Multiplex microRNA imaging in living cells using DNA-capped-Au assembled hydrogels

DNA Hydrogels for Cancer Diagnosis and Therapy

Nucleic acids, because of their precise pairing and simple composition, have emerged as excellent materials for the formation of gels. The application of DNA hydrogels in the diagnosis and therapy of cancer has expanded significantly through research on the properties and functions of nucleic acids. Functional nucleic acids (FNAs) such as aptamers, Small interfering RNA (siRNA), and DNAzymes have been incorporated into DNA hydrogels to enhance their diagnostic and therapeutic capabilities. This review discusses various methods for forming DNA hydrogels, with a focus on pure DNA hydrogels. We then explore the innovative applications of DNA hydrogels in cancer diagnosis and therapy. DNA hydrogels have become essential biomedical materials, and this review provides an overview of current research findings and the status of DNA hydrogels in the diagnosis and therapy of cancer, while also exploring future research directions.

A cancer-targeted glutathione-gated probe for self-sufficient ST/CDT combination therapy and FRET-based miRNA imaging

A cancer-targeted glutathione (GSH)-gated theranostic probe (CGT probe) for intracellular miRNA imaging and combined treatment of self-sufficient starvation therapy (ST) and chemodynamic therapy (CDT) was developed. The CGT probe is constructed using MnO2 nanosheet (MS) as carrier material to adsorb the elaborately designed functional DNAs. It can be internalized by cancer cells via specific recognition between the AS1411 aptamer and nucleolin. After CGT probe entering the cancer cells, the overexpressed GSH, as gate-control, can degrade MS to Mn2+ which can be used for CDT by Fenton-like reaction. Simultaneously, Mn2+-mediated CDT can further cascade with the enzyme-like activities (catalase-like activity and glucose oxidase-like activity) of CGT probe, achieving self-sufficient ST/CDT synergistic therapy. Meanwhile, the anchored DNAs are released, achieving in situ signal amplification via disubstituted-catalytic hairpin assembly (DCHA) and FRET (fluorescence resonance energy transfer) imaging of miR-21. The in vitro and in vivo experiments demonstrated that accurate and sensitive miRNA detection can be achieved using the CGT probe. Overall, the ingenious CGT probe opens a new avenue for the development of early clinical diagnosis and cancer therapy.

An acid-responsive DNA hydrogel-mediated cascaded enzymatic nucleic acid amplification system for the sensitive imaging of alkaline phosphatase in living cells

Alkaline phosphatase (ALP) is a class of hydrolase that catalyzes the dephosphorylation of phosphorylated species in biological tissues, playing an important role in many physiological and pathological processes. Sensitive imaging of ALP activity in living cells is contributory to the research on these processes. Herein, we propose an acid-responsive DNA hydrogel to deliver a cascaded enzymatic nucleic acid amplification system into cells for the sensitive imaging of intracellular ALP activity. The DNA hydrogel is formed by two kinds of Y-shaped DNA monomers and acid-responsive cytosine-rich linkers. The amplification system contained Bst DNA polymerase (Bst DP), Nt.BbvCI endonuclease, a Recognition Probe (RP, containing a DNAzyme sequence, a Nt.BbvCI recognition sequence, and a phosphate group at the 3'-end), and a Signal Probe (SP, containing a cleavage site for DNAzyme, Cy3 and BHQ2 at the two ends). The amplification system was trapped into the DNA hydrogel and taken up by cells, and the cytosine-rich linkers folded into a quadruplex i-motif in the acidic lysosomes, leading to the collapse of the hydrogel and releasing the amplification system. The phosphate groups on RPs were recognized and removed by the target ALP, triggering a polymerization-nicking cycle to produce large numbers of DNAzyme sequences, which then cleaved multiple SPs, restoring Cy3 fluorescence to indicate the ALP activity. This strategy achieved sensitive imaging of ALP in living HeLa, MCF-7, and NCM460 cells, and realized the sensitive detection of ALP in vitro with a detection limit of 2.0 × 10-5 U mL-1, providing a potential tool for the research of ALP-related physiological and pathological processes.

A review of DNA nanoparticles-encapsulated drug/gene/protein for advanced controlled drug release: Current status and future perspective over emerging therapy approaches

In the last ten years, the field of nanomedicine has experienced significant progress in creating novel drug delivery systems (DDSs). An effective strategy involves employing DNA nanoparticles (NPs) as carriers to encapsulate drugs, genes, or proteins, facilitating regulated drug release. This abstract examines the utilization of DNA NPs and their potential applications in strategies for controlled drug release. Researchers have utilized the distinctive characteristics of DNA molecules, including their ability to self-assemble and their compatibility with living organisms, to create NPs specifically for the purpose of delivering drugs. The DNA NPs possess numerous benefits compared to conventional drug carriers, such as exceptional stability, adjustable dimensions and structure, and convenient customization. Researchers have successfully achieved a highly efficient encapsulation of different therapeutic agents by carefully designing their structure and composition. This advancement enables precise and targeted delivery of drugs. The incorporation of drugs, genes, or proteins into DNA NPs provides notable advantages in terms of augmenting therapeutic effectiveness while reducing adverse effects. DNA NPs serve as a protective barrier for the enclosed payloads, preventing their degradation and extending their duration in the body. The protective effect is especially vital for delicate biologics, such as proteins or gene-based therapies that could otherwise be vulnerable to enzymatic degradation or quick elimination. Moreover, the surface of DNA NPs can be altered to facilitate specific targeting towards particular tissues or cells, thereby augmenting the accuracy of delivery. A significant benefit of DNA NPs is their capacity to regulate the kinetics of drug release. Through the manipulation of the DNA NPs structure, scientists can regulate the rate at which the enclosed cargo is released, enabling a prolonged and regulated dispensation of medication. This control is crucial for medications with limited therapeutic ranges or those necessitating uninterrupted administration to attain optimal therapeutic results. In addition, DNA NPs have the ability to react to external factors, including alterations in temperature, pH, or light, which can initiate the release of the payload at precise locations or moments. This feature enhances the precision of drug release control. The potential uses of DNA NPs in the controlled release of medicines are extensive. The NPs have the ability to transport various therapeutic substances, for example, drugs, peptides, NAs (NAs), and proteins. They exhibit potential for the therapeutic management of diverse ailments, including cancer, genetic disorders, and infectious diseases. In addition, DNA NPs can be employed for targeted drug delivery, traversing biological barriers, and surpassing the constraints of conventional drug administration methods.

