Binary System for MicroRNA-Targeted Imaging in Single Cells and Photothermal Cancer Therapy

A multi-channel responsive AuNP@COF core-shell nanoprobe for simultaneous subcellular profiling of multiple cancer biomarkers

The abnormal change in the expression profile of multiple cancer biomarkers is closely related to tumor progression and therapeutic effect. Due to their low abundance in living cells and the limitations of existing imaging techniques, simultaneous imaging of multiple cancer biomarkers has remained a significant challenge. Here, we proposed a multi-modal imaging strategy to detect the correlated expression of multiple cancer biomarkers, MUC1, microRNA-21 (miRNA-21) and reactive oxygen (ROS) in living cells, based on a porous covalent organic framework (COF) wrapped gold nanoparticles (AuNPs) core-shell nanoprobe. The nanoprobe is functionalized with Cy5-labeled MUC1 aptamer, a ROS-responsive molecule (2-MHQ), and a miRNA-21-response hairpin DNA tagged by FITC as the reporters for different biomarkers. The target-specific recognition can induce the orthogonal molecular change of these reporters, producing fluorescence and Raman signals for imaging the expression profiles of membrane MUC1 (red fluorescence channel), intracellular miRNA-21 (green fluorescence channel), and intracellular ROS (SERS channel). We further demonstrate the capability of the cooperative expression of these biomarkers, along with the activation of NF-κB pathway. Our research provides a robust platform for imaging multiple cancer biomarkers, with broad potential applications in cancer clinical diagnosis and drug discovery.

DNA-functionalized gold nanoparticles: Modification, characterization, and biomedical applications

With the development of technologies based on gold nanoparticles (AuNPs), bare AuNPs cannot meet the increasing requirements of biomedical applications. Modifications with different functional ligands are usually needed. DNA is not only the main genetic material, but also a good biological material, which has excellent biocompatibility, facile design, and accurate identification. DNA is a perfect ligand candidate for AuNPs, which can make up for the shortcoming of bare AuNPs. DNA-modified AuNPs (DNA-AuNPs) have exciting features and bright prospects in many fields, which have been intensively investigated in the past decade. In this review, we summarize the various approaches for the immobilization of DNA strands on the surface of AuNPs. Representative studies for biomedical applications based on DNA-AuNPs are also discussed. Finally, we present the challenges and future directions.

Gold Nanoconjugates for miRNA Modulation in Cancer Therapy: From miRNA Silencing to miRNA Mimics

Cancer is a major healthcare burden and cause of death worldwide, with an estimated 19.3 million new cancer cases and 10 million cancer deaths globally only in 2020. While several anticancer therapeutics are available to date, many of these still show low treatment efficacy and high off-target effects and adverse reactions. This prompts a serious need to develop novel therapies that can decrease the side effects and increase treatment efficacy. MicroRNAs (miRNAs) can have a role in tumor development and progression, making them important targets for the improvement of anticancer therapies. In this context, gold nanoparticles have been widely studied for different clinical applications due to their biocompatibility and possibility of customization, and gold nanoconjugates targeting miRNAs are being developed for cancer diagnosis and treatment. Here we summarize the research developed so far and how it can contribute to cancer treatment, discuss how it can be improved, and present the current challenges and future perspectives on their design and application.

Self-Protected DNAzyme Walker with a Circular Bulging DNA Shield for Amplified Imaging of miRNAs in Living Cells and Mice

Abnormal expression of miRNAs is often detected in various human cancers. DNAzyme machines combined with gold nanoparticles (AuNPs) hold promise for detecting specific miRNAs in living cells but show short circulation time due to the fragility of catalytic core. Using miRNA-21 as the model target, by introducing a circular bulging DNA shield into the middle of the catalytic core, we report herein a self-protected DNAzyme (E) walker capable of fully stepping on the substrate (S)-modified AuNP for imaging intracellular miRNAs. The DNAzyme walker exhibits 5-fold enhanced serum resistance and more than 8-fold enhanced catalytic activity, contributing to the capability to image miRNAs much higher than commercial transfection reagent and well-known FISH technique. Diseased cells can accurately be distinguished from healthy cells. Due to its universality, DNAzyme walker can be extended for imaging other miRNAs only by changing target binding domain, indicating a promising tool for cancer diagnosis and prognosis.

DNAzyme-Functionalized Nanomaterials: Recent Preparation, Current Applications, and Future Challenges

DNAzyme-nanomaterial bioconjugates are a popular hybrid and have received major attention for diverse biomedical applications, such as bioimaging, biosensor development, cancer therapy, and drug delivery. Therefore, significant efforts are made to develop different strategies for the preparation of inorganic and organic nanoparticles (NPs) with specific morphologies and properties. DNAzymes functionalized with metal-organic frameworks (MOFs), gold nanoparticles (AuNPs), graphene oxide (GO), and molybdenum disulfide (MoS₂ ) are introduced and summarized in detail in this review. Moreover, the focus is on representative examples of applications of DNAzyme-nanomaterials over recent years, especially in bioimaging, biosensing, phototherapy, and stimulation response delivery in living systems, with their several advantages and drawbacks. Finally, the perspective regarding the future directions of research addressing these challenges is also discussed and highlighted.

