchers to imagine sensing beyond the metaphorical light bulb and light switch combination.

A Ratiometric Fluorescent Bioprobe Based on Carbon Dots and Acridone Derivate for Signal Amplification Detection Exosomal microRNA

Recently, sensitive and selective detection of exosomal microRNAs (miRNAs) has been garnering significant attention, because it is related to many complex diseases, including cancer. Herein, we report a ratiometric fluorescent bioprobe based on DNA-labeled carbon dots (DNA-CDs) and 5,7-dinitro-2-sulfo-acridone (DSA) coupling with the target-catalyzing signal amplification for the detection of exosomal miRNA-21. There was high fluorescence resonance energy transfer (FRET) efficiency between carbon dots (CDs) and DSA when the bioprobe was assembled. However, in the presence of the target, with disassembling of the fluorescent bioprobe, the fluorescence intensities of CDs and DSA were changed simultaneously. Because of the ratio of dual fluorescence intensities, this ratiometric fluorescent bioprobe was able to cancel out environmental fluctuations by calculating emission intensity ratio at two different wavelengths, being robust and stable enough for detection of exosomal miRNA-21. In addition, we displayed that a single miRNA-21 can catalyze the disassembly of multiple CDs with DSA theoretically, yielding significant change in the fluorescence ratio for the detection of miRNA-21. With this signal amplification strategy, the limit of detection was as low as 3.0 fM. Furthermore, because of the introduction of lock nucleic acid to mediate the strand displacement reaction, the selectivity of this strategy was improved remarkably, even against single base mismatch sequence. More importantly, our strategy could monitor the dynamic change of exosomal miRNA-21, which maybe becomes a potential tool to distinguish cancer exosomes and nontumorigenic exosomes. In a short, this ratiometric fluorescence bioprobe possessed high stability, sensitivity and selectivity coupling with ease of operation and cost efficiency, leading to great potential for wide application.

Normalizing Tumor Microenvironment Based on Photosynthetic Abiotic/Biotic Nanoparticles

Tumor hypoxia has attained the status of a core hallmark of cancer that globally affects the entire tumor phenotype. Reversing tumor hypoxia might offer alternative therapeutic opportunities for current anticancer therapies. In this research, a photosynthetic leaf-inspired abiotic/biotic nano-thylakoid (PLANT) system was designed by fusing the thylakoid membrane with synthetic nanoparticles for efficient O₂ generation in vivo. Under 660 nm laser irradiation, the PLANT system exhibited intracellular O₂ generation and the anaerobic respiration of the multicellular tumor spheroid was suppressed by PLANT as well. In vivo, it was found that PLANT could not only normalize the entire metabolic network but also adjust the abnormal structure and function of the tumor vasculature. It was demonstrated that PLANT could significantly enhance the efficacy of phototherapy or antiangiogenesis therapy. This facile approach for normalizing the tumor microenvironment will find great potential in tumor therapy.

Ratiometric Fluorescent Biosensor for Visual Discrimination of Cancer Cells with Different Telomerase Expression Levels

Telomerase is inactive in normal somatic cells but highly activated in tumor cells to maintain their indefinite proliferation and immortal phenotype. As a specific marker for the generation and progress of almost all tumors, the detection of telomerase activity by classical PCR techniques has served in the biological research of tumors. However, the detection of in situ telomerase activity in cell extracts to evaluate the malignancy, progress, and metastasis of tumors remains a daunting challenge. Here, a precisely designed FRET-based ratiometric fluorescent oligonucleotide probe has achieved high-fidelity detection of telomerase activity for accurate discrimination of different cancer cells toward advanced diagnosis of tumors. Our method is superior to other methods in its capabilities to quantify telomerase activity in cell extracts and visualize various tumor cell extracts with different telomerase expression levels by the naked eye for clinical diagnosis. In particular, the ratiometric fluorescent probe used in the assay could exclude other experimental factors influence, and further avoid false positive signal generation. The method reported here could provide a reliable, accurate, and convenient way in medical diagnostics and therapeutic response assessment.