Intracellular MicroRNA Imaging and Specific Discrimination of Prostate Cancer Circulating Tumor Cells Using Multifunctional Gold Nanoprobe-Based Thermophoretic Assay

Circulating tumor cells (CTCs) have emerged as powerful biomarkers for diagnosis of prostate cancer. However, the effective identification and concurrently accurate imaging of CTCs for early screening of prostate cancer have been rarely explored. Herein, we reported a multifunctional gold nanoprobe-based thermophoretic assay for simultaneous specific distinguishing of prostate cancer CTCs and sensitive imaging of intracellular microRNA (miR-21), achieving the rapid and precise detection of prostate cancer. The multifunctional gold nanoprobe (GNP-DNA/Ab) was modified by two types of prostate-specific antibodies, anti-PSMA and anti-EpCAM, which could effectively recognize the targeting CTCs, and meanwhile linked double-stranded DNA for further visually imaging intracellular miR-21. Upon the specific internalization of GNP-DNA/Ab by PC-3 cells, target aberrant miR-21 could displace the signal strand to recover the fluorescence signal for sensitive detection at the single-cell level, achieving single PC-3 cell imaging benefiting from the thermophoresis-mediated signal amplification procedure. Taking advantage of the sensitive miR-21 imaging performance, GNP-DNA/Ab could be employed to discriminate the PC-3 and Jurkat cells because of the different expression levels of miR-21. Notably, PC-3 cells were efficiently recognized from white blood cells, exhibiting promising potential for the early diagnosis of prostate cancer. Furthermore, GNP-DNA/Ab possessed good biocompatibility and stability. Therefore, this work provides a great tool for aberrant miRNA-related detection and specific discrimination of CTCs, achieving the early and accurate diagnosis of prostate cancer.

Simultaneous Proximity DNAzyme-Activated Duplexed Protein-Specific Glycosylation Imaging on Cell Surface via Bioorthogonal Chemistry

Due to the scarcity of strategies to evaluate the multiple subtype monosaccharides in one specific protein simultaneously within a single assay, understanding the glycosylation mechanisms and revealing their roles in disease development become extremely challenging. Herein, a strategy of proximity DNAzyme-activated fluorescence imaging of multiplex saccharides in a protein on the cell surface via bio-orthogonal chemistry is reported. The multichannel proximity DNAzyme-activated fluorescence recovery enabled the highly selective and effective imaging analysis of multiplexed protein-specific glycosylation in situ and has been demonstrated. This strategy is successfully applied to visualize the sialylation and fucosylation in four specific proteins on different cell lines and evaluate the variations of protein-specific glycosylation in response to the alterations of the cellular physiological status. More importantly, the quantitative tracking of the terminal sialyation and fucosylation changes at the single-protein level is realized by assigning the target protein as the native reference, which has the potential to be a versatile platform for glycobiology research and clinical diagnosis.

Aptamer/Peptide-Functionalized Nanoprobe for Detecting Multiple miRNAs in Circulating Malignant Cells to Study Tumor Heterogeneity

Identification of diverse biomarkers in heterogenic circulating malignant cells (CMCs) such as circulating tumor cells (CTCs) and circulating tumor endothelial cells (CTECs) has crucial significance in tumor diagnosis. However, it remains a substantial challenge to achieve in situ detection of multiple miRNA markers in living cells in blood. Herein, we demonstrate that an aptamer/peptide-functionalized vector can deliver molecular beacons into targeted living CMCs in peripheral blood of patients for in situ detection of multiple cancer biomarkers, including miRNA-21 (miR-21) and miRNA-221 (miR-221). Based on miR-21 and miR-221 levels, heterogenic CMCs are identified for both nondistant metastatic and distant metastatic cancer patients. CMCs from nondistant metastatic and distant metastatic cancer patients exhibit similar miR-21 levels, while the miR-221 level in CMCs of the distant metastatic cancer patient is higher than that of the nondistant metastatic cancer patient. With the capability to realize precise probing of multiple intracellular biomarkers in living CMCs at the single-cell resolution, the nanoprobe can reveal the tumor heterogeneity and provide useful information for diagnosis and prognosis. The nanoprobe we developed would accelerate the progress toward noninvasive precise cancer diagnosis.

Low-Background Signal-On Homogeneous Electrochemiluminescence Biosensor for Hepatitis B Virus Detection Based on the Regulation of the Length of DNA Modified on the Nanoparticles by CRISPR/Cas12a and Hybridization Chain Reaction

In this work, combined with the high amplification efficiency of hybridization chain reaction (HCR), high specificity of the CRISPR/Cas12a system, and convenience of the homogeneous electrochemiluminescence (ECL) assay based on the regulation of negative charge on the reporting probes, a sensitive ECL biosensor for hepatitis B virus DNA (chosen as a model target) had been developed. The initiator chain trigger DNA that can induce HCR amplification is modified on the surface of ruthenium bipyridine-doped silica nanoparticles (Ru@SiO2 NPs) first, and large amounts of negative charges modified on the particles were achieved through the HCR amplification reaction. The efficiency of the nanoparticles reaching the negatively charged working electrode can be regulated and realize the change of the ECL signal. In addition, long DNA on the surface of the luminescent body may prevent the coreactant from entering the pore to react with ruthenium bipyridine. These factors combine to produce a low-background system. The presence of the target can activate the CRISPR/Cas12a system and make trigger DNA disappear from the nanoparticle surface, and strong ECL can be detected. The sensor does not require a complex electrode modification; therefore, it has better reproducibility. Additionally, due to dual signal amplification, the sensor has a high sensitivity. In the range of 10 fM to 10 nM, the ECL intensity exhibits a strong linear relationship with the logarithm of the target concentration, and the detection limit is 7.41 fM. This sensor has shown high accuracy in detecting clinical samples, which holds significant potential for application in clinical testing.

Advances and Trends in miRNA Analysis Using DNAzyme-Based Biosensors

miRNAs are endogenous small, non-coding RNA molecules that function in post-transcriptional regulation of gene expression. Because miRNA plays a pivotal role in maintaining the intracellular environment, and abnormal expression has been found in many cancer diseases, detection of miRNA as a biomarker is important for early diagnosis of disease and study of miRNA function. However, because miRNA is present in extremely low concentrations in cells and many types of miRNAs with similar sequences are mixed, traditional gene detection methods are not suitable for miRNA detection. Therefore, in order to overcome this limitation, a signal amplification process is essential for high sensitivity. In particular, enzyme-free signal amplification systems such as DNAzyme systems have been developed for miRNA analysis with high specificity. DNAzymes have the advantage of being more stable in the physiological environment than enzymes, easy to chemically synthesize, and biocompatible. In this review, we summarize and introduce the methods using DNAzyme-based biosensors, especially with regard to various signal amplification methods for high sensitivity and strategies for improving detection specificity. We also discuss the current challenges and trends of these DNAzyme-based biosensors.