Involvement of microRNAs as a Response to Phototherapy and Photodynamic Therapy: A Literature Review

The current knowledge about the mechanisms of action of light-based treatments (chiefly photodynamic therapy and phototherapy) in skin diseases leans to the possible involvement of epigenetic and oxidative stress mechanisms. To better understand and exploit, to the fullest, these relatively safe and reproducible treatments, several studies have focused on miRNAs, small non-encoding RNAs (22–24 nucleotides), after light-based treatments. The current narrative review focused on 25 articles. A meta-analysis was not deemed appropriate. The results gather the most recurrent skin-related miRNAs up- or downregulated after light treatment. Five of these, miR-21, -29, -125, -145 and -155, are either the most consistently related to efficacy/resistance to treatment or identified as helpful diagnostic tools. A specific class of miRNAs (angioMIRs) requires further studies. Future treatments and imaging techniques could benefit greatly from the use of antagomirs as a possible co-adjuvant therapy along with light-based treatments.

Gold nanostructures as mediators of hyperthermia therapies in breast cancer

Breast cancer is the leading cause of cancer-related deaths among women. Due to the limitations of the current therapeutics, new treatment options are needed. Hyperthermia is a promising approach to improve breast cancer therapy, particularly when combined with chemo and radiotherapy. This area has gained more attention following association with nanotechnology, with the emergence of modalities, such as photothermal therapy (PTT). PTT is a simple, minimally invasive technique that requires a near infrared (NIR) light source and a PTT agent. Gold nanostructures are excellent PTT agents as they offer biocompatibility, versatility, high photothermal conversion efficiency, imaging contrast and an easily-modified surface. In this review, we describe the molecular basis and the current clinical aspects of hyperthermia-based therapies. The emergent area of nanoparticle-induced hyperthermia will be explored, in particular gold nanostructure-mediated PTT, focusing on recent preclinical studies for breast cancer management.

A two-photon fluorescence silica nanoparticle-based FRET nanoprobe platform for effective ratiometric bioimaging of intracellular endogenous adenosine triphosphate

Two-photon fluorescence imaging is one of the most attractive imaging techniques for monitoring important biomolecules in the biomedical field due to its advantages of low light scattering, high penetration depth, and suppressed photodamage/phototoxicity under near-infrared excitation. However, in actual biological imaging, organic two-photon fluorescent dyes have disadvantages such as high biological toxicity and their fluorescence efficiency is easily affected by the complex environment in organisms. In this study, a novel nanoprobe platform with two-photon dye-doped silica nanoparticles was developed for FRET-based ratiometric biosensing and bioimaging, with endogenous ATP chosen as the target for detection. The nanoprobe has three components: (1) a two-photon dye-doped silica nanoparticle core, which serves as an energy donor for FRET; (2) amino-modified hairpin primers with carboxy fluorescein as an energy acceptor for FRET; (3) an aptamer acting as a recognition unit to realize the probing function. The nanoprobe showed ratiometric fluorescence responses for ATP detection with high sensitivity and high selectivity in vivo. Moreover, the nanoprobe showed satisfactory ratiometric two-photon fluorescence imaging of endogenous ATP in living cells and tissues (penetration depth of 190 nm). These results indicated that novel two-photon silica nanoparticles can be constructed by doping a two-photon fluorescent dye into silica nanoparticles, and they can effectively solve the disadvantages of two-photon fluorescent dyes. These excellent performances indicate that this novel nanoprobe platform will become a very valuable molecular imaging tool, which can be widely used in the biomedical field for drug screening and disease diagnosis and other related research.

Ratiometric fluorescent detection and imaging of microRNA in living cells with manganese dioxide nanosheet-active DNAzyme

MicroRNAs (miRNAs) play an important role in multiple biological processes and can be used as biomarkers for clinical disease diagnosis, so their detection is of great importance. Here, manganese dioxide (MnO₂) nanosheet acts as carrier to deliver DNAzyme probes into cells through endocytosis, where intracellular glutathione (GSH) reduces the MnO₂ nanosheet to manganese ions (Mn²⁺) and releases the probes. The generated Mn²⁺ can be further used as an effective cofactor to activate the DNAzyme probe, and cleave the DNA strand into two fragments. Then, the miRNA-155 in the cells can hybridize with the cleaved fragment to cause the fluorescence signal change of the probe. The proposed proportional fluorescent method has been applied to the imaging of miRNA-155 in HeLa cells and HepG2 cells with the estimated detection limit (LOD) as 1.6 × 10^-12 M. The new method can provide great help for cancer diagnosis and biological research related to miRNA.

