A network of acetyl phosphate-dependent modification modulates c-di-AMP homeostasis in Actinobacteria.

Cyclic purine nucleotides are important signal transduction molecules across all domains of life. 3',5'-cyclic di-adenosine monophosphate (c-di-AMP) has roles in both prokaryotes and eukaryotes, while the signals that adjust intracellular c-di-AMP and the molecular machinery enabling a network-wide homeostatic response remain largely unknown. Here, we present evidence for an acetyl phosphate (AcP)-governed network responsible for c-di-AMP homeostasis through two distinct substrates, the diadenylate cyclase DNA integrity scanning protein (DisA) and its newly identified transcriptional repressor, DasR. Correspondingly, we found that AcP-induced acetylation exerts these regulatory actions by disrupting protein multimerization, thus impairing c-di-AMP synthesis via K66 acetylation of DisA. Conversely, the transcriptional inhibition of disA was relieved during DasR acetylation at K78. These findings establish a pivotal physiological role for AcP as a mediator to balance c-di-AMP homeostasis. Further studies revealed that acetylated DisA and DasR undergo conformational changes that play crucial roles in differentiation. Considering the broad distribution of AcP-induced acetylation in response to environmental stress, as well as the high conservation of the identified key sites, we propose that this unique regulation of c-di-AMP homeostasis may constitute a fundamental property of central circuits in Actinobacteria and thus the global control of cellular physiology.IMPORTANCESince the identification of c-di-AMP is required for bacterial growth and cellular physiology, a major challenge is the cell signals and stimuli that feed into the decision-making process of c-di-AMP concentration and how that information is integrated into the regulatory pathways. Using the bacterium Saccharopolyspora erythraea as a model, we established that AcP-dependent acetylation of the diadenylate cyclase DisA and its newly identified transcriptional repressor DasR is involved in coordinating environmental and intracellular signals, which are crucial for c-di-AMP homeostasis. Specifically, DisA acetylated at K66 directly inactivates its diadenylate cyclase activity, hence the production of c-di-AMP, whereas DasR acetylation at K78 leads to increased disA expression and c-di-AMP levels. Thus, AcP represents an essential molecular switch in c-di-AMP maintenance, responding to environmental changes and possibly hampering efficient development. Therefore, AcP-mediated posttranslational processes constitute a network beyond the usual and well-characterized synthetase/hydrolase governing c-di-AMP homeostasis.

RNase H-Driven crRNA Switch Circuits for Rapid and Sensitive Detection of Various Analytical Targets.

The clustered regularly interspaced short palindromic repeats (CRISPR/Cas12a) system has exhibited great promise in the rapid and sensitive molecular diagnostics for its trans-cleavage property. However, most CRISPR/Cas system-based detection methods are designed for nucleic acids and require target preamplification to improve sensitivity and detection limits. Here, we propose a generic crRNA switch circuit-regulated CRISPR/Cas sensor for the sensitive detection of various targets. The crRNA switch is engineered and designed in a blocked state but can be activated in the presence of triggers, which are target-induced association DNA to initiate the trans-cleavage activity of Cas12a for signal reporting. Additionally, RNase H is introduced to specifically hydrolyze RNA duplexed with the DNA trigger, resulting in the regeneration of the trigger to activate more crRNA switches. Such a combination provides a generic and sensitive strategy for the effective sensing of the p53 sequence, thrombin, and adenosine triphosphate. The design is incorporated with nucleic acid nanotechnology and extensively broadens the application scope of the CRISPR technology in biosensing.

Universal DNA-Based Sensing Toolbox for Programming Cell Functions.

By recombining natural cell signaling systems and further reprogramming cell functions, use of genetically engineered cells and bacteria as therapies is an innovative emerging concept. However, the inherent properties and structures of the natural signal sensing and response pathways constrain further development. We present a universal DNA-based sensing toolbox on the cell surface to endow new signal sensing abilities for cells, control cell states, and reprogram multiple cell functions. The sensing toolbox contains a triangular-prismatic-shaped DNA origami framework and a sensing core anchored inside the internal confined space to enhance the specificity and efficacy of the toolbox. As a proof of principle, the sensing toolbox uses the customizable sensing core with signal sensing switches and converters to recognize unconventional signal inputs, deliver functional components to cells, and then control cell responses, including specific tumor cell death, immune cell disinhibition and adhesion, and bacterial expression. This work expands the diversity of cell sensing signals and reprograms biological functions by constructing nanomechanical-natural hybrid cells, providing new strategies for engineering cells and bacteria in diagnosis and treatment applications.