DNA hydrogels and nanogels for diagnostics, therapeutics, and theragnostics of various cancers

As an efficient class of hydrogel-based therapeutic drug delivery systems, deoxyribonucleic acid (DNA) hydrogels (particularly DNA nanogels) have attracted massive attention in the last five years. The main contributor to this is the programmability of these 3-dimensional (3D) scaffolds that creates fundamental effects, especially in treating cancer diseases. Like other active biological ingredients (ABIs), DNA hydrogels can be functionalized with other active agents that play a role in targeting drug delivery and modifying the half-life of the therapeutic cargoes in the body's internal environment. Considering the brilliant advantages of DNA hydrogels, in this survey, we intend to submit an informative collection of feasible methods for the design and preparation of DNA hydrogels and nanogels, and the responsivity of the immune system to these therapeutic cargoes. Moreover, the interactions of DNA hydrogels with cancer biomarkers are discussed in this account. Theragnostic DNA nanogels as an advanced species for both detection and therapeutic purposes are also briefly reviewed.

Contractile Hairpin DNA-Mediated Dual-Mode Strategy for Simultaneous Quantification of Lactoferrin and Iron Ion by Surface-Enhanced Raman Scattering and Fluorescence Analysis

DNA-mediated self-assembly technology with good sensitivity and affinity ability has been rapidly developed in the field of probe sensing. The efficient and accurate quantification of lactoferrin (Lac) and iron ions (Fe³⁺) in human serum and milk samples by the probe sensing method can provide useful clues for human health and early diagnosis of anemia. In this paper, contractile hairpin DNA-mediated dual-mode probes of Fe₃O₄/Ag-ZIF8/graphitic quantum dot (Fe₃O₄/Ag-ZIF8/GQD) NPs were prepared to realize the simultaneous quantification of Lac by surface-enhanced Raman scattering (SERS) and Fe³⁺ by fluorescence (FL). In the presence of targets, these dual-mode probes would be triggered by the recognition of aptamer and release GQDs to produce FL response. Meanwhile, the complementary DNA began to shrink and form a new hairpin structure on the surface of Fe₃O₄/Ag, which produced hot spots and generated a good SERS response. Thus, the proposed dual-mode analytical strategy possessed excellent selectivity, sensitivity, and accuracy due to the dual-mode switchable signals from "off" to "on" in SERS mode and from "on" to "off" in FL mode. Under the optimized conditions, a good linear range was obtained in the range of 0.5-100.0 μg/L for Lac and 0.01-5.0 μmol/L for Fe³⁺ and with detection limits of 0.14 μg/L and 3.8 nmol/L, respectively. Finally, the contractile hairpin DNA-mediated SERS-FL dual-mode probes were successfully applied in the simultaneous quantification of iron ion and Lac in human serum and milk samples.

Design and application of stimuli-responsive DNA hydrogels: A review

Deoxyribonucleic acid (DNA) hydrogels combine the properties of DNAs and hydrogels, and adding functionalized DNAs is key to the wide application of DNA hydrogels. In stimuli-responsive DNA hydrogels, the DNA transcends its application in genetics and bridges the gap between different fields. Specifically, the DNA acts as both an information carrier and a bridge in constructing DNA hydrogels. The programmability and biocompatibility of DNA hydrogel make it change macroscopically in response to a variety of stimuli. In order to meet the needs of different scenarios, DNA hydrogels were also designed into microcapsules, beads, membranes, microneedle patches, and other forms. In this study, the stimuli were classified into single biological and non-biological stimuli and composite stimuli. Stimuli-responsive DNA hydrogels from the past five years were summarized, including but not limited to their design and application, in particular logic gate pathways and signal amplification mechanisms. Stimuli-responsive DNA hydrogels have been applied to fields such as sensing, nanorobots, information carriers, controlled drug release, and disease treatment. Different potential applications and the developmental pro-spects of stimuli-responsive DNA hydrogels were discussed.

Biomolecule-Based Optical Metamaterials: Design and Applications

Metamaterials are broadly defined as artificial, electromagnetically homogeneous structures that exhibit unusual physical properties that are not present in nature. They possess extraordinary capabilities to bend electromagnetic waves. Their size, shape and composition can be engineered to modify their characteristics, such as iridescence, color shift, absorbance at different wavelengths, etc., and harness them as biosensors. Metamaterial construction from biological sources such as carbohydrates, proteins and nucleic acids represents a low-cost alternative, rendering high quantities and yields. In addition, the malleability of these biomaterials makes it possible to fabricate an endless number of structured materials such as composited nanoparticles, biofilms, nanofibers, quantum dots, and many others, with very specific, invaluable and tremendously useful optical characteristics. The intrinsic characteristics observed in biomaterials make them suitable for biomedical applications. This review addresses the optical characteristics of metamaterials obtained from the major macromolecules found in nature: carbohydrates, proteins and DNA, highlighting their biosensor field use, and pointing out their physical properties and production paths.

Dual-Locked DNAzyme Platform for In Vitro and In Vivo Discrimination of Cancer Cells

Imaging of tumor-associated microRNAs (miRNAs) can provide abundant information for cancer diagnosis, whereas the occurrence of trace amounts of miRNAs in normal cells inevitably causes an undesired false-positive signal in the discrimination of cancer cells during miRNA imaging. In this study, we propose a dual-locked (D-locked) platform consisting of the enzyme/miRNA-D-locked DNAzyme sensor and the honeycomb MnO₂ nanosponge (hMNS) nanocarrier for highly specific cancer cell imaging. For a proof-of-concept demonstration, apurinic/apyrimidinic endonuclease 1 (APE1) and miR-21 were chosen as key models. The hMNS nanocarrier can efficiently release the D-locked DNAzyme sensor in living cells due to the decomposition of hMNS by glutathione, which can also supply Mn²⁺ for DNAzyme cleavage. Ascribing to the smart design of the D-locked DNAzyme sensor, the fluorescence signal can only be generated by the synergistic response of APE1 and miR-21 that are overexpressed in cancer cells. Compared with the miRNA single-locked DNAzyme sensor and the small-molecule (ATP)/miRNA D-locked DNAzyme sensor, the proposed enzyme (APE1)/miRNA D-locked DNAzyme sensor exhibited 2.6-fold and 2.4-fold higher discrimination ratio (F_cancer/F_normal) for cancer cell discrimination, respectively. Owing to the superior performance, the D-locked strategy can selectively generate a fluorescence signal in cancer cells, facilitating accurate discrimination of cancer both in vitro and in vivo. Furthermore, this D-locked platform is easily adaptable toward other target molecules by redesigning the DNA sequences. The outstanding performance and expansibility of this D-locked platform holds promising prospects for cancer diagnosis and related biomedical applications.