Hybrid Nanosystems for Biomedical Applications

Inorganic/organic hybrid nanosystems have been increasingly developed for their versatility and efficacy at overcoming obstacles not readily surmounted by nonhybridized counterparts. Currently, hybrid nanosystems are implemented for gene therapy, drug delivery, and phototherapy in addition to tissue regeneration, vaccines, antibacterials, biomolecule detection, imaging probes, and theranostics. Though diverse, these nanosystems can be classified according to foundational inorganic/organic components, accessory moieties, and architecture of hybridization. Within this Review, we begin by providing a historical context for the development of biomedical hybrid nanosystems before describing the properties, synthesis, and characterization of their component building blocks. Afterward, we introduce the architectures of hybridization and highlight recent biomedical nanosystem developments by area of application, emphasizing hybrids of distinctive utility and innovation. Finally, we draw attention to ongoing clinical trials before recapping our discussion of hybrid nanosystems and providing a perspective on the future of the field.

Individual Plasmonic Nanoprobes for Biosensing and Bioimaging: Recent Advances and Perspectives

With the advent of nanofabrication techniques, plasmonic nanoparticles (PNPs) have been widely applied in various research fields ranging from photocatalysis to chemical and bio-sensing. PNPs efficiently convert chemical or physical stimuli in their local environment into optical signals. PNPs also have excellent properties, including good biocompatibility, large surfaces for the attachment of biomolecules, tunable optical properties, strong and stable scattering light, and good conductivity. Thus, single optical biosensors with plasmonic properties enable a broad range of uses of optical imaging techniques in biological sensing and imaging with high spatial and temporal resolution. This work provides a comprehensive overview on the optical properties of single PNPs, the description of five types of commonly used optical imaging techniques, including surface plasmon resonance (SPR) microscopy, surface-enhanced Raman scattering (SERS) technique, differential interference contrast (DIC) microscopy, total internal reflection scattering (TIRS) microscopy, and dark-field microscopy (DFM) technique, with an emphasis on their single plasmonic nanoprobes and mechanisms for applications in biological imaging and sensing, as well as the challenges and future trends of these fields.

Fluorescent-Raman Binary Star Ratio Probe for MicroRNA Detection and Imaging in Living Cells

The expression of microRNAs (miRNAs) is critical in gene regulation and has been counted into disease diagnosis marks. Precise imaging and quantification of miRNAs could afford the important information for clinical diagnosis. Here, two smart binary star ratio (BSR) probes were designed and constructed, and miRNA triggered the connection of the binary star probes and the reciprocal changes of dual signals in living cells. This multifunctional probe integrates fluorescence and surface enhanced Raman scattering (SERS) imaging, with enzyme-free numerator signal amplification for dual-mode imaging and dual-signal quantitative analysis of miRNA. First, compared with the single-mode ratio imaging method, using fluorescence-SERS complementary ratio imaging, this probe enables more accurate imaging contrast for direct visualization signal changes in living cells. Multiscale information about the dynamic behavior of miRNA and the probe is acquired. Next, via SERS reverse signal ratio response and a novel enzyme-free numerator signal amplification, the amplified signal and reduced black value were achieved in the quantification of miRNA. More importantly, BSR probes showed good stability in cells and were successfully used for accurate tracing and quantification of miR-203 from MCF-7 cells. Therefore, the reported BSR probe is a potential tool for the reliable monitoring of biomolecule dynamics in living cells.

DSN/TdT recycling digestion based cyclic amplification strategy for microRNA assay

Sensitive and specific detection of microRNAs (miRNAs) is of great significance for early cancer diagnosis. Here we report a simple and sensitive fluorescence signal amplification strategy that based on DSN/TdT recycling digestion for miRNA detection. DSN initiates DNA digestion on 3'-phosphate-primer/miRNA heteroduplex which causes miRNA recycle. The digested DNA strands with 3'-OH ends enable TdT to synthesize a polydeoxyguanylic tails on the 3'-end. The DNAs with polydeoxyguanylic tails are converted to double-stranded-DNA prior to initiation of DSN/TdT recycling digestion. With the cooperation of TdT and DSN, a new round of digestion and extension is triggered, leading to massive fluorophores separating and signal amplification. The amplification strategy produces large amounts of 3'-OH probes that can be used directly for dsDNA enrichment and DSN digestion. Moreover, both DSN digestion and TdT extension are sequence-independent reaction without the need of complex sequences design. In addition, this strategy is utilized to analyze miRNA samples from MCF-7 cell lysates and Cu (II) ion samples, indicating its potential application in actual sample analysis. The method shows a promising analytical platform for DNA nicking-related studies and tumor biomarkers measuring in clinical diagnostics.

DNA Walking and Rolling Nanomachine for Electrochemical Detection of miRNA

miRNAs, a class of endogenous noncoding RNAs, are involved in many crucial biological processes, which have emerged as a new set of biomarkers for disease theranostics. Exploring efficient signal amplification strategy is highly desired to pursue a highly sensitive miRNA biosensing platform. DNA nanotechnology shows great promise in the fabrication of amplified miRNA biosensors. In this work, a novel DNA walking and rolling nanomachine is developed for highly sensitive and selective detection of miRNA. Particularly, this approach programs two forms of dynamic DNA nanomachines powered by corresponding enzymes, which are well integrated. It is able to achieve a limit of detection as low as 39 × 10^-18 m, along with excellent anti-interfering performance and clinical applications. In addition, by designing pH-controlled detachable intermolecular DNA triplex, the main sensing elements can be conveniently reset, which fulfills the requirements of point-of-care profiling of miRNA. The high consistency between the proposed approach and quantitative real-time polymerase chain reaction validates the robustness and reliability. Therefore, it is anticipated that the DNA walking and rolling nanomachine has attractive application prospects in miRNA assay for biological researches and clinical diagnosis.

