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.

Genetically Encoded Double-Stranded DNA-Based Nanostructure Folded by a Covalently Bivalent CRISPR/dCas System.

DNA nanotechnology has been widely employed in the construction of various functional nanostructures. However, most DNA nanostructures rely on hybridization between multiple single-stranded DNAs. Herein, we report a general strategy for the construction of a double-stranded DNA-ribonucleoprotein (RNP) hybrid nanostructure by folding double-stranded DNA with a covalently bivalent clustered regularly interspaced short palindromic repeats (CRISPR)/nuclease-dead CRISPR-associated protein (dCas) system. In our design, dCas9 and dCas12a can be efficiently fused together through a flexible and stimuli-responsive peptide linker. After activation by guide RNAs, the covalently bivalent dCas9-12a RNPs (staples) can precisely recognize their target sequences in the double-stranded DNA scaffold and pull them together to construct a series of double-stranded DNA-RNP hybrid nanostructures. The genetically encoded hybrid nanostructure can protect genetic information in the folded state, similar to the natural DNA-protein hybrids present in chromosomes, and elicit efficient stimuli-responsive gene transcription in the unfolded form. This rationally developed double-stranded DNA folding and unfolding strategy presents a new avenue for the development of DNA nanotechnology.

Recent Progress of DNA Nanostructures on Amphiphilic Membranes.

Employing DNA nanostructures mimicking membrane proteins on artificial amphiphilic membranes have been widely developed to understand the structures and functions of the natural membrane systems. In this review, the recent developments in artificial systems constructed by amphiphilic membranes and DNA nanostructures are summarized. First, the preparations and properties of the amphipathic bilayer models are introduced. Second, the interactions are discussed between the membrane and the DNA nanostructures, as well as their coassembly behaviors. Next, the alternative systems related to membrane protein-mediated signal transmission, selective distribution, transmembrane channels, and membrane fusion are also introduced. Moreover, the constructions of membrane skeleton protein-mimicking DNA nanostructures are also highlighted.

Construction of a Novel Biosensor Based on the Self-assembly of Dual-Enzyme Cascade Amplification-Induced Copper Nanoparticles for Ultrasensitive Detection of MicroRNA153.

MicroRNAs (miRNAs) have received extensive attention because of their potential as biomarkers for cancer diagnosis and monitoring, and their effective detection is very significant. Here, a specific, one-pot, rapid, femtomolar sensitive miRNAs detection biosensor was developed based on the target-triggered three-way junction (3-WJ) and terminal deoxynucleotide transferase (TDT)/Nt.BspQI in combination with activated copper nanoparticles (CuNPs) self-assembly. To this end, a 3-WJ hairpin probe and helper probe were designed to selectively identify the target miRNA, so as to form a stable 3-WJ structure that further triggered the double-enzyme cycling to produce poly T to activate the self-assembly of CuNPs. Based on the simplicity of CuNPs generation, the poly T template fluorescence CuNPs can detect the minimum detection limit of 1 fm within 1.75 h. In addition, the applicability of this method in complex samples was demonstrated by analyzing the whole-blood RNA extraction from Parkinson patients, consisting of the results of commercial miRNA kits. The developed strategy performs powerful implications for miRNA detection, which may be beneficial for the effective diagnostic assays and biological research of Parkinson's disease.

Construction of Liposomes Mimicking Cell Membrane Structure through Frame-Guided Assembly.

The shape of eukaryotic cells is determined by the cytoskeleton associated with membrane proteins; however, the detailed mechanism of how the integral morphologies with structural stability is generated and maintained is still not fully understood. Here, based on the Frame-Guided Assembly (FGA) strategy, we successfully prepared hetero-liposomes with structural composition similar to that of eukaryotic cells by screening a series of transmembrane peptides as the leading hydrophobic groups (LHGs). It was demonstrated that the conformation and transmembrane mode of the LHGs played dominant roles during the FGA process. The FGA liposomes were formed with excellent stability, which may further provide evidence for the cytoskeleton-membrane protein-lipid bilayer model. Taking advantage of the biocompatibility and stability, the FGA liposomes were also applied to prepare novel drug delivery vehicles, which is promising in diagnostic imaging and cancer therapy applications.

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.

A novel template repairing-PCR (TR-PCR) reaction platform for microRNA detection using translesional synthesis on DNA templates containing abasic sites.

A novel template repairing-PCR technology based on miRNA-primed bypass synthesis at the abasic sites on the PCR template is developed as a sensitive and selective platform for miRNA detection. The assay is expected to show great promise for reverse transcription-free RNA PCR amplification and target-based coding analysis.

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.

A review of fluorescent signal-based lateral flow immunochromatographic strips.

Fluorescent signal-based lateral flow immunochromatographic strips (FLFICS) have received great expectations since they effectively improve detection sensitivity with quantitative analysis, and still retain the advantages of simplicity, rapidness, and portability of a common lateral flow immunochromatographic strip (LFICS). Diverse fluorescent reporters have promoted development of FLFICS, such as fluorescent dyes, quantum dots (QDs), an up-converting phosphor (UCP), lanthanide labels, and other fluorescence nanoparticles. In this work, we discuss the different fluorescent reporters applied with LFICS and their unique properties as well as signal amplification strategies helping to enhance detection performance. Benefitting from these sensitive and accurate fluorescent labels, FLFICS commendably satisfies requirements for detecting different disease biomarkers in medical diagnosis, strict supervision of food safety, and water pollution. This work also gives a short introduction to trends in the development of future FLFICS technology.