Cross-Platform Cancer Cell Identification Using Telomerase-Specific Spherical Nucleic Acids

Distinguishing tumor cells from normal cells holds the key to precision diagnosis and effective intervention of cancers. The fundamental difficulties, however, are the heterogeneity of tumor cells and the lack of truly specific and ideally universal cancer biomarkers. Here, we report a concept of tumor cell detection, bypassing the specific genotypic and phenotypic features of different tumor cell types and directly going toward the hallmark of cancer, uncontrollable growth. Combining spherical nucleic acids (SNAs) with exquisitely engineered molecular beacons (SNA beacons, dubbed SNAB technology) is capable of identifying tumor cells from normal cells based on the molecular phenotype of telomerase activity, largely bypassing the heterogeneity problem of cancers. Owing to the cell-entry capability of SNAs, the SNAB probe readily achieves tumor cell detection across multiple platforms, ranging from solution-based assay, to single cell imaging and in vivo solid tumor imaging (unlike PCR that is restricted to cell lysates). We envision the SNAB technology will impact cancer diagnosis, therapeutic response assessment, and image-guided surgery.

Ratiometric optical nanoprobes enable accurate molecular detection and imaging

Exploring and understanding biological and pathological changes are of great significance for early diagnosis and therapy of diseases. Optical sensing and imaging approaches have experienced major progress in this field. Particularly, an emergence of various functional optical nanoprobes has provided enhanced sensitivity, specificity, targeting ability, as well as multiplexing and multimodal capabilities due to improvements in their intrinsic physicochemical and optical properties. However, one of the biggest challenges of conventional optical nanoprobes is their absolute intensity-dependent signal readout, which causes inaccurate sensing and imaging results due to the presence of various analyte-independent factors that can cause fluctuations in their absolute signal intensity. Ratiometric measurements provide built-in self-calibration for signal correction, enabling more sensitive and reliable detection. Optimizing nanoprobe designs with ratiometric strategies can surmount many of the limitations encountered by traditional optical nanoprobes. This review first elaborates upon existing optical nanoprobes that exploit ratiometric measurements for improved sensing and imaging, including fluorescence, surface enhanced Raman scattering (SERS), and photoacoustic nanoprobes. Next, a thorough discussion is provided on design strategies for these nanoprobes, and their potential biomedical applications for targeting specific biomolecule populations (e.g. cancer biomarkers and small molecules with physiological relevance), for imaging the tumor microenvironment (e.g. pH, reactive oxygen species, hypoxia, enzyme and metal ions), as well as for intraoperative image guidance of tumor-resection procedures.

Abnormal scar identification with spherical-nucleic-acid technology

The accurate diagnosis of scar type and severity relies on histopathology of biopsied tissue, which is invasive and time-consuming, causes discomfort and may exacerbate scarring. Here, we show that imaging nanoprobes for the live-cell detection of intracellular messenger RNA (mRNA) (also known as NanoFlares) enable measurements of the expression of connective tissue growth factor (CTGF) as a visual indicator of hypertrophic scars and keloids. During cell culture, NanoFlares enabled the distinction of hypertrophic and keloidal fibroblasts from normal fibroblasts, and the detection of changes in CTGF expression resulting from the regulatory effects of transforming growth factor-β (TGF-β) agonists and TGF-β antagonists. We also applied the NanoFlares topically to the skin of live mice and rabbits, and to ex vivo human skin models. Transepidermal penetration of the NanoFlares enabled the visual and spectroscopic quantification of underlying abnormal fibroblasts on the basis of CTGF mRNA expression. Our proof-of-concept studies of topically applied NanoFlare technology as a means of biopsy-free scar diagnosis may eventually inform therapeutic decisions on the basis of the mRNA-expression patterns of skin disorders.

Avoiding Thiol Compound Interference: A Nanoplatform Based on High-Fidelity Au-Se Bonds for Biological Applications

Gold nanoparticles (Au NPs) assembled through Au-S covalent bonds have been widely used in biomolecule-sensing technologies. However, during the process, detection distortions caused by high levels of thiol compounds can still significantly influence the result and this problem has not really been solved. Based on the higher stability of Au-Se bonds compared to Au-S bonds, we prepared selenol-modified Au NPs as an Au-Se nanoplatform (NPF). Compared with the Au-S NPF, the Au-Se NPF exhibits excellent anti-interference properties in the presence of millimolar levels of glutathione (GSH). Such an Au-Se NPF that can effectively avoid detection distortions caused by high levels of thiols thus offers a new perspective in future nanomaterial design, as well as a novel platform with higher stability and selectivity for the in vivo application of chemical sensing and clinical therapies.