Overcoming Multidrug Resistance by Base-Editing-Induced Codon Mutation.

Multidrug resistance (MDR) is the main obstacle in cancer chemotherapy. ATP binding cassette (ABC) transporters on the MDR cell membrane can transport a wide range of antitumor drugs out of cells, which is one of the main causes of MDR. Therefore, disturbing ABC transporters becomes the key to reversing MDR. In this study, we implement a cytosine base editor (CBE) system to knock out the gene encoding ABC transporters by base editing. When the CBE system works in MDR cells, the MDR cells are manipulated, and the genes encoding ABC transporters can be inactivated by precisely changing single in-frame nucleotides to induce stop (iSTOP) codons. In this way, the expression of ABC efflux transporters is reduced and intracellular drug retention is significantly increased in MDR cells. Ultimately, the drug shows considerable cytotoxicity to the MDR cancer cells. Moreover, the substantial downregulation of P-glycoprotein (P-gp) and breast cancer resistance protein (BCRP) implies the successful application of the CBE system in the knockout of different ABC efflux transporters. The recovery of chemosensitivity of MDR cancer cells to the chemotherapeutic drugs revealed that the system has a satisfactory universality and applicability. We believe that the CBE system will provide valuable clues for the use of CRISPR technology to defeat the MDR of cancer cells.

Switching the Activity of CRISPR/Cas12a Using an Allosteric Inhibitory Aptamer for Biosensing.

The current CRISPR/Cas12a-based diagnostic techniques focus on designing the crRNA or substrate DNA elements to indirectly switch the trans-cleavage activity of Cas12a responsive to target information. Here, we propose the use of an allosteric DNA probe to directly regulate the trans-cleavage activity of Cas12a and present a method for sensing different types of analytes. An allosteric inhibitor probe is rationally designed to couple the target recognition sequence with the inhibitory aptamer of the CRISPR/Cas12a system and enables binding to a specific target to induce the change of conformation, which leads to the loss of its inhibitory function on Cas12a. As a result, the structure-switchable probe can regulate the degree of activity of Cas12a depending on the dose of target. Scalability of our strategy can be achieved by simply replacing the loop domain with different target recognition sequences. The proposed method was validated by detecting adenosine triphosphate and let-7a, giving the detection limits of 490 nM and 26 pM, respectively, and showing an excellent specificity. We believe that this work exploits a viable approach to use the inhibitory aptamer of Cas12a as a regulatory element for biosensing purposes, enriching the arsenal of CRISPR/Cas12a-based methods for molecular diagnostics and spurring further development and application of aptamers of the CRISPR/Cas system.

Nano-Biohybrid DNA Engager That Reprograms the T-Cell Receptor.

Although engineered T cells with transgenic chimeric antigen receptors (CARs) have made a breakthrough in cancer therapeutics, this approach still faces many challenges in the specificity, efficacy, and self-safety of genetic engineering. Here, we developed a nano-biohybrid DNA engager-reprogrammed T-cell receptor (EN-TCR) system to improve the specificity and efficacy, mitigate the excessive activation, and shield against risks from transgenesis, thus achieving a diversiform and precise control of the T-cell response. Utilizing modular assembly, the EN-TCR system can graft different specificities on T cells via antibody assembly. Besides, the designability of DNA hybridization enables precise target recognition by the library of multiantigen cell recognition circuits and allows gradual tuning of the T-cell activation level by the signaling switch and independent control over different types of T cells. Furthermore, we demonstrated the effectiveness of the system in tumor models. Together, this study provides a nongenetic T-cell engineering strategy to overcome major hindrances in T-cell therapy and may be extended to a general and convenient cell engineering strategy.

An Ultrasensitive, One-Pot RNA Detection Method Based on Rationally Engineered Cas9 Nickase-Assisted Isothermal Amplification Reaction.

RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR) have revolutionized molecular diagnostics by offering versatile Cas effectors. We previously developed an isothermal amplification reaction method using Cas9 nickase (Cas9 nAR) to detect genomic DNA. However, slow dissociation of Cas9n from nicked double-stranded DNA (dsDNA) substrates dramatically hampers the cooperation between Cas9n and DNA polymerase, leading to low amplification efficiency. Here, we use structure-guided protein engineering to generate a Cas9n variant with faster kinetics and enhanced targeting specificity, and apply it to develop Cas9 nAR version 2 (Cas9 nAR-v2) by deftly merging reverse transcription with nicking-extension-displacement-based amplification for isothermal, one-pot RNA detection. This assay is validated by detecting Salmonella typhimurium 16S rRNA, Escherichia coli O157:H7 16S rRNA, synthetic SARS-CoV-2 genes, and HIV virus RNA, showing a quantitative analysis over a wide, linear range and a detection limit as low as fewer than ten copies of RNA molecules per reaction (20 µL volume). It also shows an excellent nucleotide-mutation discrimination capability in detecting SARS-CoV-2 variants. Furthermore, Cas9 nAR-v2 is compatible with low-cost point-of-care (POC) tests based on fluorescence and lateral-flow readouts. In summary, this method provides a new paradigm for sensitive, direct RNA detection and would spur the exploration of engineered Cas effectors with improved properties for a wide range of biological applications.

A programmable and sensitive CRISPR/Cas12a-based MicroRNA detection platform combined with hybridization chain reaction.

MicroRNAs (miRNAs) play an essential role in cancer diagnosis and prognosis. Developing a new method for sensitive detection of miRNA is constantly in demand. CRISPR/Cas12a system can nonspecifically cleave single-stranded DNA after specific recognition of target DNA, showing tremendous potential in molecular diagnostics. However, CRISPR-based detection methods require synthesizing different crRNAs for detecting different targets, which limit their widespread application. Herein, we design a versatile and sensitive miRNA detection platform based on CRISPR/Cas12a system combined with a hybridization chain reaction (HCR) circuit. In this design, the HCR circuit as the signal transducer converts each miRNA into multiple DNA duplexes, which act as the activators to activate the trans-cleavage activity of Cas12a for further signal amplification. More importantly, this platform can sensitively detect different miRNAs without changing the spacer sequence of crRNA due to the fixed activators formed by HCR. In addition, the consistency between the proposed platform and RT-qPCR in miRNA detection extracted from different cell lines validated its practicability, demonstrating the potential in clinical diagnosis of cancers and monitoring therapy.

Delivery of siRNA based on engineered exosomes for glioblastoma therapy by targeting STAT3.

Small interfering RNA (siRNA) therapy has been considered as a promising strategy for treatment of glioblastoma (GBM), which is an aggressive brain disease with poor prognosis. However, siRNA therapy for GBM is seriously hindered by a multitude of barriers including possible immunogenicity, poor cellular uptake, short blood circulation, poor blood stability and low blood-brain barrier (BBB) penetration. This paper reports Angiopep-2 (An2)-functionalized signal transducers and activators of transcription 3 (STAT3) siRNA-loaded exosomes (Exo-An2-siRNA) as potential therapeutic agents to improve GBM therapy. The experimental results indicate that Exo-An2-siRNA displays high blood stability, efficient cellular uptake, and outstanding BBB penetration ability. Exo-An2-siRNA also exhibits excellent in vitro anti-GBM therapeutic effects due to the exosomes for siRNA protection and An2 modification for GBM targeting and BBB penetration. Such superior properties of Exo-An2-siRNA are responsible for favorable inhibition of the proliferation of orthotopic U87MG xenografts with limited side effects, significantly enhancing the median survival time (MST) of U87MG-bearing nude mice. The developed siRNA therapy featuring An2-functionalized exosomes as nanoplatforms is a safe and effective GBM treatment strategy.

Simultaneous imaging of cancer biomarkers in live cells based on DNA-engineered exosomes.

Cancer biomarkers are directly related to the development of cancers. Noninvasive identification of the location and expression levels of these biomarkers in live cancer cells offers great potential for accurate early-stage cancer diagnosis and cancer metastasis monitoring. Herein, we propose a DNA-engineered exosome (DNA-Exo) nanoplatform to image dual cancer biomarkers at the single-cell level, in which DNA probes were modified with the cholesterol group to facilely anchor on the exosomal membrane through hydrophobic interaction. Fluorophore-labeled DNA aptamer and hairpin probes targeting two kinds of cancer biomarkers of transmembrane glycoprotein mucin 1 (MUC1) and cytoplasmic microRNA-21 (miR-21), respectively, were employed for convenient dual-fluorescence imaging of cancer cells. The cellular uptake of DNA-Exos induced the specific recognition of MUC1 and miR-21, allowing the acquisition of the expression levels and spatial distributions of these two biomarkers in three tested cell lines. Our work demonstrated that the proposed DNA-Exos with designable functions have the capacity to visually discriminate different cell types based on the specific recognition of analytes.