Recent Advances in Near-Infrared-II Fluorescence Imaging for Deep-Tissue Molecular Analysis and Cancer Diagnosis

Fluorescence imaging with high sensitivity and minimal invasiveness has received tremendous attention, which can accomplish visualized monitoring and evaluation of cancer progression. Compared with the conventional first near-infrared (NIR-I) optical window (650-950 nm), fluorescence imaging in the second NIR optical window (NIR-II, 950-1700 nm) exhibits deeper tissue penetration capability and higher temporal-spatial resolution with lower background interference for achieving deep-tissue in vivo imaging and real-time monitoring of cancer development. Encouraged by the significant preponderances, a variety of multifunctional NIR-II fluorophores have been designed and fabricated for sensitively imaging biomarkers in vivo and visualizing the treatment procedure of cancers. In this review, the differences between NIR-I and NIR-II fluorescence imaging are briefly introduced, especially the advantages of NIR-II fluorescence imaging for the real-time visualization of tumors in vivo and cancer diagnosis. An important focus is to summarize the NIR-II fluorescence imaging for deep-tissue biomarker analysis in vivo and tumor tissue visualization, and a brief introduction of NIR-II fluorescence imaging-guided cancer therapy is also presented. Finally, the significant challenges and reasonable prospects of NIR-II fluorescence imaging for cancer diagnosis in clinical applications are outlined.

Detection of mRNAs of Ribosomal Protein L15 and E-Cadherin in Living Circulating Tumor Cells at Single Cell Resolution To Study Tumor Heterogeneity

To study the heterogeneity of circulating tumor cells (CTCs) is of crucial importance to analyze cancer progression and metastasis. However, in situ detection of highly heterogeneous CTCs in peripheral blood still faces an elusive challenge. Here, we show direct detection of two metastasis-related mRNAs of diverse CTCs in whole blood by a triple-targeting nanoprobe. In the nanoprobe, two kinds of molecular beacons, MB1 to detect RPL15 mRNA and MB2 to detect E-cadherin (E-cad) mRNA, are loaded in a highly efficient delivery vector decorated with EpCAM-targeted SYL3C, EGFR-targeted CL4, and CD44-targeted hyaluronic acid chains to specifically deliver MB1/MB2 into epithelial, mesenchymal, and stem CTCs in unprocessed peripheral blood. The numbers of RPL15⁺ and E-cad⁺ CTCs are positively correlated with the metastasis stages of cancer patients. This study provides an effective strategy to realize direct observation on diverse metastasis-related genes in living CTCs with different phenotypes to provide accurate information on cancer heterogeneity and metastasis.

Stochastic Collision Electrochemistry from Single Pt Nanoparticles: Electrocatalytic Amplification and MicroRNA Sensing

Single-particle collisions have made many achievements in basic research, but challenges still exist due to their low collision frequency and selectivity in complex samples. In this work, we developed an "on-off-on" strategy based on Pt nanoparticles (PtNPs) that catalyze N₂H₄ collision signals on the surface of carbon ultramicroelectrodes and established a new method for the detection of miRNA21 with high selectivity and sensitivity. PtNPs catalyze the reduction of N₂H₄ on the surface of carbon ultramicroelectrodes to generate a stepped collision signal, which is in the "on" state. The single-stranded DNA paired with miRNA21 is coupled with PtNPs to form the complex DNA/PtNPs. Because PtNPs are covered by DNA, the electrocatalytic collision of N₂H₄ oxidation is inhibited. At this time, the signal is in the "off" state. When miRNA21 is added, the strong complementary pairing between miRNA21 and DNA destroys the electrostatic adsorption of DNA/PtNP conjugates and restores the electrocatalytic performance of PtNPs, and the signal is in the "on" state again. Based on this, a new method for detecting miRNA21 was established. It provides a new way for small-molecule sensing and has a wide range of applications in electroanalysis, electrocatalysis, and biosensing.

Sense and Validate: Fluorophore/Mass Dual-Encoded Nanoprobes for Fluorescence Imaging and MS Quantification of Intracellular Multiple MicroRNAs

Simultaneously monitoring and quantifying intracellular multiple microRNAs (miRNAs) is highly essential to clinical diagnosis and pathological research. However, revealing the intracellular distribution of multiple miRNAs while determining their content in a multiplex and quantitative format remains challenging. Considering the respective technical merit of fluorescence imaging and mass spectrometry (MS) in in situ detection and multiplex assaying, we herein propose fluorophore/mass dual-encoded nanoprobes (FMNPs) that can execute target-triggered hairpin self-assembly to enable in situ amplified imaging and follow-up MS quantification of intracellular multiple miRNAs. The FMNPs responsive to the target miRNA were constructed by codecorating gold nanoparticles (AuNPs) with locked hairpin DNA probes (LH1) and corresponding mass tags (MTs) for fluorescent and mass spectrometric dual-modal readout. Cellular miRNAs can separately trigger recycled hairpin self-assembly, leading to the continuous liberation of fluorophore-labeled bolt DNA (bDNA) for fluorescence imaging in cells. Moreover, the postreaction FMNPs afford an extra chance to validate the fluorescence output of miRNA-21 and miRNA-141 by accurate MS quantification relying on the ion signal of the barcoded MTs. Fluorescence imaging and MS quantification of miRNA-21 and miRNA-141 have also been successfully accomplished in different cell lines, highlighting its potential in cell subtyping. This "sense-and-validate" strategy creates a new modality for assaying multiple intracellular miRNAs and holds great promise in unveiling multicomponent-involved events in cellular processes and determining multiple biomarkers in accurate clinical diagnosis.