Spiny Nanorod and Upconversion Nanoparticle Satellite Assemblies for Ultrasensitive Detection of Messenger RNA in Living Cells

Quantitation and in situ monitoring of target mRNA (mRNA) in living cells remains a significant challenge for the chemical and biomedical communities. To quantitatively detect mRNA expression levels in living cells, we have developed DNA-driven gold nanorod coated platinum-upconversion nanoparticle satellite assemblies (termed Au NR@Pt-UCNP satellites) for intracellular thymidine kinase 1 (TK1) mRNA analysis. The nanostructures were capable of recognizing target mRNA in a sequence-specific manner as luminescence of UCNPs was effectively quenched by Au NR@Pt within the assemblies. Following recognition, UCNPs detached from Au NR@Pt, resulting in luminescence restoration to achieve effective in situ imaging and quantifiable detection of target mRNA. The upconversional luminescence intensity of confocal images showed a good linear relationship with intracellular TK1 mRNA ranging from 1.17 to 65.21 fmol/10 μg RNA and a limit of detection (LOD) of 0.67 fmol/10 μg RNA. We believe that our present assay can be broadly applied for detection of endogenous biomolecules at the cellular and tissue levels and restoration of tissue homeostasis in vivo.

Au-Se-Bond-Based Nanoprobe for Imaging MMP-2 in Tumor Cells under a High-Thiol Environment

The gold nanosensors based on the Au-S bond have been widely applied to biochemical detections. However, signal distortion caused by biothiols has been seldom mentioned and urgently needs to be solved. Herein, we designed a novel but easily assembled gold nanoprobe by coupling a selenol-modified peptide with FITC onto the gold nanoparticle's surface via an Au-Se bond for fluorescence imaging of a tumor marker matrix, metalloproteinases 2 (MMP-2). Compared to the Au-S probes, the Au-Se probes display high thermal stability and a very good anti-interference ability toward glutathione under simulated physiological conditions. More importantly, the Au-Se nanoprobe exhibits a high-fidelity fluorescent signal toward MMP-2, effectively avoiding interference caused by high levels of thiol compounds in vivo. In addition, in vivo experiments further proved that no significant signal intensity change for the tumor cells treated by the Au-Se probes was observed before and after eliminating glutathione. Hence, we believe such Au-Se probes with in vivo glutathione interfering resistance offer new routes and perspectives in biology and medicine in the future.

Aptamer-based FRET nanoflares for imaging potassium ions in living cells

Due to the effective properties of the FRET signal and K⁺-sensitive recognition of G-quadruplex, aptamer-based FRET nanoflares were developed to sense intracellular potassium ions.

A Responsive "Nano String Light" for Highly Efficient mRNA Imaging in Living Cells via Accelerated DNA Cascade Reaction

Nonenzymatic DNA catalytic amplification strategies have greatly benefited bioanalysis. However, long period incubation is usually required due to its relatively low reaction rate and efficiency, which limits its in vivo application. Here we design a responsive DNA nano string light (DNSL) by interval hybridization of modified hairpin DNA probe pairs to a DNA nanowire generated by rolling circle amplification and realize accelerated DNA cascade reaction (DCR) for fast and highly efficient mRNA imaging in living cells. Target mRNA initiates interval hybridization of two paired hairpin probes sequentially along the DNA nanowire and results in instant lighting up of the whole DNA nanowire with high signal gain due to the fast opening of all the self-quenched hairpins. The reaction time is about 6.7 times shorter compared with a regular DNA cascade reaction due to the acceleration based on domino effect. The cell delivery is achieved by modifying one of the hairpin probes with folic acid, and this intracellular imaging strategy is verified using human HeLa cells and intracellular survivin mRNA with a series of suppressed expressions as model, which provides a useful platform for fast and highly efficient detection of low-abundance nucleic acids in living cells.