A Cas12a-mediated cascade amplification method for microRNA detection.

MicroRNAs (miRNAs) play a vital role in various biological processes and act as important biomarkers for clinical cancer diagnosis, prognosis, and therapy. Here, we took advantage of Cas12a trans-cleavage activity to develop an enzyme-assisted cascade amplification method for isothermal miRNA detection. A target miRNA-initiated ligation reaction would allow for the production of transcription templates that triggered the transcriptional amplification of RNA strands. These RNA strands were cleaved by the 8-17E DNAzyme to generate crRNAs and recycled RNAs which have the same sequence as the target miRNA. The amplified abundant crRNAs bound to Cas12a and dsDNA activators to form the complex, which trans-cleaved the ssDNA reporters to generate a fluorescence signal for miRNA quantitative analysis. The proposed method exhibits a femtomolar limit of detection and a good specificity in distinguishing the homologous sequences of miRNAs. Its practical application ability was further tested in different cell lines.

A telomerase-responsive nanoprobe with theranostic properties in tumor cells.

Multidrug resistance (MDR) is the main cause of treatment failure in clinical cancer chemotherapy due to the presence of P-glycoproteins (P-gp), which widely exist in stubborn drug-resistant tumor membranes and actively pump drugs from inside the tumor cell to the outside. In this study, we report a novel telomerase-responsive nanoprobe with theranostic properties for inhibiting P-gp expression and reversing MDR by gene silencing. This nanoprobe is composed of an AuNP assembled with telomerase primer, antisense oligonucleotide (ASO), and doxorubicin (Dox). When the designed nanoprobe is uptaken by the MDR cancer cells, the Dox and ASO are specifically released due to the extension of telomerase primer triggered by telomerase. The released ASO specifically hybridizes with multidrug resistance 1 (MDR1) mRNA sequence, which encodes the P-gp. As a result, the expression of P-gp is inhibited and the efflux of Dox is prevented with reduced MDR in cancerous cells. The results demonstrate that the nanoprobe based on telomerase switching for drug release and gene silencing, can both target cancer cells for delivering drugs and overcome the effect of efflux pumps. This work presents a novel paradigm for theranostics of MDR cancer and enhances the efficacy of chemotherapeutics.

Multiple and sensitive SERS detection of cancer-related exosomes based on gold-silver bimetallic nanotrepangs.

Exosomes are endogenous vesicles of cells, and can be used as important biomarkers for cancers. In this work, we developed a sensitive and reliable SERS sensor for simultaneous detection of multiple cancer-related exosomes. The SERS detection probes were made of bimetallic SERS-active nanotags, gold-silver-silver core-shell-shell nanotrepangs (GSSNTs), which were composed of bumpy surface nanorod (gold nanotrepang, GNT) cores and bilayer silver shells, and decorated with linker DNAs, which were complementary to the aptamer targeting exosomes. Three kinds of SERS detection probes were designed via the adoption of different Raman reporter molecules and linker DNAs. The capture probes were prepared by modifying specific aptamers of the target exosomes on magnetic beads (MBs). In the absence of target exosomes, SERS detection probes were coupled with MBs via specific DNA hybridization for use as aptamer-based SERS sensors. In the presence of target exosomes, the aptamer specifically recognized and captured the exosomes, and GSSNTs were subsequently released into the supernatant. Therefore, attenuated SERS signals were detected on the MBs, indicating the presence of target exosomes. The proposed aptamer-based SERS sensor is expected to be a facile and sensitive method for the multiplex detection of cancer biomarkers and has potential future applications in clinical diagnosis.

Construction of a DNA-AuNP-based satellite network for exosome analysis.

As exosomes have been playing an increasingly important role in the diagnosis, treatment and prognosis of diseases, the analysis of exosome contents becomes more crucial. Therefore, the development of a cost-effective and simple exosome separation method that achieves high purity is urgently needed, and it is vital for further research in cancer. In this work, we constructed a DNA-AuNP-based satellite network which integrates low-speed centrifugal exosome isolation, detection and protein analysis. The rolling circle amplification (RCA) reaction is used to produce a long-chain DNA hairpin structure comprising a plurality of functional domains, such as CD63 aptamer sequences, linker sequences, and spacer sequences with complementary base pairs to form a hairpin structure. When the CD63 aptamers bind to exosomes, the hairpin structure changes its conformation, exposing the linker sequences (AuNP binding sequence). Then the probe on the surface of AuNPs combines with the long-chain DNA by the toehold-mediated strand displacement reaction, releasing the fluorescent labeled complementary probe as the detection signal and simultaneously forming the DNA-AuNP-based satellite network. Thus, exosomes can be isolated by low-speed centrifugation. The formation of the DNA-AuNP-based satellite network was confirmed by transmission electron microscopy and confocal fluorescence microscopy. In addition, we established a standard curve for exosome detection which showed good linearity of the fluorescence ratio vs. log(exosome concentration). LC/MS for protein profiling of the captured exosomes demonstrated that our method has potential application in the field of exosome research.