Sensitive detection of intracellular telomerase activity via double signal amplification and ratiometric fluorescence resonance energy transfer

As an important and universal tumor marker, the reliable and in situ detection of intracellular telomerase activity is crucial for cancer diagnosis. Herein, a ratiometric fluorescence resonance energy transfer (FRET) method was developed for detecting intracellular telomerase activity. It takes full advantage of manganese dioxide nanosheets (MnO2NS) that can carry DNA probes with different conformations into cells and then completely release the DNA probes via decomposition of MnO2NS by intracellular reduced glutathione (GSH). In the presence of telomerase, a telomere substrate (TS) could be extended to form long telomerase extension products (TEPs), which trigger the cycling strand displacement reaction (SDR) between two fluorophore-labeled hairpin DNA probes to form lots of DNA duplexes. The close contact of two fluorophores led to an effective ratiometric FRET for reliable detection of telomerase activity. Fluorescence confocal imaging demonstrated that the activity of telomerase in tumor cells was reliably detected. The inhibition of telomerase activity by an inhibitor resulted in a decrease in FRET signal. For extracellular detection, the FRET ratio (FA/FD) shows a good linear relationship with the number of HeLa cells in the range of 20-1000 cells. Therefore, it offers a more facile method for reliable and sensitive detection of intracellular telomerase activity.

Facile Strategy To Enhance Specificity and Sensitivity of Molecular Beacons by an Aptamer-Functionalized Delivery Vector

To enhance the specificity and sensitivity of molecular beacons (MBs) in detecting mRNA in living tumor cells, we introduced an aptamer (AS1411) to the delivery system of MBs to form an aptamer-decorated nanoprobe (ANP), which was prepared through self-assembly between AS1411-conjugated carboxymethyl chitosan (ACMC) with protamine sulfate (PS)/CaCO₃/MB cores. Owing to the specific binding of AS1411 to nucleolin, which is overexpressed in tumor cell membranes and nuclei, an AS1411-decorated MB-delivery system leads to dramatically increased cell uptake of MBs for probing survivin mRNA and thus induces strong intracellular fluorescence emission in targeted tumorous cells and cell nuclei. Furthermore, we demonstrate that ANP can efficiently detect survivin mRNA in mitochondria. In other words, the effective delivery of MBs ensures the precise detection of mRNA distribution in diverse organelles. In addition, we evaluated the efficiency of ANP in probing tumor cells in simulated blood as well as in peripheral blood from a healthy donor and found that the nanoprobe can specifically deliver MBs to tumor cells and identify tumor cells in blood. The targeting delivery system we constructed holds promising applications in precise detection of subcellular distribution of mRNA in living tumor cells as well as in fluorescence-guided cancer detection in liquid biopsy technology. This study provides a facile strategy to effectively improve the specificity and sensitivity of conventional molecular beacons.

Multifunctional Fe3O4@Polydopamine@DNA-Fueled Molecular Machine for Magnetically Targeted Intracellular Zn2+ Imaging and Fluorescence/MRI Guided Photodynamic-Photothermal Therapy

For the precise treatment of tumors, it is necessary to develop a theranostic nanoplatform that has both diagnostic and therapeutic functions. In this article, we designed a new theranostic probe for fluorescence imaging of Zn²⁺ and fluorescence/MRI guided magnetically targeted photodynamic-photothermal therapy. The fluorescence imaging of Zn²⁺ was based on an endogenous ATP-driven DNA nanomachine that could perform repetitive stand displacement reaction. It modifies all units on a single PDA/Fe₃O₄ nanoparticle containing a hairpin-locked initiated strand activated by a target molecule in cells, a two-stranded fuel DNA triggered by ATP, and a two-stranded DNA track responding to an initiated strand and fuel DNA. After entering the cell, the intracellular target Zn²⁺ initiates the nanomachine via an autocatalytic cleavage reaction, and the machine programmatically and gradually runs on the assembled DNA track via fuel DNA driving and the intramolecular toehold-mediated stand displacement reaction. The Fe₃O₄ core first exhibits magnetic targeting, increasing the ability of nanoparticles to enter tumor cells at the tumor site. The Fe₃O₄ could also be employed as a powerful magnetic resonance imaging (MRI) contrast agent and guided therapy. Using 808 nm laser and 635 nm laser irradiation together at the tumor site, the PDA nanoshell produced an excellent photothermal effect and the TMPyP4 molecules entering the cell generated reactive oxygen species, followed by cell damage. A series of reliable experiments suggested that the Fe₃O₄@PDA@DNA nanoprobe showed superior fluorescence specificity, MRI, a remarkable photothermal/photodynamic therapy effect, and favorable biocompatibility. This theranostic nanoplatform offered a split-new insight into tumor fluorescence and MRI diagnosis as well as effective tumor therapy.