Light-Harvesting Fluorescent Spherical Nucleic Acids Self-Assembled from a DNA-Grafted Conjugated Polymer for Amplified Detection of Nucleic Acids

The ultralow concentration of nucleic acids in complex biological samples requires fluorescence probes with high specificity and sensitivity. Herein, a new kind of spherical nucleic acids (SNAs) is developed by using fluorescent π-conjugated polymers (FCPs) as a light-harvesting antenna to enhance the signal transduction of nucleic acid detection. Specifically, amphiphilic DNA-grafted FCPs are synthesized and self-assemble into FCP-SNA structures. Tuning the hydrophobicity of the graft copolymer can adjust the size and light-harvesting capability of the FCP-SNAs. We observe that more efficient signal amplification occurs in larger FCP-SNAs, as more chromophores are involved, and the energy transfer can go beyond the Förster radius. Accordingly, the optimized FCP-SNA shows an antenna effect of up to 37-fold signal amplification and the limit of detection down to 1.7 pM in microRNA detection. Consequently, the FCP-SNA is applied to amplified in situ nucleic acid detecting and imaging at the single-cell level.

A high-integrated DNA biocomputing platform for MicroRNA sensing in living cells

DNA logic computing has captured increasing interest due to its ability to assemble programmable DNA computing elements for disease diagnosis, gene regulation, and targeted therapy. In this work, we developed an aptamer-equipped high-integrated DNA biocomputing platform (HIDBP-A) with a dual-recognition function that enabled cancer cell targeting. Dual microRNAs were the input signals and can perform AND logic operations. Compared to the free DNA biocomputing platform (FDBP), the integration of all computing elements into the same DNA tetrahedron greatly improved logic computing speed and efficiency owing to the confinement effect reflected by the high local concentration of computing elements. As a proof of concept, the utilization of microRNA as the input signal was beneficial for improving the scalability and flexibility of the sequence design of the logic nano-platform. Given that the different microRNAs were over-expressed in cancer cells, this new HIDBP-A has great promise in accurate diagnosis and logic-controlled disease treatment.

Shedding Light on DNA-Based Nanoprobes for Live-Cell MicroRNA Imaging

DNA-based nanoprobes integrated with various imaging signals have been employed for fabricating versatile biosensor platforms for the study of intracellular biological process and biomarker detection. The nanoprobes developments also provide opportunities for endogenous microRNA (miRNA) in situ analysis. In this review, the authors are primarily interested in various DNA-based nanoprobes for miRNA biosensors and declare strategies to reveal how to customize the desired nanoplatforms. Initially, various delivery vehicles for nanoprobe architectures transmembrane transport are delineated, and their biosecurity and ability for resisting the complex cellular environment are evaluated. Then, the novel strategies for designing DNA sequences as target miRNA specific recognition and signal amplification modules for miRNA detection are presented. Afterward, recent advances in imaging technologies to accurately respond and produce significant signal output are summarized. Finally, the challenges and future directions in the field are discussed.

Framework Nucleic Acid-Based Spatial-Confinement Amplifier for miRNA Imaging in Living Cells

Real-time in situ monitoring of miRNAs in living cells is often appealed to signal amplifiers to tackle their low abundance challenges. However, the poor kinetics of amplifiers and potential interferences from the complex intracellular environment hamper its widespread applications in vivo. Herein, we report a framework nucleic acid (FNA)-based nonenzymatic spatial-confinement amplifier for rapid and reliable intracellular miRNA imaging. The amplifier consists of a localized catalytic hairpin assembly (L-CHA) reactor encapsulated in the inner cavity of an FNA (a 20 bp cube). The L-CHA reactor is certainly confined to the internal frame by integrating two probes (H1 and H2) of the L-CHA within a DNA strand and harnessing it to the opposite angles of the cube. We find that the stability of the amplifier is remarkably improved due to the protection of the FNA. More importantly, the spatial-confinement effect of the FNA can endow the confined L-CHA amplifier with enhanced local concentrations of reagents (5000-fold), thereby accelerating the reaction rate and improving the dynamic performance (up to 14.34-fold). With these advantages, the proposed amplifier can enable accurate and effective monitoring of miRNA expression levels in living cells and poses great potential in medical diagnostics and biomedical research.

Multiple amplified microRNAs monitoring in living cells based on fluorescence quenching of Mo2B and hybridization chain reaction

Imaging intracellular microRNAs (miRNAs) demonstrated an essential role in exposing their biological and pathological functions. However, the detection of sequence-specific miRNAs in living cells remains a key challenge. Herein, a facile amplified multiple intracellular miRNAs imaging platform was constructed based on Mo₂B nanosheets (NSs) fluorescence (FL) quenching and hybridization chain reaction (HCR). The Mo₂B NSs demonstrated strong interaction with the hairpin probes (HPs), ssDNA loop, and excellent multiple FL dyes quenching performance, achieving ultralow background signal. After transfection, the HPs recognized specific targets miRNAs, the corresponding HCR was triggered to produce tremendous DNA-miRNA duplex helixes, which dissociated from the surface of the Mo₂B NSs to produce strong FL for miRNAs detection. It realized to image multiple miRNAs biomarkers in different cells to discriminate cancer cells from normal cells owing to the excellent sensitivity, and the regulated expression change of miRNAs in cancer cells was also successfully monitored. The facile and versatile Mo₂B-based FL quenching platform open an avenue to profile miRNAs expression pattern in living cells, and has great applications in miRNAs based biological and biomedical research.

Development of the DNA-based biosensors for high performance in detection of molecular biomarkers: More rapid, sensitive, and universal

The molecular biomarkers are molecules that are closely related to specific physiological states. Numerous molecular biomarkers have been identified as targets for disease diagnosis and biological research. To date, developing highly efficient probes for the precise detection of biomarkers has become an attractive research field which is very important for biological and biochemical studies. During the past decades, not only the small chemical probe molecules but also the biomacromolecules such as enzymes, antibodies, and nucleic acids have been introduced to construct of biosensor platform to achieve the detection of biomarkers in a highly specific and highly efficient way. Nevertheless, improving the performance of the biosensors, especially in clinical applications, is still in urgent demand in this field. A noteworthy example is the Corona Virus Disease 2019 (COVID-19) that breaks out globally in a short time in 2020. The COVID-19 was caused by the virus called SARS-CoV-2. Early diagnosis is very important to block the infection of the virus. Therefore, during these months scientists have developed dozens of methods to achieve rapid and sensitive detection of the virus. Nowadays some of these new methods have been applied for producing the commercial detection kit and help people against the disease worldwide. DNA-based biosensors are useful tools that have been widely applied in the detection of molecular biomarkers. The good stability, high specificity, and excellent biocompatibility make the DNA-based biosensors versatile in application both in vitro and in vivo. In this paper, we will review the major methods that emerged in recent years on the design of DNA-based biosensors and their applications. Moreover, we will also briefly discuss the possible future direction of DNA-based biosensors design. We believe this is helpful for people interested in not only the biosensor field but also in the field of analytical chemistry, DNA nanotechnology, biology, and disease diagnosis.

