Engineered crRNA for CRISPR/Cas-assisted biosensing.

CRISPR/Cas-based diagnostics (CRISPR-Dx) face challenges, including difficulty in detecting ultrashort nucleotides, preamplification dependency, cross-contamination, insufficiency in on-pot detection paradigms, and inconvenience in detecting non-nucleic acid targets. This forum outlines the advances in engineered CRISPR RNA (crRNA) that address the aforementioned problems, highlighting challenges, opportunities, and future directions.

Semiarbitrary qPCR for Sensitive Detection of Circulating miRNA via Terminal Deoxynucleotidyl Transferase-Assisted RNA-Primed DNA Polymerization.

Circulating microRNAs (miRNAs) have recently emerged as noninvasive disease biomarkers. Quantitative detection of circulating miRNAs could offer significant information for clinical diagnosis due to its significance in the development of biological processes. In response to the current challenges of circulating miRNA detection, we introduce a sensitive, selective, and versatile circulating miRNA detection strategy using terminal deoxynucleotidyl transferase (TdT)-catalyzed RNA-primed DNA polymerization (TCRDP) coupled with semiarbitrary qPCR (SAPCR). Semiarbitrary qPCR was first developed here to detect long fragment targets with only a short-known sequence or to detect a short fragment target after extension with terminal transferase. Besides, the subsequent results show that TdT has a preference for RNA, particularly for extending RNAs with purine-rich and unstructured ends. Consequently, utilizing this assay, we have successfully applied it to the quantitative analysis of circulating miR-122 in animal models, a sensitive and informative biomarker for drug-induced liver injury, and as low as 200 zmol of the target is detected with desirable specificity and sensitivity, indicating that the TCRDP-SAPCR can offer a promising platform for nucleic acids analysis.

Recent Advances of DNA-Templated Metal Nanoclusters for Food Safety Detection: From Synthesis, Applications, Challenges, and Beyond.

Food safety concerns have become a significant threat to human health and well-being, catching global attention in recent years. As a result, it is imperative to research conceptually novel biosensing and effective techniques for food matrices detection. Currently, DNA-templated metal nanoclusters (DNA-MNCs) are considered as one of the most promising nanomaterials due to their excellent properties in biosensing. While DNA-MNCs have garnered increasing interest, the reviews of design strategies, applications, and futuristic prospects for biosensing have been hardly found especially in food safety. The synthesis of DNA-MNCs and their use as biosensing materials in food contamination detection, including pathogenic bacteria, toxins, heavy metals, residues of pesticides, and others were comprehensively reviewed. In addition, we summarize the properties of DNA-MNCs briefly and discuss the challenges and future trends. The application of DNA-MNCs powered biosensing has been demonstrated and actively studied, which is a promising paradigm for food safety testing that can supplement or even replace current existing methods. Despite the challenges of difficulty regulating accurately, poor stability, low quantum yield, and difficult commercial transformation, the application prospects of DNA-MNCs biosensors are promising. This review aims to provide insights and directions for the future development of DNA-MNCs based food detection technology.

pH-Responsive Mucus-Penetrating Nanoparticles for Enhanced Cellular Internalization by Local Administration in Vaginal Tissue.

Low mucus penetration ability and cellular uptake seriously limit the effectiveness of local vaginal drug administration because of the rapid foreign particulate and pathogen removal property of the mucus layer. Our previous work proved that nanoparticles with a highly dense polyethylene glycol (PEG) coating can penetrate mucus rapidly (mucus-penetrating nanoparticles, MPPs) and improve drug distribution and retention at mucosal surfaces. However, the "stealth-effect" of the PEG coating also restricts cellular uptake of MPPs. In this work, we designed pH-responsive mucus-penetrating nanoparticles (pMPPs) with hydrazone bonds as the linker to conjugate a dense PEG surface coating, which enabled the pMPPs to rapidly penetrate through the mucus layer. More importantly, the acidic environment of the vaginal mucus induces slow shedding of the PEG layer, leading to a positive charge exposure to facilitate cellular uptake. Overall, pMPPs demonstrate potential as an effective delivery platform for the prophylactic and therapeutic treatment of female reproductive diseases.

A lateral flow strip biosensor platform based on cascade nucleic acid amplification technology for ultrasensitive detection of OSCC-associated salivary MicroRNA.