A Dual-Signal Twinkling Probe for Fluorescence-SERS Dual Spectrum Imaging and Detection of miRNA in Single Living Cell via Absolute Value Coupling of Reciprocal Signals

Imaging and detecting microRNAs (miRNAs) is of central importance in tumor cell analysis. It stays challenging to establish simple, accurate, and sensitive analytical assays for imaging and detection of miRNA in a single living cell, because of intracellular complex environment and miRNA sequence similarity. Herein, we designed a dual-signal twinkling probe (DSTP) with triplex-stem structure which employed a fluorescence-SERS signal reciprocal switch. The spatiotemporal dynamics of the miRNA molecular and intracellular uptake of the probe are monitored by fluorescence-SERS signal switch of the DSTP. Meanwhile, using the surface-enhanced Raman scattering (SERS) signals of DSTP, the measure of absolute value coupling of reciprocal signals is first used to real-time detection of miRNA. Through simultaneous enhancing the target response signal value and reducing blank value, this work deducted the background effect, and showed high sensitivity and reproducibility. Moreover, the probe shows excellent reversibility and specificity in real quantitative detection of intracellular miRNA. miR-203 was successfully monitored in MCF-7, in accord with the results in vitro as well as in cell lysates. We anticipate that this new dual-signal twinkling and dual-spectrum switch method will be generally useful to image and detect various types of biomolecules in single living cell.

Prussian blue-modified ferritin nanoparticles for effective tumor chemo-photothermal combination therapy via enhancing reactive oxygen species production

To realize the photothermal therapy ability of Prussian blue-modified ferritin nanoparticles (PB-Ft NPs) and its synergistic effect with chemotherapy, PB-Ft NPs were synthesized by a simple surface double decomposition reaction. Mean sizes of ferritin and PB-Ft NPs were 10.4 nm and 12.6 nm, respectively. The obtained PB-Ft NPs were verified to have both the photothermal conversion ability of Prussian blue and the morphology of ferritin. The in vitro and in vivo photothermal therapy results confirm PB-Ft NPs can successfully inhibit the growth of murine breast cancer cell line (4T1) without any obvious side effect. Moreover, taking use of the peroxidase-like activity of PB-Ft NPs, the photothermal therapy effect of PB-Ft NPs effectively improved the curative effect of gemcitabine (GEM) via enhancing reactive oxygen species production. The obtained PB-Ft NPs can be served as a useful and safe photothermal therapy agent in breast cancer. Moreover, PB-Ft NPs-assisted photothermal therapy can be applied as an adjunctive therapy with various established cancer treatments such as chemotherapy.

A DNA encoding loop program: the snowball effect enhanced microRNA visualization in living cells

A DNA encoding loop program (DELP); an Illustration of the DELP clustering process. In the presence of miRNA, multiple seed probes and fuel probes form enlarged GNP clusters, and the fluorescence of the FAM molecules recovers due to the opening of the hairpin DNA.

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.

Dynamic Single Molecular Rulers: Toward Quantitative Detection of MicroRNA-21 in Living Cells

Innovative techniques to measure microRNA (miRNA) in vivo could greatly improve the fundamental understanding of complex cellular processes. Herein, we report a novel method for real-time, quantitative miRNA detection inside living cells based on core-satellite plasmon rulers (PRs). This approach allows for the statistical analysis of single hybridization event caused by target miRNA. We investigated hundreds of satellite leaving events and found that the distribution of the time range for one strand displacement event is miRNA concentration-dependent, which obeyed Poisson statistics. Probing several such PRs under dark-field microscopy would provide precise determination of miRNA in vitro and in living cells, without photobleaching or blinking of the fluorophores. We believe the simple and practical approach on the basis of dynamic PRs with single-molecule sensitivity combined with statistical analysis hold promising potential to visualize native nucleic acids with short sequence and low-abundance.

Construction of a Cytosine-Adjusted Electrochemiluminescence Resonance Energy Transfer System for MicroRNA Detection

The cytosines in cluster-nucleation sequences play a vital role in the formation of silver nanoclusters (Ag NCs). Here, an innovative electrochemiluminescence (ECL) resonance energy transfer (RET) sensing system was developed using CdS quantum dots (QDs) as ECL donor and Ag NCs as ECL acceptor. Modulation of the number of cytosines in the cluster-nucleation sequences allowed tuning of Ag NCs absorption bands to match with the ECL emission spectrum of CdS QDs, yielding effective ECL-RET. The sensitivity of detection was improved by dual-target recycling amplification based on duplex-specific nuclease (DSN) and catalytic hairpin assembly. In the presence of target microRNA-21 (miRNA-21), DSN selectively cleaved the complementary DNA section (S1), resulting in the release of the transduction section (S2) and the reuse of miRNA-21 in the next recycling amplification. Interaction of the stem-loop structure of the DNA1 segment (H1) on CdS QDs-modified electrode with S2 led to the opening of the hairpin structure of H1 and the formation of H1:S2 duplex. Then, hairpin DNA2 encapsulated Ag NCs hybridized with the remaining single-stranded DNA segment of H1, and the S2 strand was replaced. Finally, the dissociated S2 participated in subsequent reaction cycles, introducing Ag NCs to the electrode surface and leading to ECL signal quenching of the CdS QDs. The proposed sensor showed excellent performance in detecting miRNA-21 at a wide linear range from 1 fM to 100 pM. The practical application ability of the strategy was tested in HeLa cells with acceptable results, suggesting that the detection platform is a promising approach for disease diagnosis and molecular biology research.