An aptamer-tethered DNA origami amplifier for sensitive and accurate imaging of intracellular microRNA

Accurate detection and imaging of low-abundance microRNA (miRNA) in living cells are essential for the diagnosis and prognosis of diseases. Designing nanoprobes with resistance to enzyme degradation, effective cell-binding, and efficient signal amplification is crucial for in vivo imaging. In this study, we present an aptamer-tethered DNA origami amplifier (ADOA) that functions inside living cells to detect miRNA with high sensitivity and stability. In the design, cancer cell-targeting aptamers were tethered onto the border of the DNA origami to improve the discrimination between cancer cells and normal cells. Two substrate modules for the intramolecular entropy-driven reaction (EDR) circuit were alternately arranged on the DNA origami plane. The target miRNA will initiate the sequential hybridization of the two substrate modules on the DNA origami, generating amplified fluorescence signals. The proposed ADOA achieved an accelerated cascade reaction due to the "confinement effect" and significantly enhanced the sensitivity compared with a traditional EDR. Meanwhile, with the rigid structure of the DNA origami, the ADOA possessed excellent signalling stability in living cells. Therefore, the ADOA could expand the application of DNA origami in miRNA sensing and has potential value in early-stage clinical diagnosis.

DNA nanolantern-mediated catalytic hairpin assembly nanoamplifiers for simultaneous detection of multiple microRNAs

Simultaneous detection of multiple microRNAs (miRNAs) with high sensitivity can give accurate and reliable information for clinical applications. By uniformly anchoring hairpin probes on the surface of DNA nanolantern, a three-dimensional DNA nanostructure contains abundant and adjustable modification sites, highly integrated DNA nanoprobes were designed and developed as catalytic hairpin assembly (CHA)-based signal amplifiers for enzyme-free signal amplification detection of target miRNAs. The nanolantern-based CHA (NLC) amplifiers, which were facilely prepared via a simple "one-pot" annealing method, showed enhanced biostability, improved cell internalization efficiency, accelerated CHA reaction kinetics, and increased signal amplification capability compared to the single-stranded DNA hairpin probes used in traditional CHA reaction. By co-assembling multiple hairpin probes on a DNA nanolantern surface, as-prepared NLC amplifiers were demonstrated to work well for highly sensitive and specific imaging, expression level fluctuation analysis of two miRNAs in living cells, and miRNAs-guided tumor imaging in living mice. The proposed DNA nanolantern-based nanoamplifier strategy might provide a feasible way to promote the cellular and in vivo applications of nucleic acid probes.

Advances in the DNA Nanotechnology for the Cancer Biomarkers Analysis: Attributes and Applications

The most commonly used clinical methods are enzyme-linked immunosorbent assay (ELISA) and quantitative PCR (qPCR) in which ELISA was applied for the detection of protein biomarkers and qPCR was especially applied for nucleic acid biomarker analysis. Although these constructed methods have been applied in wide range, they also showed some inherent shortcomings such as low sensitivity, large sample volume and complex operations. At present, many methods have been successfully constructed on the basis of DNA nanotechnology with the merits of high accuracy, rapid and simple operation for cancer biomarkers assay. In this review, we summarized the bioassay strategies based on DNA nanotechnology from the perspective of the analytical attributes for the first time and discussed and the feasibility of the reported strategies for clinical application in the future.

DNA Logic Circuits for Multiple Tumor Cells Identification Using Intracellular MicroRNA Molecular Bispecific Recognition

The aberrant expression level of intracellular microRNAs (miRNAs) holds great promise for differentiating cell types at the molecular level. However, cell subtype discrimination based on a single miRNA molecular level is not sufficient and reliable. Herein, multiple identifiable and reporting modules are integrated into a single DNA circuit for multiple cancer cell subtypes identification based on miRNAs bispecific recognition. The DNA three-dimensional (3D) logic gate nano-hexahedron framework extends three recognition modules and three reporting modules to form three "AND" logic gates. Each Boolean operator "AND" returns an "ON" signal in the presence of bispecific miRNAs, simultaneously enabling three types of cell subtype identification. It not only enables the discrimination of cancer cells A549 and MCF-7 from normal cells NHDF but also successfully distinguishes different types of cancer cells. The bispecific intracellular miRNA controllable DNA circuit, with low signal-to-noise ratio, easily extends to various cell type discrimination by adjusting the miRNA species, provides huge opportunities for accurately differentiating multiple cell types at the molecular level.

From Passive Signal Output to Intelligent Response: "On-Demand" Precise Imaging Controlled by Near-Infrared Light

"On-demand" accurate imaging of multiple intracellular miRNAs will significantly improve the detection reliability and accuracy. However, the "always-active" design of traditional multicomponent detection probes enables them to passively recognize and output signals as soon as they encounter targets, which will inevitably impair the detection accuracy and, inevitably, result in false-positive signals. To address this scientific problem, in this work, we developed a near-infrared (NIR) light-activated multicomponent detection intelligent nanoprobe for spatially and temporally controlled on-demand accurate imaging of multiple intracellular miRNAs. The proposed intelligent nanoprobe is composed of a rationally designed UV light-responsive triangular DNA nano sucker (TDS) and upconversion nanoparticles (UCNPs), named UCNPs@TDS (UTDS), which can enter cells autonomously through endocytosis and enable remote regulation of on-demand accurate imaging for multiple intracellular miRNAs using NIR light illumination at a chosen time and place. It is worth noting that the most important highlight of the UTDS we designed in this work is that it can resist nonspecific activation as well as effectively avoid false-positive signals and improve the accuracy of imaging of multiple intracellular miRNAs. Moreover, distinguishing different kinds of cell lines with different miRNA expressions levels can be also achieved through this NIR light-activated intelligent UTDS, showing feasible prospects in precise imaging and disease diagnosis.