Ultrasensitive SERS detection of specific oligonucleotides based on Au@AgAg bimetallic nanorods.

We synthesized a novel and sensitive Au/Ag bimetallic SERS-active nanotag, Au-Ag-Ag core-shell-shell nanorod (Au@AgAgNR). The Au@AgAgNR nanotag exhibited a strong SERS signal and was easily assembled from bilayer silver shells on an Au nanorod (AuNR) core with embedded Raman reporter molecules in the core-shell-shell gaps. The SERS activity of the nanotags was investigated with 2-mercaptopyridine (2-Mpy) as a Raman reporter, which could form pyridine/Ag+ coordination complexes to mediate the formation of silver shells. Specific enhancement of Raman signals was observed in the following order: AuNR < Au@AgNR < Au@AgAgNR. Then, Au@AgAgNR nanotags were coupled with magnetic beads (MBs) via specific DNA hybridization as a SERS sensor with a detection limit of 1 fM for a segment of the gene HPV-16. Factors affecting sensitivity and selectivity were investigated, including Raman dye concentration, silver nitrate dosage and the response to similar oligonucleotides. The proposed SERS sensor is expected to be a facile and sensitive method for specific gene detection.

A dual signal amplification method for exosome detection based on DNA dendrimer self-assembly.

An increasing number of studies have found that circulating exosomes play a vital role in the occurrence and metastasis of cancer. Therefore, a direct, sensitive and specific method for detection of tumor exosomes will contribute to the diagnosis and prognosis of cancer. In this work, we take advantage of the facile adaptability of aptamers to design an exosome quantitative method, which converts an exosome capture event to nucleic acid detection. With the help of a hairpin DNA cascade reaction (HDCR) and easy accessibility of DNA dendrimer self-assembly, dual signal amplification was achieved. A CD63 aptamer linked via a DNA probe to magnetic beads acts as the capture component. In the presence of target exosomes, aptamers identify and combine with exosomes, releasing the DNA probe as a trigger to initiate the HDCR (the first signal amplification process) by opening hairpin DNA (HP1) bound to gold nanoparticles (AuNPs). Fluorescently-labeled DNA dendrimers concatenate with HP1 as the second signal amplification stage to increase the signal-to-noise ratio. Under the optimal conditions, our method achieved a good linear response for HepG2 cell-derived exosomes in a concentration range from 1.75 × 103 to 7.0 × 106 particles per µL with a detection limit of 1.16 × 103 particles per µL. It also shows a good performance for detection of exosomes in biological samples.

Highly sensitive detection of exosomes by SERS using gold nanostar@Raman reporter@nanoshell structures modified with a bivalent cholesterol-labeled DNA anchor.

Exosomes, as important signal transmitters, play a key role in intercellular communication, especially in cancer metastasis. There is considerable evidence that exosomes can be used as an indicator of cancer. However, convenient and sensitive methods for detecting exosomes are still technically challenging. Here, we present a convenient and highly sensitive surface-enhanced Raman scattering (SERS) based method by combining immunoaffinity, SERS nanoprobes, and portable Raman devices for specific isolation and accurate quantification of exosomes. To construct the SERS-based biosensor, the surfaces of gold nanostar@4-mercaptobenzoic acid@nanoshell structures (AuNS@4-MBA@Au) are modified with a bivalent cholesterol (B-Chol)-labeled DNA anchor to prepare SERS nanoprobes. Exosomes are specifically captured by immunomagnetic beads, and then SERS nanoprobes are fixed on the surface of exosomes by hydrophobic interactions between cholesterol and lipid membranes, thus forming a sandwich-type immunocomplex. The immunocomplex can be magnetically captured and produce enhanced SERS signals. In the absence of exosomes, the sandwich-type immunocomplex cannot be formed, and thus negligible SERS signals are detected. The degree of immunocomplex assembly and the corresponding SERS signals are positively correlated with the exosome concentration over a wide linear range of 40 to 4 × 107 particles per µL and the limit of detection is as low as 27 particles per µL. Consequently, a sensitive and simple strategy for detection of exosomes is successfully constructed. We believe that our biosensor has considerable potential as a convenient and highly sensitive quantification tool to detect exosomes in biological samples.