Oral squamous cell carcinoma (OSCC) is the well-known malignancy and poses a serious threat to human health with high morbidity and mortality. Early detection and treatment can improve the recovery rate and reduce complications of OSCC. Therefore, we designed a lateral flow strip biosensor platform (HRCA-strip) based on the cascade nucleic acid amplification technology (HRCA) for colorimetric analysis of OSCC-associated has-microRNA 31-5p (miRNA 31). In this work, the target miRNA 31 mediated the formation of the sandwich complex structure on the surface of magnetic beads (MBs). Then, the sandwich complex structure could activate cascade amplification reaction between hybridization chain reaction (HCR) and rolling-circle amplification (RCA) to generate numerous G-quadruplex structures. The G-quadruplex structures combined with hemin to form hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme (H/G-HRP mimic enzyme) which were enriched on the T-line and catalyzed the oxidation of chromogenic substrates to generate colorimetric signal on the strip. The HRCA-strip platform could achieve highly sensitive and specific miRNA 31 detection with the limit of detection (LOD) as low as 3.21 fM. Moreover, the designed HRCA-strip platform also enabled portable detection of miRNA 31 in clinical sample which might show good potential for early clinical diagnosis of OSCC.

An amplified fluorescent biosensor for Ag+ detection through the hybridization chain reactions.

Ag is widely distributed in nature and it is used in almost all areas of human life. However, due to the widespread use of Ag materials, Ag+ pollution seriously threatens the human health and environment. The traditional detection methods for Ag+ suffer from disadvantages including high operational cost, complicated operating unit and instrument, and high requirements for professionals. Thus, in this study, a new type of Ag+ detection biosensor based on the hybridization signal amplification was designed to overcome these problems. Combining cytosine-Ag+-cytosine mismatch structure with the hybridization chain reaction, this biosensor converted the conventional detection signal into the nucleic acid amplification signal, which realized efficient, rapid, sensitive, and specific detection of Ag+. The limit-of-detection of this sensor reached 0.69 pM, which is much less than the maximum concentration (0.1 mg L-1, 927 nM) suggested for drinking water by the World Health Organization, and the maximum concentration (0.05 mg L-1, 464 nM) suggested by the United States Environmental Protection Agency. This method provides a promising new platform for detecting Ag+ concentrations at ultralow levels.

MicroRNA-Responsive DNA-Programmed Nanomedicine with Controllability of Cascaded Events for Cancer Therapy Enhancement.

Chemotherapy is a prime tool for cancer clinical therapy. The effectiveness has been improved considerably with the assistance of nanotechnology. However, it still meets the challenge of unsatisfied therapeutic effects caused by multidrug resistance and uncontrollable drug release. For further enhancement of the treatment performance, we develop a kind of microRNA-responsive nanomedicine that uses the biomarker microRNA-21 as a trigger of cascaded killing effects on cancer cells, including chemotherapy and gene silencing. The nanomedicine consists of a gold nanoparticle core and a DNA layer. Strand migrations within the layer can accurately control the events of anticancer drug doxorubicin release and multidrug-resistant-associated protein 1 downregulation, yielding an alleviation of multidrug resistance and enhanced killing on cancer cells. This work demonstrates a microRNA-responsive nanomedicine in combination with chemotherapy and gene silencing, which paves the way to the advancement of DNA-based nanomedicine for cancer theranostics.

High fluorescence quenching probe-based reverse fluorescence enhancement LFTS coupling with IS-primer amplification reaction for the rapid and sensitive Parkinson Disease-associated MicroRNA detection.

Parkinson Disease (PD) is the second-most common neurodegenerative disorder in the population. Recent researches indicated that hsa-microRNA 5010-3p (miR-5010) and hsa-microRNA 331-5p (miR-331) were significantly important for the detection of PD. So, in this work, a kind of high fluorescence quenching probe-based reverse fluorescence enhancement lateral flow test strip (rLFTS) was constructed to realize the synchronous detection of miR-5010 and miR-331. The formation of black hole quencher 2 (BHQ2) coating gold nanoparticles (AuNPs) effectively enhanced the fluorescence quenching property of the probes so as to significantly improve the detection sensitivity. This rLFTS also coupled with "invading stacking primer" (IS-primer) isothermal amplification reaction (ISAR) to accomplish rapid, sensitive, specific, and synchronous detection of PD-associated microRNA (miRNA). The whole detection time was shorter (35 min), and the limit-of-detection (LOD) reached to fM level. For the high accuracy diagnosis of PD, the synchronous determination of miR-5010 and miR-331 was successfully realized on one rLFTS by labeling fluorescent molecules to different T-line. This rLFTS also allowed for miRNA detection in total microRNA extracts from whole blood samples of PD patients, which performed important value in PD diagnosis and biomedical research.