Advances in the Functional Nucleic Acid Biosensors for Detection of Lead Ions

Lead ions (Pb²⁺) are destructive to the natural environment and public health, so the efficient detection of Pb²⁺ is particularly important. Although the instrumental analysis methods have high accuracy, they require high cost and precise operation, which limits their wide application. Therefore, many strategies have been extensively studied for detecting Pb²⁺ by biosensors. Functional nucleic acids have become an efficient tool in this field. This review focuses on the recent biosensors of detecting Pb²⁺ based on functional nucleic acids from 2010 to 2020, in which DNAzyme, DNA G-quadruplex and aptamer will be introduced. The biosensors are divided into three categories that colorimetric, fluorometric and electrochemical biosensors according to the different reported signals. The action mechanism and detection effect of each biosensor are explained. Finally, the present situation of nucleic acid biosensor for the detection of Pb²⁺ is summarized and the future research direction is prospected.

Nucleic Acid Tests for Clinical Translation

Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.

Smart and Functionalized Development of Nucleic Acid-Based Hydrogels: Assembly Strategies, Recent Advances, and Challenges

Nucleic acid-based hydrogels that integrate intrinsic biological properties of nucleic acids and mechanical behavior of their advanced assemblies are appealing bioanalysis and biomedical studies for the development of new-generation smart biomaterials. It is inseparable from development and incorporation of novel structural and functional units. This review highlights different functional units of nucleic acids, polymers, and novel nanomaterials in the order of structures, properties, and functions, and their assembly strategies for the fabrication of nucleic acid-based hydrogels. Also, recent advances in the design of multifunctional and stimuli-responsive nucleic acid-based hydrogels in bioanalysis and biomedical science are discussed, focusing on the applications of customized hydrogels for emerging directions, including 3D cell cultivation and 3D bioprinting. Finally, the key challenge and future perspectives are outlined.

A One-Two-Three Multifunctional System for Enhanced Imaging and Detection of Intracellular MicroRNA and Chemogene Therapy

Simultaneous imaging, diagnosis, and therapy can offer an effective strategy for cancer treatment. However, the complex probe design, poor drug release efficiency, and multidrug resistance remain tremendous challenges to cancer treatment. Here, a novel one-two-three system is built for enhanced imaging and detection of miRNA-21 (miR-21) overexpressed in cancer cell and chemogene therapy. The system consists of dual-mode DNA robot nanoprobes assembled by two types of hairpin DNAs and three-way branch DNAs modified on gold nanoparticles, with intercalating anticancer drugs (doxorubicin), into DNA duplex GC base pairs. In the system, via intracellular ATP-accelerated cyclic reaction triggered by miR-21, fluorescence and SERS signals were alternated with DNA structure switch, and the precise SERS detection of miRNA and fluorescence imaging oriented "on-demand" release of two types of anticancer drugs (anti-miR-21 and Dox) are achieved. Thus, "one-two-three" means one kind of miR-21-triggered endogenous substance accelerated cyclic reaction, two modes of signal switch, and three functions including enhanced imaging, detection, and comprehensive treatment. The one-two-three system has some notable merits. First, ATP as an endogenous substance promotes DNA structure switching and accelerates the cyclic reaction. Second, the treatment with a dual-mode signal switch is more reliable and accurate and can provide more abundant information than a single-mode treatment platform. Thus, the imaging and detection of intracellular miRNA and effective comprehensive therapy are realized. In vivo results indicate that the system can provide new insights and strategies for diagnosis and therapy.

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.

Recent progress of SERS optical nanosensors for miRNA analysis

This review focuses on emerging applications of surface-enhanced Raman spectroscopy (SERS) optical nanosensors for miRNA analysis, in which the key enhancement factors of the SERS signal, i.e. SERS-active substrates, SERS nanoprobes and nano-assembly strategy, are emphasized. This article includes many nanomaterials for miRNA analysis by the SERS technique. We summarize these reported nanomaterials mainly according to their function in the miRNA assay biosensor. We also briefly summarize the research progress of these nanomaterials in SERS detection of intracellular miRNA. Finally, we discussed the prospect and limitations of SERS nanosensors for analyzing miRNA.

Self-assembled nanomaterials for biosensing and therapeutics: recent advances and challenges

Self-assembled nanomaterials (SANs) exhibit designable biofunctions owing to their tunable nanostructures and modifiable surface. Various constituent units and multi-dimensional structures of SANs provide unlimited possibilities for numerous applications. This review emphasizes the recent development of SANs in the fields of biosensing, bioimaging, and nano-drug engineering. The unit type, design concepts, material advantages, assembly driving force, nanostructure effects, drug loading performance, etc. are discussed and summarized. Finally, we briefly summarize how to assemble unique nanomaterials and point out the key challenges in this field.

From prevention to diagnosis and treatment: Biomedical applications of metal nanoparticle-hydrogel composites

Recent advances in biomaterials integrate metal nanoparticles with hydrogels to generate composite materials that exhibit new or improved properties. By precisely controlling the composition, arrangement and interactions of their constituents, these hybrid materials facilitate biomedical applications through myriad approaches. In this work we seek to highlight three popular frameworks for designing metal nanoparticle-hydrogel hybrid materials for biomedical applications. In the first approach, the properties of metal nanoparticles are incorporated into a hydrogel matrix such that the composite is selectively responsive to stimuli such as light and magnetic flux, enabling precisely activated therapeutics and self-healing biomaterials. The second approach mediates the dynamic reorganization of metal nanoparticles based on environment-directed changes in hydrogel structure, leading to chemosensing, microbial and viral detection, and drug-delivery capabilities. In the third approach, the hydrogel matrix spatially arranges metal nanoparticles to produce metamaterials or passively enhance nanoparticle properties to generate improved substrates for biomedical applications including tissue engineering and wound healing. This article reviews the construction, properties and biomedical applications of metal nanoparticle-hydrogel composites, with a focus on how they help to prevent, diagnose and treat diseases. Discussion includes how the composites lead to new or improved properties, how current biomedical research leverages these properties and the emerging directions in this growing field.

Advances in multiplexed techniques for the detection and quantification of microRNAs

MicroRNA detection is currently a crucial analytical chemistry challenge: almost 2000 papers were referenced in PubMed in 2018 and 2019 for the keywords "miRNA detection method". MicroRNAs are potential biomarkers for multiple diseases including cancers, neurodegenerative and cardiovascular diseases. Since miRNAs are stably released in bodily fluids, they are of prime interest for the development of non-invasive diagnosis methods, such as liquid biopsies. Their detection is however challenging, as high levels of sensitivity, specificity and robustness are required. The analysis also needs to be quantitative, since the aim is to detect miRNA concentration changes. Moreover, a high multiplexing capability is also of crucial importance, since the clinical potential of miRNAs probably lays in our ability to perform parallel mapping of multiple miRNA concentrations and recognize typical disease signature from this profile. A plethora of biochemical innovative detection methods have been reported recently and some of them provide new solutions to the problem of sensitive multiplex detection. In this review, we propose to analyze in particular the new developments in multiplexed approaches to miRNA detection. The main aspects of these methods (including sensitivity and specificity) will be analyzed, with a particular focus on the demonstrated multiplexing capability and potential of each of these methods.