Direct Exosome Quantification via Bivalent-Cholesterol-Labeled DNA Anchor for Signal Amplification.

Exosomes, as an important subpopulation of extracellular vesicles (EVs), play an important role in intercellular communications in various important pathophysiological processes, especially cancer-related. However, reliable and convenient quantitative methods for their determination are still technically challenging. In this study, we developed an efficient and direct method by combining immunoaffinity and lipid membrane surface modification into a single platform for specific isolation and accurate quantification of exosomes. Exosomes are specifically captured by immunomagnetic beads, and then a bivalent-cholesterol (B-Chol)-labeled DNA anchor with high affinity is spontaneously inserted into the exosome membrane. The rationally designed sticky end of the anchor acts as the initiator for the subsequent horseradish peroxidase (HRP)-linked hybridization chain reaction (HCR) for signal amplification. Detection is based on the color change of HRP-catalyzed H2O2-mediated oxidation of 3,3',5,5'- tetramethyl benzidine (TMB), which can be conveniently observed by the naked eye and monitored by UV-vis spectrometry. This proposed method enables sensitive detection of 2.2 × 103 exosomes per microliter with a relative standard deviation of <5.6%, with 100-fold higher sensitivity compared to conventional ELISA. We believe that our assay has considerable potential as a routine bioassay (cost-efficient, reliable, and easy to operate) for the accurate quantification of exosomes in clinical samples.

Simultaneous Surface-Enhanced Raman Spectroscopy Detection of Multiplexed MicroRNA Biomarkers.

Simultaneous detection of cancer biomarkers holds great promise for the early diagnosis of cancer. In the present work, an ultrasensitive and reliable surface-enhanced Raman scattering (SERS) sensor has been developed for simultaneous detection of multiple liver cancer related microRNA (miRNA) biomarkers. We first proposed a novel strategy for the synthesis of nanogap-based SERS nanotags by modifying gold nanoparticles (AuNPs) with thiolated DNA and nonfluorescent small encoding molecules. We also explored a simple approach to a green synthesis of hollow silver microspheres (Ag-HMSs) with bacteria as templates. On the basis of the sandwich hybridization assay, probe DNA-conjugated SERS nanotags used as SERS nanoprobes and capture DNA-conjugated Ag-HMSs used as capture substrates were developed for the detection of target miRNA with a detection limit of 10 fM. Multiplexing capability for simultaneous detection of the three liver cancer related miRNAs with the high sensitivity and specificity was demonstrated using the proposed SERS sensor. Furthermore, the practicability of the SERS sensor was supported by the successful determination of target miRNA in cancer cells. The experimental results indicated that the proposed strategy holds significant potential for multiplex detection of cancer biomarkers and offers the opportunity for future applications in clinical diagnosis.

A novel polydopamine-based chemiluminescence resonance energy transfer method for microRNA detection coupling duplex-specific nuclease-aided target recycling strategy.

MicroRNAs (miRNAs), functioning as oncogenes or tumor suppressors, play significant regulatory roles in regulating gene expression and become as biomarkers for disease diagnostics and therapeutics. In this work, we have coupled a polydopamine (PDA) nanosphere-assisted chemiluminescence resonance energy transfer (CRET) platform and a duplex-specific nuclease (DSN)-assisted signal amplification strategy to develop a novel method for specific miRNA detection. With the assistance of hemin, luminol, and H2O2, the horseradish peroxidase (HRP)-mimicking G-rich sequence in the sensing probe produces chemiluminescence, which is quickly quenched by the CRET effect between PDA as energy acceptor and excited luminol as energy donor. The target miRNA triggers DSN to partially degrade the sensing probe in the DNA-miRNA heteroduplex to repeatedly release G-quadruplex formed by G-rich sequence from PDA for the production of chemiluminescence. The method allows quantitative detection of target miRNA in the range of 80 pM-50 nM with a detection limit of 49.6 pM. The method also shows excellent specificity to discriminate single-base differences, and can accurately quantify miRNA in biological samples, with good agreement with the result from a commercial miRNA detection kit. The procedure requires no organic dyes or labels, and is a simple and cost-effective method for miRNA detection for early clinical diagnosis.