Nonenzyme Cascaded Amplification Biosensor Based on Effective Aggregation Luminescence Caused by Disintegration of Silver Nanoparticles.

Sensitive and portable quantification of biomarkers has particular significance in the monitoring and treatment of clinical diseases. Conventional immunoassays were accustomed to introducing or incorporating enzymes for signal amplification, which commonly suffered from poor stability and inferior tolerance. Herein, we constructed a novel nonenzyme amplification methodology based on fluorogenic Ag+-tetrazolate aggregation coupled with silver corrosion sensitization for biomarker determination. A significant cascade enhancement strategy was achieved by the valid aggregation luminescence caused by the potent disintegration of silver nanoparticles. Furthermore, efficient magnetic separation was also combined and performed for the rapidity and simplicity of operation. As the target, the detection limit of prostate-specific antigen was 15.66 pg/mL in our designed biosensor. Besides, a good linear relationship was obtained. The designed biosensor demonstrated good specificity and was successfully applied to clinical serum sample detection.

A fluorescent signal "removal" sensor via duplex-specific nuclease-aided cleavage for miRNA detection in flow cytometry.

Considered as the next-generation biomarkers, microRNAs play an important role in the early diagnosis of cancers. Here, we designed a fluorescent signal "removal" sensor for one-step, sensitive and specific detection of multiple microRNAs by flow cytometry (FCM). In this work, single-stranded DNA (ssDNA), working as the interlinkage, immobilized the fluorescent nanosphere (FS) onto the SiO2 microspheres surface to form the SiO2-ssDNA-FS probes. When target miRNAs integrated with SiO2-ssDNA-FS probes, the duplex-specific nuclease (DSN) could cleave the ssDNA selectively and release FS with numerous cycles to enhance the fluorescent signal attenuation of SiO2-ssDNA-FS, so as to remarkably improve the analysis sensitivity. It achieved a simple, accurate and quantitative microRNA-21 detection for clinical blood samples. Parallel multi-target detection of microRNA-21 and Let-7d was also realized by different color labeled FS. Moreover, our designed sensor was suitable for other targets' detection with the corresponding probes.

Reusable Bioluminescent Sensor for Ultrasensitive MicroRNA Detection Based on a Target-Introducing "Fuel-Loading" Mechanism.

As a kind of important potential biomarkers, the expression level of some microRNAs (miRNAs) is closely related to cancer development and progression. Herein, a reusable ultra-sensitive "fuel-loadings" bioluminescent sensor was constructed to detect the trace miRNA based on the cascading signal amplification, which combined the target-introducing "fuel-loading" mechanism and cyclic bioluminescence assay. In this sensor, magnetic beads labeled with hairpin DNA probes (hDNA) could specifically hybridize with the target miRNA and isolate these targets from samples. Then, the target-introducing "fuel loading" mechanism worked because the poly(A) polymerase can catalyze the template-independent sequential addition of adenosine monophosphate (AMP) to the 3' ends of the miRNA targets to produce long poly(A) tails. The long poly(A) tails provided lots of 5'AMPs (cleaved by Exonuclease T), which further as fuels were converted into adenosine-triphosphate (ATP) to generate an enhanced bioluminescent signal by cyclic AMP pyrophosphorylation-ATP dephosphorylation. The "fuel-loadings" bioluminescent sensor realized a high sensitivity with a limit-of-detection of about 22.6 aM for miRNA 21. Moreover, this "fuel-loadings" bioluminescent sensor not only achieved regenerable and reusable measurement in the same microwell to decrease the analysis costs, but also could directly detect miRNA 21 in the serum without complicated extraction procedures. It showed excellent coherence with quantitative reverse transcription polymerase chain reaction for miRNA 21 detection of cancer patients' samples, indicating clinical translation potential for miRNA detection.