Novel Protease-Free Long-Lasting Chemiluminescence System Based on the Dox-ABEI Chimeric Magnetic DNA Hydrogel for Ultrasensitive Immunoassay

Most of chemiluminescence (CL) substrates exhibit the flash-type light emission. Therefore, the long-lasting CL system is always the crown in the field of CL-based analysis methodology. In this work, we constructed a Dox-ABEI chimeric magnetic DNA hydrogel (MDH) as a novel protease-free long-lasting CL reaction system. The functional MDH can transform flash-type ABEI/H₂O₂/CO²⁺ reaction into a glow-type CL system because of its block effect on delaying the diffusion rate of co-reactants, making the CL reaction gradually occur. More importantly, the functional MDH possessed the advantages of biocompatibility and controllability and could be well-designed to incorporate different biosensing strategies. Subsequently, we established a functional MDH-based long-lasting CL immunoassay system for ultrasensitive and highly specific detection of d-dimer and fibrin degradation products (FDPs). The designed CL immunoassay can detect d-dimer and FDP down to 53.7 and 31.6 fg/mL, respectively, with a wide line ranging from 100 fg/mL to 100 ng/mL, which was superior to the previously reported CL biosensing strategies. Moreover, benefiting from the magnetic separation of MDH and excellent CL performance, the developed immunoassaying method was successfully applied in the detection of clinical samples, which showed a close correlation with clinical reference technology. Thus, this functional MDH proved to be an excellent long-lasting CL system and a potential technical platform for clinical bioanalysis applications.

Targeted and direct intracellular delivery of native DNAzymes enables highly specific gene silencing

DNAzymes exhibit high potential as gene silencing agents for therapeutic applications. Such purposes, however, are significantly challenged by the targeted and successful delivery of unmodified DNAzymes into cells with minimal side effects. Here, we set out to formulate and demonstrate a new stimuli-responsive and constrained aptamer/DNAzyme (Apt/Dz) catenane nanostructure for highly specific gene silencing. The rational design of the Apt/Dz catenane nanostructure with the respective integration of the aptamer sequence and the completely closed catenane format enables both the targeted capability and significantly improved nuclease resistance, facilitating the stable and targeted delivery of unmodified Dz into cancer cells. Moreover, the Dz enzymatic activity in the constrained structure can only be conditionally regulated by the specific intracellular mRNA sequences to silence the target gene with highly reduced side effects. Results show that the Apt/Dz catenane nanostructure can effectively inhibit the expression of the target gene and the proliferation of cancer cells with high specificity.

A Janus 3D DNA nanomachine for simultaneous and sensitive fluorescence detection and imaging of dual microRNAs in cancer cells

Herein, a Janus three-dimensional (3D) DNA nanomachine was constructed for the simultaneous and sensitive fluorescence detection and imaging of dual microRNAs (miRNAs) in cancer cells, which could effectively eliminate signal interference in a homogeneous nanoparticle-based 3D DNA nanostructure caused by the proximity of the two different signal probes to achieve accurate co-location in the same position of living cancer cells. In this system, the Janus nanoparticles were synthesized as the carrier for immobilizing two different oligonucleotides on two different functionalized hemispheres of the nanoparticles to form a Janus 3D DNA nanostructure, which could convert trace amounts of miRNA-21 and miRNA-155 targets into massive FAM and Cy5-labeled duplexes to induce two remarkable fluorescence emissions by the catalytic hairpin assembly (CHA) and 3D DNA walker cascade nucleic acid amplification strategy, realizing sensitive detection and imaging of miRNA targets in cancer cells. Impressively, in comparison with current miRNA imaging methods based on nanoparticle assemblies, the proposed strategy could efficiently eliminate “false positive” results obtained in single type miRNA detection and distinctly increase the immobilization concentration of two different signal probes using Janus nanoparticles as the carrier to further enhance fluorescence intensity, resulting in accurate co-location in the same position of living cells. Meanwhile, the proposed fluorescence imaging technology makes it possible to visualize low concentrations of miRNAs with tiny change associated with some cancers, which could significantly improve the accuracy and precision compared to those of the conventional fluorescence in situ hybridization (FISH) approach. Therefore, it could serve as persuasive evidence for supplying accurate information to better understand biological processes and investigate mechanisms of various biomolecules and subcellular organelles, resulting in the further validation of their function in tumor proliferation and differentiation. This strategy provided an innovative approach to design new generations of nanomachines with ultimate applications in bioanalysis and clinical diagnoses.

A Janus three-dimensional DNA nanomachine was constructed for the simultaneous and sensitive fluorescent detection and imaging of dual microRNAs in the cancer cells.

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

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

Multi-Dimensionally Extended Functionalization Innovates to an Entropy-Driven Detection of Multi-miRNAs for One-Step Cancer Screening and Diagnosis in Living Cells

Compared with tedious multi-step detections, multi-functional nanoprobes are effective for one-step screening and diagnosis of cancers by multi-detection of microRNAs (miRNAs). However, limited probe density, spatial mutual interference, and low target-triggered hybridization efficiency of nanoprobes will hinder intracellular applications. Here, for obtaining high loading density but low spatial mutual interference between functional biomolecules on nanoprobes, an extended biofunctionalization in three dimensions (the two-dimensional surface and a special "height" direction) is designed. Therefore, a multi-functional probe is constructed for one-step detection of multi-miRNAs for cancer screening and diagnosis. With linker-bridged multiple single-stranded DNAs swung out rigidly, multi-dimensionally extended upconversion nanorods (ME-UCNRs) covered by chitosan are constructed to load and deliver multiple biomolecules into living cells. Escaping from endolysosomes, ME-UCNRs maintain good biological activities of functionalized DNAs for effective detection of multi-miRNAs in living cells. Thereby, with multiple targets of miRNAs, toehold-mediated entropy-driven strand displacements are employed to give respectively changed fluorescent signals via fluorescence resonance energy transfer. Thus, a universal cancer biomarker of miR-21 and two specific liver-cancer biomarkers (miR-199a and miR-224) are efficiently detected through a one-step detection. By discriminating cancer cells from normal ones and determining liver-cancer cells simultaneously, this work innovates an efficient and definite one-step strategy for fast screening and early cancer diagnosis.