Exploration of the Kinetics of Toehold-Mediated Strand Displacement via Plasmon Rulers

DNA/RNA strand displacement is one of the most fundamental reactions in DNA and RNA circuits and nanomachines. In this work, we reported an exploration of the dynamic process of the toehold-mediated strand displacement via core-satellite plasmon rulers at the single-molecule level. Applying plasmon rulers with unlimited lifetime, single-strand displacement triggered by the invader that resulted in stepwise leaving of satellite from the core was continuously monitored by changes of scattering signal for hours. The kinetics of strand displacement in vitro with three different toehold lengths have been investigated. Also, the study revealed the difference in the kinetics of strand displacement between DNA/RNA and DNA/DNA duplexes. For the kinetics study in vivo, influence from the surrounding medium has been evaluated using both phosphate buffer and cell lysate. Applying core-satellite plasmon rulers with high signal/noise ratio, kinetics study in living cells proceeded for the first time, which was not possible by conventional methods with a fluorescent reporter. The plasmon rulers, which are flexible, easily constructed, and robust, have proven to be effective tools in exploring the dynamical behaviors of biochemical reactions in vivo.

MoS2 quantum dots modified with a labeled molecular beacon as a ratiometric fluorescent gene probe for FRET based detection and imaging of microRNA

A dual-channel ratiometric nanoprobe is described for detection and imaging of microRNA. It was prepared from MoS₂ quantum dots (QDs; with blue emission and excitation/emission peaks at 310/398 nm) which acts as both the gene carrier and as a donor in fluorescence resonance energy transfer (FRET). Molecular beacons containing loops for molecular recognition of microRNA and labeled with carboxyfluorescein (FAM) were covalently attached to the MoS₂ QDs and serve as the FRET acceptor. In the absence of microRNA, the nanoprobe exhibits low FRET efficiency due to the close distance between the FAM tag and the QDs. Hybridization with microRNA enlarges the distance between QD and beacon. This results in an enhancement of the FRET efficiency of the nanoprobe. The ratio of green and blue fluorescence (I₅₂₀/I₃₉₈) increases linearly in the 5 to 150 nM microRNA concentration range in both aqueous solution and diluted artificial cerebrospinal fluid. The limit of detection (LOD) is as low as 0.38 nM and 0.52 nM, respectively. Other features of this nanoprobe include (a) excellent resistance to nuclease-induced false positive signals and (b) the option to use it for distinguishing different cell lines by in-situ imaging of intracellular microRNAs. Graphical abstract Schematic of a dual-channel photoluminescence nanoprobe for the determination of microRNA-21 (miR-21) by monitoring the microRNA-triggered enhancement of the fluorescence resonance energy transfer (FRET) efficiency between MoS₂ QDs and carboxyfluorescein-labeled molecular beacons.

Recent progress in live cell mRNA/microRNA imaging probes based on smart and versatile nanomaterials

We summarize the recent progress in live cell mRNA/miRNA imaging probes based on various versatile nanomaterials, describing their structures and their working principles of bio-imaging applications.

DNAzyme Based Nanomachine for in Situ Detection of MicroRNA in Living Cells

The capability of in situ detection of microRNA in living cells with signal amplification strategy is of fundamental importance, and it will open up a new opportunity in development of diagnosis and prognosis of many diseases. Herein we report a swing DNA nanomachine for intracellular microRNA detection. The surfaces of Au nanoparticles (NPs) are modified by two hairpin DNA. We observe that one DNA (MB2) will open its hairpin structure upon partial hybridization with target miR-21 after entering into cells, and the other part of its hairpin structure could further react with the other hairpin DNA (MB1) to form a Zn²⁺-specific DNAzyme. This results in the disruption of MB1 through shearing action and the release of fluorescein Cy5. To provide an intelligent DNA nanomachine, MB2 is available again with the shearing action to bind with MB1, which provides effective signal amplification. This target-responsive, DNA nanomachine-based method showed a detection limit of 0.1 nM in vitro, and this approach could be an important step toward intracellular amplified detection and imaging of various analytes in living cells.