Enzyme-free colorimetric detection of MicroRNA-21 using metal chelator as label for signal generation and amplification.

MicroRNAs (miRNAs) were reported to be potential tumor markers for early diagnosis of cancer. Due to its short sequence, low expression level and high susceptibility to degradation, the stable and sensitive detection method of miRNAs is arduous to establish. In this work, we designed a metal chelator (ethylenediamine tetraacetic acid disodium salt, EDTA•2Na) labeled oligonucleotides as the plasmonic signal supraregulator probe to control the generation of gold nanoparticles (AuNPs). Based on another complementary oligonucleotides of target miRNA labeling SiO2 microparticles (SiO2MPs) as the detecting platform, EDTA•2Na labeled oligonucleotide probes were immobilized on the SiO2 platform through the sandwich structure in the presence of target miRNA. The sandwich chelating device could further chelate Au3+ to regulate the generation of AuNPs, resulting in colorimetric signal to qualitatively and quantitatively detect the concentration of microRNA-21 (miR-21). The results indicate that the proposed metal chelator -labeled signal amplification method has outstanding sensitivity (LOD = 8.9 fM) and excellent stability, which will be benefit for the early accurate diagnosis of miRNAs.

An innovative "unlocked mechanism" by a double key avenue for one-pot detection of microRNA-21 and microRNA-141.

The accurate and quantitative detection of microRNAs (miRNAs) as next-generation, reliable biomarkers will provide vital information for cancer research and treatment. However, their unique, intrinsic features pose quite a challenge for miRNA profiling, especially for multiplexed detection. Thus, there is a strong and an ever-growing need to develop an accurate, simple, sensitive and specific miRNA sensing method. Methods: In this study, a simple and novel sensor is presented that uses a flow cytometry (FCM) method based on the double key "unlocked mechanism" and a fluorescence enrichment signal amplification strategy. The "unlocked mechanism" was cleverly designed via using hairpin DNA probes (HDs) labeled by fluorescent particles (FS) as the lock to block part of them, which can specifically hybridize with the probe on polystyrene microparticles (PS). The target miRNA and duplex-specific nuclease (DSN) forming the double key can specifically open the HDs and cleave a single-stranded DNA (ssDNA) into DNA/RNA dimers circularly in order to unlock the special part of the HDs to be specially enriched further on the PS. Results: The designed sensor with a hairpin structure and DSN special performance was found to have a high specificity. The circularly unlocking fluorescent probes and fluorescent signal enrichment can be beneficial for achieving a high sensitivity with a detection limit of 3.39 fM for miRNA-21. Meanwhile, the performance of multiplexing was estimated by simultaneous detection of miR-21 and miR-141, and the method also allowed for miR-21 detection in breast cancer blood samples. Conclusion: The designed sensor based on an "unlocked mechanism" and a signal enrichment strategy resulted in a one-pot, highly specific and sensitive detection of multiplex miRNAs. The whole detection without the need for a complex purification process is based on a FCM and is expected to have a great value in cancer diagnosis and biomedical research.

A Metal Chelator as a Plasmonic Signal-Generation Superregulator for Ultrasensitive Colorimetric Bioassays of Disease Biomarkers.

Enzyme-based assays have been widely applied in clinical diagnosis for decades. However, the intrinsic limitations of enzymes, such as low operation stability, mediocre sensitivity, and high cost in production and purification, heavily constrain their detection application. Here, an enzyme-free assay is reported that relies on the strong chelating capability of ethylenediamine tetraacetic acid disodium salt (EDTA•2Na, the chelator) for Au3+ ions, in which the cheap EDTA•2Na labeled by targeting moieties can selectively regulate the growth of plasmonic gold nanoparticles (AuNPs) at the target site subjecting to the concentration of analyte in samples. Independent of ambient temperature and unstable H2O2, EDTA•2Na perform superregulation in AuNPs plasmonic signal generation with distinct tonality and outstanding reliability. Upon integrating with silica nanoparticles as the signal amplifying platform, EDTA•2Na-regulated bioassay can lead to detection-sensitivity enhancements exceeding three orders of magnitude in protein detection, compared with the gold-standard assay. The limit of detection of the HBsAg and alpha fetoprotein (AFP) pushes down to 2.6 × 10-15 and 2.5 × 10-19 g mL-1, respectively. EDTA•2Na-regulated bioassay is also challenged in the clinical serum sample detection and a good consistency is found with the chemiluminescence immunoassay method in clinics.