Ratiometric electrochemical assay for sensitive detecting microRNA based on dual-amplification mechanism of duplex-specific nuclease and hybridization chain reaction

We propose a ratiometric electrochemical assay for detecting microRNA (miRNA) on the basis of dual-amplification mechanism by using distinguishable electrochemical signals from thionine (Thi) and ferrocene (Fc). The thiol-modified and ferrocene-labeled hairpin capture probes (CP) are first immobilized on an Au electrode via Au-S reaction. The target miRNA hybridizes with CP and unfolding the hairpin structure of CP to form miRNA-DNA duplexes. Then, kamchatka crab duplex specific nuclease (DSN) specifically cleaves the DNA in miRNA-DNA duplexes, leading to the release of miRNA and another cleaves cycle, meanwhile, numerous Fc leaves away from the electrode surface and leads to the signal-off of Fc. The residual fragment on electrode surface acts as a HCR primer to form dsDNA polymers through in situ HCR with the presence of the primer and two probes (HDNA and HDNA'), resulting in the capture of numerous DNA/Au NPs/Thi and the signal-on of Thi. The dual-amplification mechanism significantly amplifies the decrease of Fc signal and the increase of Thi signal for ratiometric readout (I_Thi/I_Fc), thus providing a sensitive method for the selective detection of miR-141 with a detection limit down to 11aM. The dual-signal ratiometric outputs have an intrinsic self-calibration to the effects from system, which is promising to be applied in biosensing and clinical diagnosis.

Electro-Grafted Electrode with Graphene-Oxide-Like DNA Affinity for Ratiometric Homogeneous Electrochemical Biosensing of MicroRNA

This work demonstrated for the first time a simple and rapid approach to endow the electrode with the excellent discrimination ability over single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) through the robust electrochemical grafting of in situ generated 1-naphthalenesulfonate (NS^-) diazonium salt onto the surface of indium tin oxide (ITO) electrode. On the basis of understanding the influence of sequence and length on the binding affinity of ssDNA and dsDNA toward NS^- grafted ITO (NS^--ITO) electrode, these interesting findings were successfully employed to rationally develop a ratiometric homogeneous electrochemical biosensing platform for microRNA based on the affinity-mediated signal transduction. The achievement of ultrasensitive detection of microRNA lies in a compatibly designed T7 exonuclease-assisted isothermal amplification strategy, in which the presence of target microRNA initiated the continual and opposite affinity inversion of two rationally engineered electrochemical signal reporters, methylene blue (MB) labeled hairpin reporter and ferrocene (Fc) labeled dsDNA reporter, toward NS^--ITO electrode, thereby providing the ratiometric transduction and amplification of the homogeneous electrochemical output signal. By measuring the distinct variation in the peak current intensity ratios of Fc and MB tags, this ratiometric homogeneous electrochemical microRNA biosensing platform showed a detection limit of 25 aM, which is much lower than that of the reported homogeneous electrochemical biosensors. Therefore, we envision that the proposed approach will find useful applications in disease molecular diagnoses and biomedicine.

A DNA-Fueled and Catalytic Molecule Machine Lights Up Trace Under-Expressed MicroRNAs in Living Cells

The detection of specific intracellular microRNAs (miRNAs) in living cells can potentially provide insight into the causal mechanism of cancer metastasis and invasion. However, because of the characteristic nature of miRNAs in terms of small sizes, low abundance, and similarity among family members, it is a great challenge to monitor miRNAs in living cells, especially those with much lower expression levels. In this work, we describe the establishment of a DNA-fueled and catalytic molecule machinery in cell signal amplification approach for monitoring trace and under-expressed miRNAs in living cells. The presence of the target miRNA releases the hairpin sequences from the dsDNA (containing the fluorescence resonance energy transfer (FRET) pair-labeled and unfolded hairpin sequences)-conjugated gold nanoparticles (dsDNA-AuNPs), and the DNA fuel strands assist the recycling of the target miRNA sequences via two cascaded strand displacement reactions, leading to the operation of the molecular machine in a catalytic fashion and the release of many hairpin sequences. As a result, the liberated hairpin sequences restore the folded hairpin structures and bring the FRET pair into close proximity to generate significantly amplified signals for detecting trace miRNA targets. Besides, the dsDNA-AuNP nanoprobes have good nuclease stability and show low cytotoxicity to cells, and the application of such a molecular system for monitoring trace and under-expressed miRNAs in living cells has also been demonstrated. With the advantages of in cell signal amplification and reduced background noise, the developed method thus offers new opportunities for detecting various trace intracellular miRNA species.

Simultaneously electrochemical detection of microRNAs based on multifunctional magnetic nanoparticles probe coupling with hybridization chain reaction

We report a sensor combining two distinguishable magnetic nanoprobes (DNA1/Fe₃O₄ NPs/Thi and DNA2/Fe₃O₄ NPs/Fc) with target-triggered hybridization chain reaction (HCR) strategy for the simultaneous detection of microRNA-141 (miR-141) and microRNA-21 (miR-21). In the presence of targets, the thiol-modified hairpin capture probes (HCP1 and HCP2) specifically hybridize with miR-141 and miR-21 on a gold electrode, leading to the conformation change of HCP1 and HCP2, respectively. The conformation change subsequently triggers HCR to generate plentiful bonding sequences of magnetic nanoprobes. Thus, numerous thionine (Thi) modified DNA1/Fe₃O₄ NPs/Thi and ferrocene carboxaldehyde (Fc-CHO) modified DNA2/Fe₃O₄ NPs/Fc are captured by the well-designed HCR, via DNA hybridization respectively, giving rise to the dual magnified response of currents. The increase in the electrochemical currents at different potentials of the two magnetic nanoprobes enables us to simultaneously and quantitatively detect miR-141 and miR-21. Target-triggered HCR increases the amount of captured nanoprobes due to the increasing number of bonding sequences, greatly amplifying the currents of the two magnetic nanoprobes in the presence of targets, and ultimately realizing the dual signal amplification with increased sensitivity. The sensor can be applied for detecting miRNAs in cell lysates, thus, promising to be a clinic diagnosis of cancers by means of simultaneous detection of a variety of miRNA biomarkers.

Cancer-Associated, Stimuli-Driven, Turn on Theranostics for Multimodality Imaging and Therapy

Advances in bioinformatics, genomics, proteomics, and metabolomics have facilitated the development of novel anticancer agents that have decreased side effects and increased safety. Theranostics, systems that have combined therapeutic effects and diagnostic capabilities, have garnered increasing attention recently because of their potential use in personalized medicine, including cancer-targeting treatments for patients. One interesting approach to achieving this potential involves the development of cancer-associated, stimuli-driven, turn on theranostics. Multicomponent constructs of this type would have the capability of selectively delivering therapeutic reagents into cancer cells or tumor tissues while simultaneously generating unique signals that can be readily monitored under both in vitro and in vivo conditions. Specifically, their combined anticancer activities and selective visual signal respond to cancer-associated stimuli, would make these theranostic agents more highly efficient and specific for cancer treatment and diagnosis. This article focuses on the progress of stimuli-responsive turn on theranostics that activate diagnostic signals and release therapeutic reagents in response to the cancer-associated stimuli. The present article not only provides the fundamental backgrounds of diagnostic and therapeutic tools that have been widely utilized for developing theranostic agents, but also discusses the current approaches for developing stimuli-responsive turn on theranostics.

Nanoparticles as Theranostic Vehicles in Experimental and Clinical Applications-Focus on Prostate and Breast Cancer

Prostate and breast cancer are the second most and most commonly diagnosed cancer in men and women worldwide, respectively. The American Cancer Society estimates that during 2016 in the USA around 430,000 individuals were diagnosed with one of these two types of cancers, and approximately 15% of them will die from the disease. In Europe, the rate of incidences and deaths are similar to those in the USA. Several different more or less successful diagnostic and therapeutic approaches have been developed and evaluated in order to tackle this issue and thereby decrease the death rates. By using nanoparticles as vehicles carrying both diagnostic and therapeutic molecular entities, individualized targeted theranostic nanomedicine has emerged as a promising option to increase the sensitivity and the specificity during diagnosis, as well as the likelihood of survival or prolonged survival after therapy. This article presents and discusses important and promising different kinds of nanoparticles, as well as imaging and therapy options, suitable for theranostic applications. The presentation of different nanoparticles and theranostic applications is quite general, but there is a special focus on prostate cancer. Some references and aspects regarding breast cancer are however also presented and discussed. Finally, the prostate cancer case is presented in more detail regarding diagnosis, staging, recurrence, metastases, and treatment options available today, followed by possible ways to move forward applying theranostics for both prostate and breast cancer based on promising experiments performed until today.

Fluorescence and SERS Imaging for the Simultaneous Absolute Quantification of Multiple miRNAs in Living Cells

The simultaneous imaging and quantification of multiple intracellular microRNAs (miRNAs) are particularly desirable for the early diagnosis of cancers. However, simultaneous direct imaging with absolute quantification of multiple intracellular RNAs remains a great challenge, particularly for miRNAs, which have significantly different expression levels in living cells. We designed dual-signal switchable (DSS) nanoprobes using the fluorescence-Raman signal switch. The intracellular uptake and dynamic behaviors of the probe are monitored by its fluorescence signal. Meanwhile, real-time quantitative detection of multiple miRNAs is made possible by measurements of the surface-enhanced Raman spectroscopy (SERS) ratios. Moreover, the signal 1:n ratio amplification mode only responds to low-abundance miRNA (asymmetric signal amplification mode) for simultaneous visualization and quantitative detection of significantly different levels of miRNAs in living cells. miR-21 and miR-203 were successfully detected in living MCF-7 cells, in agreement with in vitro results from the same batch of cell lysates. The reported dual-spectrum imaging method promises to offer a new strategy for the intracellular imaging and detection of various types of biomolecules.

Nano Endoscopy with Plasmon-Enhanced Fluorescence for Sensitive Sensing Inside Ultrasmall Volume Samples

Plasmon-enhanced fluorescence (PEF) generally requires the samples settled on a metal substrate and the effective enhancement distance is less than 100 nm, which limit its application in intracellular sensing. Herein, we report a nano endoscopy with PEF effect for sensing analytes inside the extremely small volume samples. The nano endoscopy was fabricated by assembling single nanoporous gold nanowire (PGNW) on the tip of a tungsten needle. It was accurately manipulated to insert into a micro droplet, and an effective sensing was realized at micrometre scale with submicrometer resolution. By taking lysozyme as a model sensing target, a 23-fold improvement of sensitivity was obtained, comparing with that of smooth gold nanowire (SGNW). These results indicated that the nano endoscopy can realize a high spatial resolution sensing, showing its potential application in intracellular sensing.