High sensitive and multiple detection of acute myocardial infarction biomarkers based on a dual-readout immunochromatography test strip.

Immunochromatography test strip (ICTS) displayed high advantages in screening acute myocardial infarction (AMI) biomarkers. However, the low sensitivity and nonquantitative results seriously limited its clinical application. Herein, we designed a highly sensitive, quantitative and dual-readout ICTS for assaying multiple AMI biomarkers based on magnetic nanoparticles (MNPs) quenching the fluorescence of Cy5, which was labeled on capture antibodies on test (T) lines. The changes of fluorescent intensity caused by MNPs nanoprobes enabled us to sensitively quantify cTnI and CK-MB for early diagnosis of AMI in 15 min with a corresponding detection limit of 0.049 ng/mL and 0.085 ng/mL, respectively. Meanwhile, the aggregations of MNPs on T lines allowed colorimetric readout in 2 min for rapid diagnosis of emergent and severe AMI patients. Furthermore, the detection results of 30 clinical serum samples were coincident with those by electrochemiluminescence immunoassay. So this approach is promising a new avenue for clinical diagnosis and prognosis of AMI.

Effective Bioactivity Retention of Low-Concentration Antibodies on HFBI-Modified Fluorescence ICTS for Sensitive and Rapid Detection of PSA.

Nowadays, increasing analytical sensitivity is still a big challenge in constructing membrane-based fluorescence immunochromatography test strips (FICTS). However, the bioactivity of antibody (Ab) immobilized on the test line (T line) of porous nitrocellulose membrane (PNM), which directly influences the analytical sensitivity, is less studied. In this work, a novel amphiphilic hydrophobin (HFBI) protein was introduced to modify the T line to effectively retain the Abs' bioactivity. The results indicated that HFBI could self-assemble on the PNM and immobilize the Abs in the "stand-up" orientation. Compared with the conventional FICTS, the HFBI-modified FICTS with only 0.2 mg/mL of monoclonal Abs on T line enable more accurate quantitative detection and better sensitivity (0.06 ng/mL for prostate specific antigen), which is more than 2 orders of magnitude lower than that of the conventional FICTS with the same concentration of monoclonal Abs on T line. Furthermore, the accuracy of this HFBI-modified FICTS was investigated by testing 150 clinical serum samples and the detection results were coincident with those by electrochemiluminescence immunoassay. Our results provide a novel and promising strategy of Ab immobilization on FICTS for near-patient and point-of-care application.

Simple and Sensitive Quantification of MicroRNAs via PS@Au Microspheres-Based DNA Probes and DSN-Assisted Signal Amplification Platform.

Identifying the microRNA (miRNA) expression level can provide critical information for early diagnosis of cancers or monitoring the cancer therapeutic efficacy. This paper focused on a kind of gold-nanoparticle-coated polystyrene microbeads (PS@Au microspheres)-based DNA probe as miRNA capture and duplex-specific nuclease (DSN) signal amplification platform based on an RGB value readout for detection of miRNAs. In virtue of the outstanding selectivity and simple experimental operation, 5'-fluorochrome-labeled molecular beacons (MBs) were immobilized on PS@Au microspheres via their 3'-thiol, in the wake of the fluorescence quenching by nanoparticle surface energy transfer (NSET). Target miRNAs were captured by the PS@Au microspheres-based DNA probe through DNA/RNA hybridization. DSN enzyme subsequently selectively cleaved the DNA to recycle the target miRNA and release of fluorophores, thereby triggering the signal amplification with more free fluorophores. The RGB value measurement enabled a detection limit of 50 fM, almost 4 orders of magnitude lower than PS@Au microspheres-based DNA probe detection without DSN. Meanwhile, by different encoding of dyes, miRNA-21 and miRNA-10b were simultaneously detected in the same sample. Considering the ability for quantitation, high sensitivity, and convenient merits, the PS@Au microspheres-based DNA probe and DSN signal amplification platform supplied valuable information for early diagnosis of cancers.

Fluorescence quenching-based signal amplification on immunochromatography test strips for dual-mode sensing of two biomarkers of breast cancer.

Recently, immunochromatography test strips (ICTS) have been fully developed for point-of-care testing (POCT). However, the intrinsic limitations including non-quantitative detection of colloidal gold ICTS and low sensitivity of fluorescence ICTS (FICTS) significantly restrict their further application in clinical diagnosis. Taking advantages of rapid colorimetric qualitative detection and fluorescence quantitation, we designed a kind of sensitive and dual-mode magnetic FICTS (mFICTS) based on PLGA@Fe3O4 super-paramagnetic nanosphere (SPMN) probes quenching multiplex fluorescer on the test line through sandwich immunoreactions. Owing to the large number of Fe3O4 nanoparticles (about 47) encapsulated in one SPMN, about 2680 Cy5 molecules were quenched by one SPMN on the test line such that to significantly improve the analytical sensitivity as well as the detection of whole blood samples via magnetic separation. Moreover, the aggregation of black SPMN on the test line enabled a quick naked-eye screening in 3 min. For high accuracy breast cancer diagnosis, combined determination of carcinoembryonic antigen (CEA) and carbohydrate antigen (CA153) was performed on one mFICTS with the limits of detection of about 0.06 ng mL-1 and 0.09 U mL-1, respectively. Then, more than 50 clinical serum samples were investigated for high-resolution screening by mFICTS, and the results were coincident with those obtained by electrochemiluminescence immunoassay (ECLIA). Thus, the designed mFICTS is suitable for point-of-care diagnostics.

The construction of a novel nucleic acids detection microplatform based on the NSET for one-step detecting TK1-DNA and microRNA-21.

Microbeads-based microchip technology has become the potential for a new generation of nucleic acids detection in a high-throughput and sensitive manner. However the specificity and operational complexity limit the microchip applied in nucleic acids detection. Herein, in this work, we designed a kind of gold-nanoparticles coated polystyrene microbeads as microplatform conjugating with the molecular beacons as probes. Due to the nanoparticle surface energy transfer of gold-nanoparticles, the fluorescence of dye on one end of molecular beacons was effectively quenched. When the target nucleic acids existed, the fluorescence of dye was quickly "turn-on" with high sensitivity. Due to the nanoparticle surface energy transfer effect of gold-nanoparticles, the designed platform performed better sensitivity than traditional microbead-based detection methods and realized quickly detection within 10min without purification steps. In addition, compared with the linear chain probes, the molecular beacons probes enabled higher specificity and wash-free operation. Through different dyes encoded, TK1-DNA and microRNA-21 were simultaneously detected in one step and finally quantified by flow cytometry. The proposed detection method was also capable of monitoring TK1-DNA and microRNA-21 levels in human serum. Our study provides the potential multidetection of DNA and RNA.

Enhanced Fluorescence ELISA Based on HAT Triggering Fluorescence "Turn-on" with Enzyme-Antibody Dual Labeled AuNP Probes for Ultrasensitive Detection of AFP and HBsAg.

At present, enzyme-linked immunosorbent assay (ELISA) is considered to be the most appropriate approach in clinical biomarker detection, with good specificity, low cost, and straightforward readout. However, unsatisfactory sensitivity severely hampers its wide application in clinical diagnosis. Herein, we designed a new kind of enhanced fluorescence enzyme-linked immunosorbent assay (FELISA) based on the human alpha-thrombin (HAT) triggering fluorescence "turn-on" signals. In this system, detection antibodies (Ab2) and HAT were labeled on the gold nanoparticles (AuNPs) to form the detection probes, and a bisamide derivative of Rhodamine110 with fluorescence quenched served as the substrate of HAT. After the sandwich immunoreaction, HAT on the sandwich structure could catalyze the cleavage of the fluorescence-quenched substrate, leading to a strong fluorescence signal for sensing ultralow levels of alpha fetoprotein (AFP) and hepatitis B virus surface antigen (HBsAg). Under the optimized reaction conditions, AFP and HBsAg were detected at the ultralow concentrations of 10-8 ng mL-1 and 5 × 10-4 IU mL-1, respectively, which were at least 104 times lower than those of the conventional fluorescence assay and 106 times lower than those of the conventional ELISA. In addition, we further discussed the efficiency of the sensitive FELISA in clinical serum samples, showing great potential in practical applications.